bwa-0.7.3a.tar

bwa-0.7.3a/000755 000767 000024 00000000000 12120745411 012263 5ustar00lh3staff000000 000000 bwa-0.7.3a/bamlite.c000644 000767 000024 00000011052 12120745361 014047 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <stdio.h>
#include "bamlite.h"

/*********************
 * from bam_endian.c *
 *********************/

static inline int bam_is_big_endian()
{
	long one= 1;
	return !(*((char *)(&one)));
}
static inline uint16_t bam_swap_endian_2(uint16_t v)
{
	return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
}
static inline void *bam_swap_endian_2p(void *x)
{
	*(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
	return x;
}
static inline uint32_t bam_swap_endian_4(uint32_t v)
{
	v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
	return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
}
static inline void *bam_swap_endian_4p(void *x)
{
	*(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
	return x;
}
static inline uint64_t bam_swap_endian_8(uint64_t v)
{
	v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
	v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
	return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
}
static inline void *bam_swap_endian_8p(void *x)
{
	*(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
	return x;
}

/**************
 * from bam.c *
 **************/

int bam_is_be;

bam_header_t *bam_header_init()
{
	bam_is_be = bam_is_big_endian();
	return (bam_header_t*)calloc(1, sizeof(bam_header_t));
}

void bam_header_destroy(bam_header_t *header)
{
	int32_t i;
	if (header == 0) return;
	if (header->target_name) {
		for (i = 0; i < header->n_targets; ++i)
			free(header->target_name[i]);
		free(header->target_name);
		free(header->target_len);
	}
	free(header->text);
	free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
	bam_header_t *header;
	char buf[4];
	int magic_len;
	int32_t i = 1, name_len;
	// read "BAM1"
	magic_len = bam_read(fp, buf, 4);
	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
		return 0;
	}
	header = bam_header_init();
	// read plain text and the number of reference sequences
	bam_read(fp, &header->l_text, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->l_text);
	header->text = (char*)calloc(header->l_text + 1, 1);
	bam_read(fp, header->text, header->l_text);
	bam_read(fp, &header->n_targets, 4);
	if (bam_is_be) bam_swap_endian_4p(&header->n_targets);
	// read reference sequence names and lengths
	header->target_name = (char**)calloc(header->n_targets, sizeof(char*));
	header->target_len = (uint32_t*)calloc(header->n_targets, 4);
	for (i = 0; i != header->n_targets; ++i) {
		bam_read(fp, &name_len, 4);
		if (bam_is_be) bam_swap_endian_4p(&name_len);
		header->target_name[i] = (char*)calloc(name_len, 1);
		bam_read(fp, header->target_name[i], name_len);
		bam_read(fp, &header->target_len[i], 4);
		if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
	}
	return header;
}

static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
{
	uint8_t *s;
	uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
	s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
	for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
	while (s < data + data_len) {
		uint8_t type;
		s += 2; // skip key
		type = toupper(*s); ++s; // skip type
		if (type == 'C' || type == 'A') ++s;
		else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
		else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
		else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
		else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
	}
}

int bam_read1(bamFile fp, bam1_t *b)
{
	bam1_core_t *c = &b->core;
	int32_t block_len, ret, i;
	uint32_t x[8];

	if ((ret = bam_read(fp, &block_len, 4)) != 4) {
		if (ret == 0) return -1; // normal end-of-file
		else return -2; // truncated
	}
	if (bam_read(fp, x, sizeof(bam1_core_t)) != sizeof(bam1_core_t)) return -3;
	if (bam_is_be) {
		bam_swap_endian_4p(&block_len);
		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
	}
	c->tid = x[0]; c->pos = x[1];
	c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
	c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
	c->l_qseq = x[4];
	c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
	b->data_len = block_len - sizeof(bam1_core_t);
	if (b->m_data < b->data_len) {
		b->m_data = b->data_len;
		kroundup32(b->m_data);
		b->data = (uint8_t*)realloc(b->data, b->m_data);
	}
	if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
	b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
	if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
	return 4 + block_len;
}
bwa-0.7.3a/bamlite.h000644 000767 000024 00000004564 12120745361 014066 0ustar00lh3staff000000 000000 #ifndef BAMLITE_H_
#define BAMLITE_H_

#include <stdint.h>
#include <zlib.h>

typedef gzFile bamFile;
#define bam_open(fn, mode) gzopen(fn, mode)
#define bam_dopen(fd, mode) gzdopen(fd, mode)
#define bam_close(fp) gzclose(fp)
#define bam_read(fp, buf, size) gzread(fp, buf, size)

typedef struct {
	int32_t n_targets;
	char **target_name;
	uint32_t *target_len;
	size_t l_text, n_text;
	char *text;
} bam_header_t;

#define BAM_FPAIRED        1
#define BAM_FPROPER_PAIR   2
#define BAM_FUNMAP         4
#define BAM_FMUNMAP        8
#define BAM_FREVERSE      16
#define BAM_FMREVERSE     32
#define BAM_FREAD1        64
#define BAM_FREAD2       128
#define BAM_FSECONDARY   256
#define BAM_FQCFAIL      512
#define BAM_FDUP        1024

#define BAM_CIGAR_SHIFT 4
#define BAM_CIGAR_MASK  ((1 << BAM_CIGAR_SHIFT) - 1)

#define BAM_CMATCH      0
#define BAM_CINS        1
#define BAM_CDEL        2
#define BAM_CREF_SKIP   3
#define BAM_CSOFT_CLIP  4
#define BAM_CHARD_CLIP  5
#define BAM_CPAD        6

typedef struct {
	int32_t tid;
	int32_t pos;
	uint32_t bin:16, qual:8, l_qname:8;
	uint32_t flag:16, n_cigar:16;
	int32_t l_qseq;
	int32_t mtid;
	int32_t mpos;
	int32_t isize;
} bam1_core_t;

typedef struct {
	bam1_core_t core;
	int l_aux, data_len, m_data;
	uint8_t *data;
} bam1_t;

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
#define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
#define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
#define bam1_qname(b) ((char*)((b)->data))
#define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
#define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
#define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)

#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
#define bam_destroy1(b) do {					\
		if (b) { free((b)->data); free(b); }	\
	} while (0)

extern int bam_is_be;

#ifdef __cplusplus
extern "C" {
#endif

	bam_header_t *bam_header_init(void);
	void bam_header_destroy(bam_header_t *header);
	bam_header_t *bam_header_read(bamFile fp);
	int bam_read1(bamFile fp, bam1_t *b);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bntseq.c000644 000767 000024 00000024676 12120745361 013746 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <unistd.h>
#include "bntseq.h"
#include "utils.h"

#include "kseq.h"
KSEQ_DECLARE(gzFile)

unsigned char nst_nt4_table[256] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 5 /*'-'*/, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

void bns_dump(const bntseq_t *bns, const char *prefix)
{
	char str[1024];
	FILE *fp;
	int i;
	{ // dump .ann
		strcpy(str, prefix); strcat(str, ".ann");
		fp = xopen(str, "w");
		fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->seed);
		for (i = 0; i != bns->n_seqs; ++i) {
			bntann1_t *p = bns->anns + i;
			fprintf(fp, "%d %s", p->gi, p->name);
			if (p->anno[0]) fprintf(fp, " %s\n", p->anno);
			else fprintf(fp, "\n");
			fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
		}
		fclose(fp);
	}
	{ // dump .amb
		strcpy(str, prefix); strcat(str, ".amb");
		fp = xopen(str, "w");
		fprintf(fp, "%lld %d %u\n", (long long)bns->l_pac, bns->n_seqs, bns->n_holes);
		for (i = 0; i != bns->n_holes; ++i) {
			bntamb1_t *p = bns->ambs + i;
			fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
		}
		fclose(fp);
	}
}

bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
{
	char str[1024];
	FILE *fp;
	bntseq_t *bns;
	long long xx;
	int i;
	bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
	{ // read .ann
		fp = xopen(ann_filename, "r");
		fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
		bns->l_pac = xx;
		bns->anns = (bntann1_t*)calloc(bns->n_seqs, sizeof(bntann1_t));
		for (i = 0; i < bns->n_seqs; ++i) {
			bntann1_t *p = bns->anns + i;
			char *q = str;
			int c;
			// read gi and sequence name
			fscanf(fp, "%u%s", &p->gi, str);
			p->name = strdup(str);
			// read fasta comments 
			while ((c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
			*q = 0;
			if (q - str > 1) p->anno = strdup(str + 1); // skip leading space
			else p->anno = strdup("");
			// read the rest
			fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
			p->offset = xx;
		}
		fclose(fp);
	}
	{ // read .amb
		int64_t l_pac;
		int32_t n_seqs;
		fp = xopen(amb_filename, "r");
		fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
		l_pac = xx;
		xassert(l_pac == bns->l_pac && n_seqs == bns->n_seqs, "inconsistent .ann and .amb files.");
		bns->ambs = bns->n_holes? (bntamb1_t*)calloc(bns->n_holes, sizeof(bntamb1_t)) : 0;
		for (i = 0; i < bns->n_holes; ++i) {
			bntamb1_t *p = bns->ambs + i;
			fscanf(fp, "%lld%d%s", &xx, &p->len, str);
			p->offset = xx;
			p->amb = str[0];
		}
		fclose(fp);
	}
	{ // open .pac
		bns->fp_pac = xopen(pac_filename, "rb");
	}
	return bns;
}

bntseq_t *bns_restore(const char *prefix)
{  
	char ann_filename[1024], amb_filename[1024], pac_filename[1024];
	strcat(strcpy(ann_filename, prefix), ".ann");
	strcat(strcpy(amb_filename, prefix), ".amb");
	strcat(strcpy(pac_filename, prefix), ".pac");
	return bns_restore_core(ann_filename, amb_filename, pac_filename);
}

void bns_destroy(bntseq_t *bns)
{
	if (bns == 0) return;
	else {
		int i;
		if (bns->fp_pac) fclose(bns->fp_pac);
		free(bns->ambs);
		for (i = 0; i < bns->n_seqs; ++i) {
			free(bns->anns[i].name);
			free(bns->anns[i].anno);
		}
		free(bns->anns);
		free(bns);
	}
}

#define _set_pac(pac, l, c) ((pac)[(l)>>2] |= (c)<<((~(l)&3)<<1))
#define _get_pac(pac, l) ((pac)[(l)>>2]>>((~(l)&3)<<1)&3)

static uint8_t *add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q)
{
	bntann1_t *p;
	int i, lasts;
	if (bns->n_seqs == *m_seqs) {
		*m_seqs <<= 1;
		bns->anns = (bntann1_t*)realloc(bns->anns, *m_seqs * sizeof(bntann1_t));
	}
	p = bns->anns + bns->n_seqs;
	p->name = strdup((char*)seq->name.s);
	p->anno = seq->comment.s? strdup((char*)seq->comment.s) : strdup("(null)");
	p->gi = 0; p->len = seq->seq.l;
	p->offset = (bns->n_seqs == 0)? 0 : (p-1)->offset + (p-1)->len;
	p->n_ambs = 0;
	for (i = lasts = 0; i < seq->seq.l; ++i) {
		int c = nst_nt4_table[(int)seq->seq.s[i]];
		if (c >= 4) { // N
			if (lasts == seq->seq.s[i]) { // contiguous N
				++(*q)->len;
			} else {
				if (bns->n_holes == *m_holes) {
					(*m_holes) <<= 1;
					bns->ambs = (bntamb1_t*)realloc(bns->ambs, (*m_holes) * sizeof(bntamb1_t));
				}
				*q = bns->ambs + bns->n_holes;
				(*q)->len = 1;
				(*q)->offset = p->offset + i;
				(*q)->amb = seq->seq.s[i];
				++p->n_ambs;
				++bns->n_holes;
			}
		}
		lasts = seq->seq.s[i];
		{ // fill buffer
			if (c >= 4) c = lrand48()&3;
			if (bns->l_pac == *m_pac) { // double the pac size
				*m_pac <<= 1;
				pac = realloc(pac, *m_pac/4);
				memset(pac + bns->l_pac/4, 0, (*m_pac - bns->l_pac)/4);
			}
			_set_pac(pac, bns->l_pac, c);
			++bns->l_pac;
		}
	}
	++bns->n_seqs;
	return pac;
}

int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only)
{
	extern void seq_reverse(int len, ubyte_t *seq, int is_comp); // in bwaseqio.c
	kseq_t *seq;
	char name[1024];
	bntseq_t *bns;
	uint8_t *pac = 0;
	int32_t m_seqs, m_holes;
	int64_t ret = -1, m_pac, l;
	bntamb1_t *q;
	FILE *fp;

	// initialization
	seq = kseq_init(fp_fa);
	bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
	bns->seed = 11; // fixed seed for random generator
	srand48(bns->seed);
	m_seqs = m_holes = 8; m_pac = 0x10000;
	bns->anns = (bntann1_t*)calloc(m_seqs, sizeof(bntann1_t));
	bns->ambs = (bntamb1_t*)calloc(m_holes, sizeof(bntamb1_t));
	pac = calloc(m_pac/4, 1);
	q = bns->ambs;
	strcpy(name, prefix); strcat(name, ".pac");
	fp = xopen(name, "wb");
	// read sequences
	while (kseq_read(seq) >= 0) pac = add1(seq, bns, pac, &m_pac, &m_seqs, &m_holes, &q);
	if (!for_only) { // add the reverse complemented sequence
		m_pac = (bns->l_pac * 2 + 3) / 4 * 4;
		pac = realloc(pac, m_pac/4);
		memset(pac + (bns->l_pac+3)/4, 0, (m_pac - (bns->l_pac+3)/4*4) / 4);
		for (l = bns->l_pac - 1; l >= 0; --l, ++bns->l_pac)
			_set_pac(pac, bns->l_pac, 3-_get_pac(pac, l));
	}
	ret = bns->l_pac;
	{ // finalize .pac file
		ubyte_t ct;
		fwrite(pac, 1, (bns->l_pac>>2) + ((bns->l_pac&3) == 0? 0 : 1), fp);
		// the following codes make the pac file size always (l_pac/4+1+1)
		if (bns->l_pac % 4 == 0) {
			ct = 0;
			fwrite(&ct, 1, 1, fp);
		}
		ct = bns->l_pac % 4;
		fwrite(&ct, 1, 1, fp);
		// close .pac file
		fclose(fp);
	}
	bns_dump(bns, prefix);
	bns_destroy(bns);
	kseq_destroy(seq);
	free(pac);
	return ret;
}

int bwa_fa2pac(int argc, char *argv[])
{
	int c, for_only = 0;
	gzFile fp;
	while ((c = getopt(argc, argv, "f")) >= 0) {
		switch (c) {
			case 'f': for_only = 1; break;
		}
	}
	if (argc == optind) {
		fprintf(stderr, "Usage: bwa fa2pac [-f] <in.fasta> [<out.prefix>]\n");
		return 1;
	}
	fp = xzopen(argv[optind], "r");
	bns_fasta2bntseq(fp, (optind+1 < argc)? argv[optind+1] : argv[optind], for_only);
	gzclose(fp);
	return 0;
}

int bns_pos2rid(const bntseq_t *bns, int64_t pos_f)
{
	int left, mid, right;
	if (pos_f >= bns->l_pac) return -1;
	left = 0; mid = 0; right = bns->n_seqs;
	while (left < right) { // binary search
		mid = (left + right) >> 1;
		if (pos_f >= bns->anns[mid].offset) {
			if (mid == bns->n_seqs - 1) break;
			if (pos_f < bns->anns[mid+1].offset) break; // bracketed
			left = mid + 1;
		} else right = mid;
	}
	return mid;
}

int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id)
{
	int left, mid, right, nn;
	if (ref_id) *ref_id = bns_pos2rid(bns, pos_f);
	left = 0; right = bns->n_holes; nn = 0;
	while (left < right) {
		mid = (left + right) >> 1;
		if (pos_f >= bns->ambs[mid].offset + bns->ambs[mid].len) left = mid + 1;
		else if (pos_f + len <= bns->ambs[mid].offset) right = mid;
		else { // overlap
			if (pos_f >= bns->ambs[mid].offset) {
				nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
					bns->ambs[mid].offset + bns->ambs[mid].len - pos_f : len;
			} else {
				nn += bns->ambs[mid].offset + bns->ambs[mid].len < pos_f + len?
					bns->ambs[mid].len : len - (bns->ambs[mid].offset - pos_f);
			}
			break;
		}
	}
	return nn;
}

uint8_t *bns_get_seq(int64_t l_pac, const uint8_t *pac, int64_t beg, int64_t end, int64_t *len)
{
	uint8_t *seq = 0;
	if (end < beg) end ^= beg, beg ^= end, end ^= beg; // if end is smaller, swap
	if (end > l_pac<<1) end = l_pac<<1;
	if (beg < 0) beg = 0;
	if (beg >= l_pac || end <= l_pac) {
		int64_t k, l = 0;
		*len = end - beg;
		seq = malloc(end - beg);
		if (beg >= l_pac) { // reverse strand
			int64_t beg_f = (l_pac<<1) - 1 - end;
			int64_t end_f = (l_pac<<1) - 1 - beg;
			for (k = end_f; k > beg_f; --k)
				seq[l++] = 3 - _get_pac(pac, k);
		} else { // forward strand
			for (k = beg; k < end; ++k)
				seq[l++] = _get_pac(pac, k);
		}
	} else *len = 0; // if bridging the forward-reverse boundary, return nothing
	return seq;
}
bwa-0.7.3a/bntseq.h000644 000767 000024 00000004775 12120745361 013751 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#ifndef BWT_BNTSEQ_H
#define BWT_BNTSEQ_H

#include <stdint.h>
#include <stdio.h>
#include <zlib.h>

#ifndef BWA_UBYTE
#define BWA_UBYTE
typedef uint8_t ubyte_t;
#endif

typedef struct {
	int64_t offset;
	int32_t len;
	int32_t n_ambs;
	uint32_t gi;
	char *name, *anno;
} bntann1_t;

typedef struct {
	int64_t offset;
	int32_t len;
	char amb;
} bntamb1_t;

typedef struct {
	int64_t l_pac;
	int32_t n_seqs;
	uint32_t seed;
	bntann1_t *anns; // n_seqs elements
	int32_t n_holes;
	bntamb1_t *ambs; // n_holes elements
	FILE *fp_pac;
} bntseq_t;

extern unsigned char nst_nt4_table[256];

#ifdef __cplusplus
extern "C" {
#endif

	void bns_dump(const bntseq_t *bns, const char *prefix);
	bntseq_t *bns_restore(const char *prefix);
	bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
	void bns_destroy(bntseq_t *bns);
	int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
	int bns_pos2rid(const bntseq_t *bns, int64_t pos_f);
	int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
	uint8_t *bns_get_seq(int64_t l_pac, const uint8_t *pac, int64_t beg, int64_t end, int64_t *len);

#ifdef __cplusplus
}
#endif

static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
{
	return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
}

#endif
bwa-0.7.3a/bwa.1000644 000767 000024 00000057122 12120745361 013131 0ustar00lh3staff000000 000000 .TH bwa 1 "15 March 2013" "bwa-0.7.3a" "Bioinformatics tools"
.SH NAME
.PP
bwa - Burrows-Wheeler Alignment Tool
.SH SYNOPSIS
.PP
bwa index ref.fa
.PP
bwa mem ref.fa reads.fq > aln-se.sam
.PP
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
.PP
bwa aln ref.fa short_read.fq > aln_sa.sai
.PP
bwa samse ref.fa aln_sa.sai short_read.fq > aln-se.sam
.PP
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
.PP
bwa bwasw ref.fa long_read.fq > aln.sam

.SH DESCRIPTION
.PP
BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome. It consists of three algorithms:
BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
sequence reads up to 100bp, while the rest two for longer sequences ranged from
70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read
support and split alignment, but BWA-MEM, which is the latest, is generally
recommended for high-quality queries as it is faster and more accurate.
BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina
reads.

For all the algorithms, BWA first needs to construct the FM-index for
the reference genome (the
.B index
command). Alignment algorithms are invoked with different sub-commands:
.BR aln / samse / sampe
for BWA-backtrack,
.B bwasw
for BWA-SW and
.B mem
for the BWA-MEM algorithm.

.SH COMMANDS AND OPTIONS
.TP
.B index
bwa index [-p prefix] [-a algoType] <in.db.fasta>

Index database sequences in the FASTA format.

.B OPTIONS:
.RS
.TP 10
.BI -p \ STR
Prefix of the output database [same as db filename]
.TP
.BI -a \ STR
Algorithm for constructing BWT index. Available options are:
.RS
.TP
.B is
IS linear-time algorithm for constructing suffix array. It requires
5.37N memory where N is the size of the database. IS is moderately fast,
but does not work with database larger than 2GB. IS is the default
algorithm due to its simplicity. The current codes for IS algorithm are
reimplemented by Yuta Mori.
.TP
.B bwtsw
Algorithm implemented in BWT-SW. This method works with the whole human
genome.
.RE
.RE

.TP
.B mem
.B bwa mem
.RB [ -aCHMpP ]
.RB [ -t
.IR nThreads ]
.RB [ -k
.IR minSeedLen ]
.RB [ -w
.IR bandWidth ]
.RB [ -d
.IR zDropoff ]
.RB [ -r
.IR seedSplitRatio ]
.RB [ -c
.IR maxOcc ]
.RB [ -A
.IR matchScore ]
.RB [ -B
.IR mmPenalty ]
.RB [ -O
.IR gapOpenPen ]
.RB [ -E
.IR gapExtPen ]
.RB [ -L
.IR clipPen ]
.RB [ -U
.IR unpairPen ]
.RB [ -R
.IR RGline ]
.RB [ -v
.IR verboseLevel ]
.I db.prefix
.I reads.fq
.RI [ mates.fq ]

Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the
algorithm works by seeding alignments with maximal exact matches (MEMs) and
then extending seeds with the affine-gap Smith-Waterman algorithm (SW).

If
.I mates.fq
file is absent and option
.B -p
is not set, this command regards input reads are single-end. If
.I mates.fq
is present, this command assumes the
.IR i -th
read in
.I reads.fq
and the
.IR i -th
read in
.I mates.fq
constitute a read pair. If
.B -p
is used, the command assumes the
.RI 2 i -th
and the
.RI (2 i +1)-th
read in
.I reads.fq
constitute a read pair (such input file is said to be interleaved). In this case,
.I mates.fq
is ignored. In the paired-end mode, the
.B mem
command will infer the read orientation and the insert size distribution from a
batch of reads.

The BWA-MEM algorithm performs local alignment. It may produce multiple primary
alignments for different part of a query sequence. This is a crucial feature
for long sequences. However, some tools such as Picard's markDuplicates does
not work with split alignments. One may consider to use option
.B -M
to flag shorter split hits as secondary.

.B OPTIONS:
.RS
.TP 10
.BI -t \ INT
Number of threads [1]
.TP
.BI -k \ INT
Minimum seed length. Matches shorter than
.I INT
will be missed. The alignment speed is usually insensitive to this value unless
it significantly deviates 20. [19]
.TP
.BI -w \ INT
Band width. Essentially, gaps longer than
.I INT
will not be found. Note that the maximum gap length is also affected by the
scoring matrix and the hit length, not solely determined by this option. [100]
.TP
.BI -d \ INT
Off-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between
the best and the current extension score is above
.RI | i - j |* A + INT ,
where
.I i
and
.I j
are the current positions of the query and reference, respectively, and
.I A
is the matching score. Z-dropoff is similar to BLAST's X-dropoff except that it
doesn't penalize gaps in one of the sequences in the alignment. Z-dropoff not
only avoids unnecessary extension, but also reduces poor alignments inside a
long good alignment. [100]
.TP
.BI -r \ FLOAT
Trigger re-seeding for a MEM longer than
.IR minSeedLen * FLOAT .
This is a key heuristic parameter for tuning the performance. Larger value
yields fewer seeds, which leads to faster alignment speed but lower accuracy. [1.5]
.TP
.BI -c \ INT
Discard a MEM if it has more than
.I INT
occurence in the genome. This is an insensitive parameter. [10000]
.TP
.B -P
In the paired-end mode, perform SW to rescue missing hits only but do not try to find
hits that fit a proper pair.
.TP
.BI -A \ INT
Matching score. [1]
.TP
.BI -B \ INT
Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]
.TP
.BI -O \ INT
Gap open penalty. [6]
.TP
.BI -E \ INT
Gap extension penalty. A gap of length k costs O + k*E (i.e.
.B -O
is for opening a zero-length gap). [1]
.TP
.BI -L \ INT
Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best
score reaching the end of query. If this score is larger than the best SW score
minus the clipping penalty, clipping will not be applied. Note that in this
case, the SAM AS tag reports the best SW score; clipping penalty is not
deducted. [5]
.TP
.BI -U \ INT
Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as
.RI scoreRead1+scoreRead2- INT
and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these
two scores to determine whether we should force pairing. [9]
.TP
.B -p
Assume the first input query file is interleaved paired-end FASTA/Q. See the command description for details.
.TP
.BI -R \ STR
Complete read group header line. '\\t' can be used in
.I STR
and will be converted to a TAB in the output SAM. The read group ID will be
attached to every read in the output. An example is '@RG\\tID:foo\\tSM:bar'.
[null]
.TP
.BI -T \ INT
Don't output alignment with score lower than
.IR INT .
This option affects output and occasionally SAM flag 2. [30]
.TP
.B -a
Output all found alignments for single-end or unpaired paired-end reads. These
alignments will be flagged as secondary alignments.
.TP
.B -C
Append append FASTA/Q comment to SAM output. This option can be used to
transfer read meta information (e.g. barcode) to the SAM output. Note that the
FASTA/Q comment (the string after a space in the header line) must conform the SAM
spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
.TP
.B -H
Use hard clipping 'H' in the SAM output. This option may dramatically reduce
the redundancy of output when mapping long contig or BAC sequences.
.TP
.B -M
Mark shorter split hits as secondary (for Picard compatibility).
.TP
.BI -v \ INT
Control the verbose level of the output. This option has not been fully
supported throughout BWA. Ideally, a value 0 for disabling all the output to
stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for
all normal messages; 4 or higher for debugging. When this option takes value
4, the output is not SAM. [3]
.RE

.TP
.B aln
bwa aln [-n maxDiff] [-o maxGapO] [-e maxGapE] [-d nDelTail] [-i
nIndelEnd] [-k maxSeedDiff] [-l seedLen] [-t nThrds] [-cRN] [-M misMsc]
[-O gapOsc] [-E gapEsc] [-q trimQual] <in.db.fasta> <in.query.fq> >
<out.sai>

Find the SA coordinates of the input reads. Maximum
.I maxSeedDiff
differences are allowed in the first
.I seedLen
subsequence and maximum
.I maxDiff
differences are allowed in the whole sequence.

.B OPTIONS:
.RS
.TP 10
.BI -n \ NUM
Maximum edit distance if the value is INT, or the fraction of missing
alignments given 2% uniform base error rate if FLOAT. In the latter
case, the maximum edit distance is automatically chosen for different
read lengths. [0.04]
.TP
.BI -o \ INT
Maximum number of gap opens [1]
.TP
.BI -e \ INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing
long gaps) [-1]
.TP
.BI -d \ INT
Disallow a long deletion within INT bp towards the 3'-end [16]
.TP
.BI -i \ INT
Disallow an indel within INT bp towards the ends [5]
.TP
.BI -l \ INT
Take the first INT subsequence as seed. If INT is larger than the query
sequence, seeding will be disabled. For long reads, this option is
typically ranged from 25 to 35 for `-k 2'. [inf]
.TP
.BI -k \ INT
Maximum edit distance in the seed [2]
.TP
.BI -t \ INT
Number of threads (multi-threading mode) [1]
.TP
.BI -M \ INT
Mismatch penalty. BWA will not search for suboptimal hits with a score
lower than (bestScore-misMsc). [3]
.TP
.BI -O \ INT
Gap open penalty [11]
.TP
.BI -E \ INT
Gap extension penalty [4]
.TP
.BI -R \ INT
Proceed with suboptimal alignments if there are no more than INT equally
best hits. This option only affects paired-end mapping. Increasing this
threshold helps to improve the pairing accuracy at the cost of speed,
especially for short reads (~32bp).
.TP
.B -c
Reverse query but not complement it, which is required for alignment in
the color space. (Disabled since 0.6.x)
.TP
.B -N
Disable iterative search. All hits with no more than
.I maxDiff
differences will be found. This mode is much slower than the default.
.TP
.BI -q \ INT
Parameter for read trimming. BWA trims a read down to
argmax_x{\\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original
read length. [0]
.TP
.B -I
The input is in the Illumina 1.3+ read format (quality equals ASCII-64).
.TP
.BI -B \ INT
Length of barcode starting from the 5'-end. When
.I INT
is positive, the barcode of each read will be trimmed before mapping and will
be written at the
.B BC
SAM tag. For paired-end reads, the barcode from both ends are concatenated. [0]
.TP
.B -b
Specify the input read sequence file is the BAM format. For paired-end
data, two ends in a pair must be grouped together and options
.B -1
or
.B -2
are usually applied to specify which end should be mapped. Typical
command lines for mapping pair-end data in the BAM format are:

    bwa aln ref.fa -b1 reads.bam > 1.sai
    bwa aln ref.fa -b2 reads.bam > 2.sai
    bwa sampe ref.fa 1.sai 2.sai reads.bam reads.bam > aln.sam
.TP
.B -0
When
.B -b
is specified, only use single-end reads in mapping.
.TP
.B -1
When
.B -b
is specified, only use the first read in a read pair in mapping (skip
single-end reads and the second reads).
.TP
.B -2
When
.B -b
is specified, only use the second read in a read pair in mapping.
.B
.RE

.TP
.B samse
bwa samse [-n maxOcc] <in.db.fasta> <in.sai> <in.fq> > <out.sam>

Generate alignments in the SAM format given single-end reads. Repetitive
hits will be randomly chosen.

.B OPTIONS:
.RS
.TP 10
.BI -n \ INT
Maximum number of alignments to output in the XA tag for reads paired
properly. If a read has more than INT hits, the XA tag will not be
written. [3]
.TP
.BI -r \ STR
Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
.RE

.TP
.B sampe
bwa sampe [-a maxInsSize] [-o maxOcc] [-n maxHitPaired] [-N maxHitDis]
[-P] <in.db.fasta> <in1.sai> <in2.sai> <in1.fq> <in2.fq> > <out.sam>

Generate alignments in the SAM format given paired-end reads. Repetitive
read pairs will be placed randomly.

.B OPTIONS:
.RS
.TP 8
.BI -a \ INT
Maximum insert size for a read pair to be considered being mapped
properly. Since 0.4.5, this option is only used when there are not
enough good alignment to infer the distribution of insert sizes. [500]
.TP
.BI -o \ INT
Maximum occurrences of a read for pairing. A read with more occurrneces
will be treated as a single-end read. Reducing this parameter helps
faster pairing. [100000]
.TP
.B -P
Load the entire FM-index into memory to reduce disk operations
(base-space reads only). With this option, at least 1.25N bytes of
memory are required, where N is the length of the genome.
.TP
.BI -n \ INT
Maximum number of alignments to output in the XA tag for reads paired
properly. If a read has more than INT hits, the XA tag will not be
written. [3]
.TP
.BI -N \ INT
Maximum number of alignments to output in the XA tag for disconcordant
read pairs (excluding singletons). If a read has more than INT hits, the
XA tag will not be written. [10]
.TP
.BI -r \ STR
Specify the read group in a format like `@RG\\tID:foo\\tSM:bar'. [null]
.RE

.TP
.B bwasw
bwa bwasw [-a matchScore] [-b mmPen] [-q gapOpenPen] [-r gapExtPen] [-t
nThreads] [-w bandWidth] [-T thres] [-s hspIntv] [-z zBest] [-N
nHspRev] [-c thresCoef] <in.db.fasta> <in.fq> [mate.fq]

Align query sequences in the
.I in.fq
file. When
.I mate.fq
is present, perform paired-end alignment. The paired-end mode only works
for reads Illumina short-insert libraries. In the paired-end mode, BWA-SW
may still output split alignments but they are all marked as not properly
paired; the mate positions will not be written if the mate has multiple
local hits.

.B OPTIONS:
.RS
.TP 10
.BI -a \ INT
Score of a match [1]
.TP
.BI -b \ INT
Mismatch penalty [3]
.TP
.BI -q \ INT
Gap open penalty [5]
.TP
.BI -r \ INT
Gap extension penalty. The penalty for a contiguous gap of size k is
q+k*r. [2]
.TP
.BI -t \ INT
Number of threads in the multi-threading mode [1]
.TP
.BI -w \ INT
Band width in the banded alignment [33]
.TP
.BI -T \ INT
Minimum score threshold divided by a [37]
.TP
.BI -c \ FLOAT
Coefficient for threshold adjustment according to query length. Given an
l-long query, the threshold for a hit to be retained is
a*max{T,c*log(l)}. [5.5]
.TP
.BI -z \ INT
Z-best heuristics. Higher -z increases accuracy at the cost of speed. [1]
.TP
.BI -s \ INT
Maximum SA interval size for initiating a seed. Higher -s increases
accuracy at the cost of speed. [3]
.TP
.BI -N \ INT
Minimum number of seeds supporting the resultant alignment to skip
reverse alignment. [5]
.RE

.SH SAM ALIGNMENT FORMAT
.PP
The output of the
.B `aln'
command is binary and designed for BWA use only. BWA outputs the final
alignment in the SAM (Sequence Alignment/Map) format. Each line consists
of:

.TS
center box;
cb | cb | cb
n | l | l .
Col	Field	Description
_
1	QNAME	Query (pair) NAME
2	FLAG	bitwise FLAG
3	RNAME	Reference sequence NAME
4	POS	1-based leftmost POSition/coordinate of clipped sequence
5	MAPQ	MAPping Quality (Phred-scaled)
6	CIAGR	extended CIGAR string
7	MRNM	Mate Reference sequence NaMe (`=' if same as RNAME)
8	MPOS	1-based Mate POSistion
9	ISIZE	Inferred insert SIZE
10	SEQ	query SEQuence on the same strand as the reference
11	QUAL	query QUALity (ASCII-33 gives the Phred base quality)
12	OPT	variable OPTional fields in the format TAG:VTYPE:VALUE
.TE

.PP
Each bit in the FLAG field is defined as:

.TS
center box;
cb | cb | cb
c | l | l .
Chr	Flag	Description
_
p	0x0001	the read is paired in sequencing
P	0x0002	the read is mapped in a proper pair
u	0x0004	the query sequence itself is unmapped
U	0x0008	the mate is unmapped
r	0x0010	strand of the query (1 for reverse)
R	0x0020	strand of the mate
1	0x0040	the read is the first read in a pair
2	0x0080	the read is the second read in a pair
s	0x0100	the alignment is not primary
f	0x0200	QC failure
d	0x0400	optical or PCR duplicate
.TE

.PP
The Please check <http://samtools.sourceforge.net> for the format
specification and the tools for post-processing the alignment.

BWA generates the following optional fields. Tags starting with `X' are
specific to BWA.

.TS
center box;
cb | cb
cB | l .
Tag	Meaning
_
NM	Edit distance
MD	Mismatching positions/bases
AS	Alignment score
BC	Barcode sequence
_
X0	Number of best hits
X1	Number of suboptimal hits found by BWA
XN	Number of ambiguous bases in the referenece
XM	Number of mismatches in the alignment
XO	Number of gap opens
XG	Number of gap extentions
XT	Type: Unique/Repeat/N/Mate-sw
XA	Alternative hits; format: /(chr,pos,CIGAR,NM;)*/
_
XS	Suboptimal alignment score
XF	Support from forward/reverse alignment
XE	Number of supporting seeds
_
XP	Alt primary hits; format: /(chr,pos,CIGAR,mapQ,NM;)+/
.TE

.PP
Note that XO and XG are generated by BWT search while the CIGAR string
by Smith-Waterman alignment. These two tags may be inconsistent with the
CIGAR string. This is not a bug.

.SH NOTES ON SHORT-READ ALIGNMENT
.SS Alignment Accuracy
.PP
When seeding is disabled, BWA guarantees to find an alignment
containing maximum
.I maxDiff
differences including
.I maxGapO
gap opens which do not occur within
.I nIndelEnd
bp towards either end of the query. Longer gaps may be found if
.I maxGapE
is positive, but it is not guaranteed to find all hits. When seeding is
enabled, BWA further requires that the first
.I seedLen
subsequence contains no more than
.I maxSeedDiff
differences.
.PP
When gapped alignment is disabled, BWA is expected to generate the same
alignment as Eland version 1, the Illumina alignment program. However, as BWA
change `N' in the database sequence to random nucleotides, hits to these
random sequences will also be counted. As a consequence, BWA may mark a
unique hit as a repeat, if the random sequences happen to be identical
to the sequences which should be unqiue in the database.
.PP
By default, if the best hit is not highly repetitive (controlled by -R), BWA
also finds all hits contains one more mismatch; otherwise, BWA finds all
equally best hits only. Base quality is NOT considered in evaluating
hits. In the paired-end mode, BWA pairs all hits it found. It further
performs Smith-Waterman alignment for unmapped reads to rescue reads with a
high erro rate, and for high-quality anomalous pairs to fix potential alignment
errors.

.SS Estimating Insert Size Distribution
.PP
BWA estimates the insert size distribution per 256*1024 read pairs. It
first collects pairs of reads with both ends mapped with a single-end
quality 20 or higher and then calculates median (Q2), lower and higher
quartile (Q1 and Q3). It estimates the mean and the variance of the
insert size distribution from pairs whose insert sizes are within
interval [Q1-2(Q3-Q1), Q3+2(Q3-Q1)]. The maximum distance x for a pair
considered to be properly paired (SAM flag 0x2) is calculated by solving
equation Phi((x-mu)/sigma)=x/L*p0, where mu is the mean, sigma is the
standard error of the insert size distribution, L is the length of the
genome, p0 is prior of anomalous pair and Phi() is the standard
cumulative distribution function. For mapping Illumina short-insert
reads to the human genome, x is about 6-7 sigma away from the
mean. Quartiles, mean, variance and x will be printed to the standard
error output.

.SS Memory Requirement
.PP
With bwtsw algorithm, 5GB memory is required for indexing the complete
human genome sequences. For short reads, the
.B aln
command uses ~3.2GB memory and the
.B sampe
command uses ~5.4GB.

.SS Speed
.PP
Indexing the human genome sequences takes 3 hours with bwtsw
algorithm. Indexing smaller genomes with IS algorithms is
faster, but requires more memory.
.PP
The speed of alignment is largely determined by the error rate of the query
sequences (r). Firstly, BWA runs much faster for near perfect hits than
for hits with many differences, and it stops searching for a hit with
l+2 differences if a l-difference hit is found. This means BWA will be
very slow if r is high because in this case BWA has to visit hits with
many differences and looking for these hits is expensive. Secondly, the
alignment algorithm behind makes the speed sensitive to [k log(N)/m],
where k is the maximum allowed differences, N the size of database and m
the length of a query. In practice, we choose k w.r.t. r and therefore r
is the leading factor. I would not recommend to use BWA on data with
r>0.02.
.PP
Pairing is slower for shorter reads. This is mainly because shorter
reads have more spurious hits and converting SA coordinates to
chromosomal coordinates are very costly.

.SH CHANGES IN BWA-0.6
.PP
Since version 0.6, BWA has been able to work with a reference genome longer than 4GB.
This feature makes it possible to integrate the forward and reverse complemented
genome in one FM-index, which speeds up both BWA-short and BWA-SW. As a tradeoff,
BWA uses more memory because it has to keep all positions and ranks in 64-bit
integers, twice larger than 32-bit integers used in the previous versions.

The latest BWA-SW also works for paired-end reads longer than 100bp. In
comparison to BWA-short, BWA-SW tends to be more accurate for highly unique
reads and more robust to relative long INDELs and structural variants.
Nonetheless, BWA-short usually has higher power to distinguish the optimal hit
from many suboptimal hits. The choice of the mapping algorithm may depend on
the application.

.SH SEE ALSO
BWA website <http://bio-bwa.sourceforge.net>, Samtools website
<http://samtools.sourceforge.net>

.SH AUTHOR
Heng Li at the Sanger Institute wrote the key source codes and
integrated the following codes for BWT construction: bwtsw
<http://i.cs.hku.hk/~ckwong3/bwtsw/>, implemented by Chi-Kwong Wong at
the University of Hong Kong and IS
<http://yuta.256.googlepages.com/sais> originally proposed by Nong Ge
<http://www.cs.sysu.edu.cn/nong/> at the Sun Yat-Sen University and
implemented by Yuta Mori.

.SH LICENSE AND CITATION
.PP
The full BWA package is distributed under GPLv3 as it uses source codes
from BWT-SW which is covered by GPL. Sorting, hash table, BWT and IS
libraries are distributed under the MIT license.
.PP
If you use the BWA-backtrack algorithm, please cite the following
paper:
.PP
Li H. and Durbin R. (2009) Fast and accurate short read alignment with
Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]
.PP
If you use the BWA-SW algorithm, please cite:
.PP
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]
.PP
If you use the fastmap component of BWA, please cite:
.PP
Li H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de
novo assembly. Bioinformatics, 28, 1838-1844. [PMID: 22569178]
.PP
The BWA-MEM algorithm has not been published yet.

.SH HISTORY
BWA is largely influenced by BWT-SW. It uses source codes from BWT-SW
and mimics its binary file formats; BWA-SW resembles BWT-SW in several
ways. The initial idea about BWT-based alignment also came from the
group who developed BWT-SW. At the same time, BWA is different enough
from BWT-SW. The short-read alignment algorithm bears no similarity to
Smith-Waterman algorithm any more. While BWA-SW learns from BWT-SW, it
introduces heuristics that can hardly be applied to the original
algorithm. In all, BWA does not guarantee to find all local hits as what
BWT-SW is designed to do, but it is much faster than BWT-SW on both
short and long query sequences.

I started to write the first piece of codes on 24 May 2008 and got the
initial stable version on 02 June 2008. During this period, I was
acquainted that Professor Tak-Wah Lam, the first author of BWT-SW paper,
was collaborating with Beijing Genomics Institute on SOAP2, the successor
to SOAP (Short Oligonucleotide Analysis Package). SOAP2 has come out in
November 2008. According to the SourceForge download page, the third
BWT-based short read aligner, bowtie, was first released in August
2008. At the time of writing this manual, at least three more BWT-based
short-read aligners are being implemented.

The BWA-SW algorithm is a new component of BWA. It was conceived in
November 2008 and implemented ten months later.

The BWA-MEM algorithm is based on an algorithm finding super-maximal exact
matches (SMEMs), which was first published with the fermi assembler paper
in 2012. I first implemented the basic SMEM algorithm in the
.B fastmap
command for an experiment and then extended the basic algorithm and added the
extension part in Feburary 2013 to make BWA-MEM a fully featured mapper.

bwa-0.7.3a/bwa.c000644 000767 000024 00000023011 12120745361 013201 0ustar00lh3staff000000 000000 #include <string.h>
#include <stdio.h>
#include <zlib.h>
#include <assert.h>
#include "bntseq.h"
#include "bwa.h"
#include "ksw.h"
#include "utils.h"

int bwa_verbose = 3;
char bwa_rg_id[256];

/************************
 * Batch FASTA/Q reader *
 ************************/

#include "kseq.h"
KSEQ_DECLARE(gzFile)

static inline void trim_readno(kstring_t *s)
{
	if (s->l > 2 && s->s[s->l-2] == '/' && isdigit(s->s[s->l-1]))
		s->l -= 2, s->s[s->l] = 0;
}

static inline void kseq2bseq1(const kseq_t *ks, bseq1_t *s)
{ // TODO: it would be better to allocate one chunk of memory, but probably it does not matter in practice
	s->name = strdup(ks->name.s);
	s->comment = ks->comment.l? strdup(ks->comment.s) : 0;
	s->seq = strdup(ks->seq.s);
	s->qual = ks->qual.l? strdup(ks->qual.s) : 0;
	s->l_seq = strlen(s->seq);
}

bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
{
	kseq_t *ks = (kseq_t*)ks1_, *ks2 = (kseq_t*)ks2_;
	int size = 0, m, n;
	bseq1_t *seqs;
	m = n = 0; seqs = 0;
	while (kseq_read(ks) >= 0) {
		if (ks2 && kseq_read(ks2) < 0) { // the 2nd file has fewer reads
			fprintf(stderr, "[W::%s] the 2nd file has fewer sequences.\n", __func__);
			break;
		}
		if (n >= m) {
			m = m? m<<1 : 256;
			seqs = realloc(seqs, m * sizeof(bseq1_t));
		}
		trim_readno(&ks->name);
		kseq2bseq1(ks, &seqs[n]);
		size += seqs[n++].l_seq;
		if (ks2) {
			trim_readno(&ks2->name);
			kseq2bseq1(ks2, &seqs[n]);
			size += seqs[n++].l_seq;
		}
		if (size >= chunk_size && (n&1) == 0) break;
	}
	if (size == 0) { // test if the 2nd file is finished
		if (ks2 && kseq_read(ks2) >= 0)
			fprintf(stderr, "[W::%s] the 1st file has fewer sequences.\n", __func__);
	}
	*n_ = n;
	return seqs;
}

/*****************
 * CIGAR related *
 *****************/

void bwa_fill_scmat(int a, int b, int8_t mat[25])
{
	int i, j, k;
	for (i = k = 0; i < 4; ++i) {
		for (j = 0; j < 4; ++j)
			mat[k++] = i == j? a : -b;
		mat[k++] = -1; // ambiguous base
	}
	for (j = 0; j < 5; ++j) mat[k++] = -1;
}

// Generate CIGAR when the alignment end points are known
uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM)
{
	uint32_t *cigar = 0;
	uint8_t tmp, *rseq;
	int i;
	int64_t rlen;
	*n_cigar = 0; *NM = -1;
	if (l_query <= 0 || rb >= re || (rb < l_pac && re > l_pac)) return 0; // reject if negative length or bridging the forward and reverse strand
	rseq = bns_get_seq(l_pac, pac, rb, re, &rlen);
	if (re - rb != rlen) goto ret_gen_cigar; // possible if out of range
	if (rb >= l_pac) { // then reverse both query and rseq; this is to ensure indels to be placed at the leftmost position
		for (i = 0; i < l_query>>1; ++i)
			tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;
		for (i = 0; i < rlen>>1; ++i)
			tmp = rseq[i], rseq[i] = rseq[rlen - 1 - i], rseq[rlen - 1 - i] = tmp;
	}
	if (l_query == re - rb && w_ == 0) { // no gap; no need to do DP
		cigar = malloc(4);
		cigar[0] = l_query<<4 | 0;
		*n_cigar = 1;
		for (i = 0, *score = 0; i < l_query; ++i)
			*score += mat[rseq[i]*5 + query[i]];
	} else {
		int w, max_gap, min_w;
		//printf("[Q] "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
		//printf("[R] "); for (i = 0; i < re - rb; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
		// set the band-width
		max_gap = (int)((double)(((l_query+1)>>1) * mat[0] - q) / r + 1.);
		max_gap = max_gap > 1? max_gap : 1;
		w = (max_gap + abs(rlen - l_query) + 1) >> 1;
		w = w < w_? w : w_;
		min_w = abs(rlen - l_query) + 3;
		w = w > min_w? w : min_w;
		// NW alignment
		*score = ksw_global(l_query, query, rlen, rseq, 5, mat, q, r, w, n_cigar, &cigar);
	}
	{// compute NM
		int k, x, y, n_mm = 0, n_gap = 0;
		for (k = 0, x = y = 0; k < *n_cigar; ++k) {
			int op  = cigar[k]&0xf;
			int len = cigar[k]>>4;
			if (op == 0) { // match
				for (i = 0; i < len; ++i)
					if (query[x + i] != rseq[y + i]) ++n_mm;
				x += len; y += len;
			} else if (op == 1) x += len, n_gap += len;
			else if (op == 2) y += len, n_gap += len;
		}
		*NM = n_mm + n_gap;
	}
	if (rb >= l_pac) // reverse back query
		for (i = 0; i < l_query>>1; ++i)
			tmp = query[i], query[i] = query[l_query - 1 - i], query[l_query - 1 - i] = tmp;

ret_gen_cigar:
	free(rseq);
	return cigar;
}

int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
{
	int ib, ie, is_rev;
	int64_t fb, fe, mid = -1;
	if (*rb < bns->l_pac && *re > bns->l_pac) { // cross the for-rev boundary
		*qb = *qe = *rb = *re = -1;
		return -1; // unable to fix
	} else {
		fb = bns_depos(bns, *rb < bns->l_pac? *rb : *re - 1, &is_rev);
		ib = bns_pos2rid(bns, fb);
		if (fb - bns->anns[ib].offset + (*re - *rb) <= bns->anns[ib].len) return 0; // no need to fix
		fe = bns_depos(bns, *re - 1 < bns->l_pac? *re - 1 : *rb, &is_rev);
		ie = bns_pos2rid(bns, fe);
		if (ie - ib > 1) { // bridge three or more references
			*qb = *qe = *rb = *re = -1;
			return -2; // unable to fix
		} else {
			int l = bns->anns[ib].offset + bns->anns[ib].len - fb;
			mid = is_rev? *re - l : *rb + l;
		}
	}
	if (mid >= 0) {
		int i, score, n_cigar, y, NM;
		uint32_t *cigar;
		int64_t x;
		cigar = bwa_gen_cigar(mat, q, r, w, bns->l_pac, pac, *qe - *qb, query + *qb, *rb, *re, &score, &n_cigar, &NM);
		for (i = 0, x = *rb, y = *qb; i < n_cigar; ++i) {
			int op = cigar[i]&0xf, len = cigar[i]>>4;
			if (op == 0) {
				if (x <= mid && mid < x + len) {
					if (mid - *rb > *re - mid) { // the first part is longer
						if (x == mid) { // need to check the previous operation
							assert(i); // mid != *rb should always stand
							if ((cigar[i-1]&0xf) == 1) *qe = y - (cigar[i-1]>>4), *re = x;
							else if ((cigar[i-1]&0xf) == 2) *qe = y, *re = x - (cigar[i-1]>>4);
							else abort(); // should not be here
						} else *qe = y + (mid - x), *re = mid;
					} else *qb = y + (mid - x), *rb = mid;
					break;
				} else x += len, y += len;
			} else if (op == 1) { // insertion
				y += len;
			} else if (op == 2) { // deletion
				if (x <= mid && mid < x + len) {
					if (mid - *rb > *re - mid) *qe = y, *re = x;
					else *qb = y, *rb = x + len;
					break;
				} else x += len;
			} else abort(); // should not be here
		}
		free(cigar);
	}
	return 1;
}

/*********************
 * Full index reader *
 *********************/

char *bwa_idx_infer_prefix(const char *hint)
{
	char *prefix;
	int l_hint;
	FILE *fp;
	l_hint = strlen(hint);
	prefix = malloc(l_hint + 3 + 4 + 1);
	strcpy(prefix, hint);
	strcpy(prefix + l_hint, ".64.bwt");
	if ((fp = fopen(prefix, "rb")) != 0) {
		fclose(fp);
		prefix[l_hint + 3] = 0;
		return prefix;
	} else {
		strcpy(prefix + l_hint, ".bwt");
		if ((fp = fopen(prefix, "rb")) == 0) {
			free(prefix);
			return 0;
		} else {
			fclose(fp);
			prefix[l_hint] = 0;
			return prefix;
		}
	}
}

bwt_t *bwa_idx_load_bwt(const char *hint)
{
	char *tmp, *prefix;
	bwt_t *bwt;
	prefix = bwa_idx_infer_prefix(hint);
	if (prefix == 0) {
		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
		return 0;
	}
	tmp = calloc(strlen(prefix) + 5, 1);
	strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
	bwt = bwt_restore_bwt(tmp);
	strcat(strcpy(tmp, prefix), ".sa");  // partial suffix array (SA)
	bwt_restore_sa(tmp, bwt);
	free(tmp); free(prefix);
	return bwt;
}

bwaidx_t *bwa_idx_load(const char *hint, int which)
{
	bwaidx_t *idx;
	char *prefix;
	prefix = bwa_idx_infer_prefix(hint);
	if (prefix == 0) {
		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
		return 0;
	}
	idx = calloc(1, sizeof(bwaidx_t));
	if (which & BWA_IDX_BWT) idx->bwt = bwa_idx_load_bwt(hint);
	if (which & BWA_IDX_BNS) {
		idx->bns = bns_restore(prefix);
		if (which & BWA_IDX_PAC) {
			idx->pac = calloc(idx->bns->l_pac/4+1, 1);
			fread(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
			fclose(idx->bns->fp_pac);
			idx->bns->fp_pac = 0;
		}
	}
	free(prefix);
	return idx;
}

void bwa_idx_destroy(bwaidx_t *idx)
{
	if (idx == 0) return;
	if (idx->bwt) bwt_destroy(idx->bwt);
	if (idx->bns) bns_destroy(idx->bns);
	if (idx->pac) free(idx->pac);
	free(idx);
}

/***********************
 * SAM header routines *
 ***********************/

void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line)
{
	int i;
	for (i = 0; i < bns->n_seqs; ++i)
		err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
	if (rg_line) err_printf("%s\n", rg_line);
}

static char *bwa_escape(char *s)
{
	char *p, *q;
	for (p = q = s; *p; ++p) {
		if (*p == '\\') {
			++p;
			if (*p == 't') *q++ = '\t';
			else if (*p == 'n') *q++ = '\n';
			else if (*p == 'r') *q++ = '\r';
			else if (*p == '\\') *q++ = '\\';
		} else *q++ = *p;
	}
	*q = '\0';
	return s;
}

char *bwa_set_rg(const char *s)
{
	char *p, *q, *r, *rg_line = 0;
	memset(bwa_rg_id, 0, 256);
	if (strstr(s, "@RG") != s) {
		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line is not started with @RG\n", __func__);
		goto err_set_rg;
	}
	rg_line = strdup(s);
	bwa_escape(rg_line);
	if ((p = strstr(rg_line, "\tID:")) == 0) {
		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] no ID at the read group line\n", __func__);
		goto err_set_rg;
	}
	p += 4;
	for (q = p; *q && *q != '\t' && *q != '\n'; ++q);
	if (q - p + 1 > 256) {
		if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] @RG:ID is longer than 255 characters\n", __func__);
		goto err_set_rg;
	}
	for (q = p, r = bwa_rg_id; *q && *q != '\t' && *q != '\n'; ++q)
		*r++ = *q;
	return rg_line;

err_set_rg:
	free(rg_line);
	return 0;
}

bwa-0.7.3a/bwa.h000644 000767 000024 00000002545 12120745361 013217 0ustar00lh3staff000000 000000 #ifndef BWA_H_
#define BWA_H_

#include <stdint.h>
#include "bntseq.h"
#include "bwt.h"

#define BWA_IDX_BWT 0x1
#define BWA_IDX_BNS 0x2
#define BWA_IDX_PAC 0x4
#define BWA_IDX_ALL 0x7

typedef struct {
	bwt_t    *bwt; // FM-index
	bntseq_t *bns; // information on the reference sequences
	uint8_t  *pac; // the actual 2-bit encoded reference sequences with 'N' converted to a random base
} bwaidx_t;

typedef struct {
	int l_seq;
	char *name, *comment, *seq, *qual, *sam;
} bseq1_t;

extern int bwa_verbose;
extern char bwa_rg_id[256];

#ifdef __cplusplus
extern "C" {
#endif

	bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_);

	void bwa_fill_scmat(int a, int b, int8_t mat[25]);
	uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar, int *NM);
	int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re);

	char *bwa_idx_infer_prefix(const char *hint);
	bwt_t *bwa_idx_load_bwt(const char *hint);

	bwaidx_t *bwa_idx_load(const char *hint, int which);
	void bwa_idx_destroy(bwaidx_t *idx);

	void bwa_print_sam_hdr(const bntseq_t *bns, const char *rg_line);
	char *bwa_set_rg(const char *s);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwamem.c000644 000767 000024 00000104206 12120745361 013706 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <assert.h>
#include <math.h>
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif

#include "kstring.h"
#include "bwamem.h"
#include "bntseq.h"
#include "ksw.h"
#include "kvec.h"
#include "ksort.h"
#include "utils.h"

/* Theory on probability and scoring *ungapped* alignment
 *
 * s'(a,b) = log[P(b|a)/P(b)] = log[4P(b|a)], assuming uniform base distribution
 * s'(a,a) = log(4), s'(a,b) = log(4e/3), where e is the error rate
 *
 * Scale s'(a,b) to s(a,a) s.t. s(a,a)=x. Then s(a,b) = x*s'(a,b)/log(4), or conversely: s'(a,b)=s(a,b)*log(4)/x
 *
 * If the matching score is x and mismatch penalty is -y, we can compute error rate e:
 *   e = .75 * exp[-log(4) * y/x]
 *
 * log P(seq) = \sum_i log P(b_i|a_i) = \sum_i {s'(a,b) - log(4)}
 *   = \sum_i { s(a,b)*log(4)/x - log(4) } = log(4) * (S/x - l)
 *
 * where S=\sum_i s(a,b) is the alignment score. Converting to the phred scale:
 *   Q(seq) = -10/log(10) * log P(seq) = 10*log(4)/log(10) * (l - S/x) = 6.02 * (l - S/x)
 *
 *
 * Gap open (zero gap): q' = log[P(gap-open)], r' = log[P(gap-ext)] (see Durbin et al. (1998) Section 4.1)
 * Then q = x*log[P(gap-open)]/log(4), r = x*log[P(gap-ext)]/log(4)
 *
 * When there are gaps, l should be the length of alignment matches (i.e. the M operator in CIGAR)
 */

mem_opt_t *mem_opt_init()
{
	mem_opt_t *o;
	o = calloc(1, sizeof(mem_opt_t));
	o->flag = 0;
	o->a = 1; o->b = 4; o->q = 6; o->r = 1; o->w = 100;
	o->T = 30;
	o->zdrop = 100;
	o->pen_unpaired = 9;
	o->pen_clip = 5;
	o->min_seed_len = 19;
	o->split_width = 10;
	o->max_occ = 10000;
	o->max_chain_gap = 10000;
	o->max_ins = 10000;
	o->mask_level = 0.50;
	o->chain_drop_ratio = 0.50;
	o->split_factor = 1.5;
	o->chunk_size = 10000000;
	o->n_threads = 1;
	o->max_matesw = 100;
	bwa_fill_scmat(o->a, o->b, o->mat);
	return o;
}

/***************************
 * SMEM iterator interface *
 ***************************/

struct __smem_i {
	const bwt_t *bwt;
	const uint8_t *query;
	int start, len;
	bwtintv_v *matches; // matches; to be returned by smem_next()
	bwtintv_v *sub;     // sub-matches inside the longest match; temporary
	bwtintv_v *tmpvec[2]; // temporary arrays
};

smem_i *smem_itr_init(const bwt_t *bwt)
{
	smem_i *itr;
	itr = calloc(1, sizeof(smem_i));
	itr->bwt = bwt;
	itr->tmpvec[0] = calloc(1, sizeof(bwtintv_v));
	itr->tmpvec[1] = calloc(1, sizeof(bwtintv_v));
	itr->matches   = calloc(1, sizeof(bwtintv_v));
	itr->sub       = calloc(1, sizeof(bwtintv_v));
	return itr;
}

void smem_itr_destroy(smem_i *itr)
{
	free(itr->tmpvec[0]->a); free(itr->tmpvec[0]);
	free(itr->tmpvec[1]->a); free(itr->tmpvec[1]);
	free(itr->matches->a);   free(itr->matches);
	free(itr->sub->a);       free(itr->sub);
	free(itr);
}

void smem_set_query(smem_i *itr, int len, const uint8_t *query)
{
	itr->query = query;
	itr->start = 0;
	itr->len = len;
}

const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width)
{
	int i, max, max_i, ori_start;
	itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = itr->sub->n = 0;
	if (itr->start >= itr->len || itr->start < 0) return 0;
	while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases
	if (itr->start == itr->len) return 0;
	ori_start = itr->start;
	itr->start = bwt_smem1(itr->bwt, itr->len, itr->query, ori_start, 1, itr->matches, itr->tmpvec); // search for SMEM
	if (itr->matches->n == 0) return itr->matches; // well, in theory, we should never come here
	for (i = max = 0, max_i = 0; i < itr->matches->n; ++i) { // look for the longest match
		bwtintv_t *p = &itr->matches->a[i];
		int len = (uint32_t)p->info - (p->info>>32);
		if (max < len) max = len, max_i = i;
	}
	if (split_len > 0 && max >= split_len && itr->matches->a[max_i].x[2] <= split_width) { // if the longest SMEM is unique and long
		int j;
		bwtintv_v *a = itr->tmpvec[0]; // reuse tmpvec[0] for merging
		bwtintv_t *p = &itr->matches->a[max_i];
		bwt_smem1(itr->bwt, itr->len, itr->query, ((uint32_t)p->info + (p->info>>32))>>1, itr->matches->a[max_i].x[2]+1, itr->sub, itr->tmpvec); // starting from the middle of the longest MEM
		i = j = 0; a->n = 0;
		while (i < itr->matches->n && j < itr->sub->n) { // ordered merge
			int64_t xi = itr->matches->a[i].info>>32<<32 | (itr->len - (uint32_t)itr->matches->a[i].info);
			int64_t xj = itr->sub->a[j].info>>32<<32 | (itr->len - (uint32_t)itr->sub->a[j].info);
			if (xi < xj) {
				kv_push(bwtintv_t, *a, itr->matches->a[i]);
				++i;
			} else if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1 && (uint32_t)itr->sub->a[j].info > ori_start) {
				kv_push(bwtintv_t, *a, itr->sub->a[j]);
				++j;
			} else ++j;
		}
		for (; i < itr->matches->n; ++i) kv_push(bwtintv_t, *a, itr->matches->a[i]);
		for (; j < itr->sub->n; ++j)
			if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1 && (uint32_t)itr->sub->a[j].info > ori_start)
				kv_push(bwtintv_t, *a, itr->sub->a[j]);
		kv_copy(bwtintv_t, *itr->matches, *a);
	}
	return itr->matches;
}

/********************************
 * Chaining while finding SMEMs *
 ********************************/

typedef struct {
	int64_t rbeg;
	int32_t qbeg, len;
} mem_seed_t;

typedef struct {
	int n, m;
	int64_t pos;
	mem_seed_t *seeds;
} mem_chain_t;

typedef struct { size_t n, m; mem_chain_t *a;  } mem_chain_v;

#include "kbtree.h"

#define chain_cmp(a, b) (((b).pos < (a).pos) - ((a).pos < (b).pos))
KBTREE_INIT(chn, mem_chain_t, chain_cmp)

static int test_and_merge(const mem_opt_t *opt, int64_t l_pac, mem_chain_t *c, const mem_seed_t *p)
{
	int64_t qend, rend, x, y;
	const mem_seed_t *last = &c->seeds[c->n-1];
	qend = last->qbeg + last->len;
	rend = last->rbeg + last->len;
	if (p->qbeg >= c->seeds[0].qbeg && p->qbeg + p->len <= qend && p->rbeg >= c->seeds[0].rbeg && p->rbeg + p->len <= rend)
		return 1; // contained seed; do nothing
	if ((last->rbeg < l_pac || c->seeds[0].rbeg < l_pac) && p->rbeg >= l_pac) return 0; // don't chain if on different strand
	x = p->qbeg - last->qbeg; // always non-negtive
	y = p->rbeg - last->rbeg;
	if (y >= 0 && x - y <= opt->w && y - x <= opt->w && x - last->len < opt->max_chain_gap && y - last->len < opt->max_chain_gap) { // grow the chain
		if (c->n == c->m) {
			c->m <<= 1;
			c->seeds = realloc(c->seeds, c->m * sizeof(mem_seed_t));
		}
		c->seeds[c->n++] = *p;
		return 1;
	}
	return 0; // request to add a new chain
}

static void mem_insert_seed(const mem_opt_t *opt, int64_t l_pac, kbtree_t(chn) *tree, smem_i *itr)
{
	const bwtintv_v *a;
	int split_len = (int)(opt->min_seed_len * opt->split_factor + .499);
	split_len = split_len < itr->len? split_len : itr->len;
	while ((a = smem_next(itr, split_len, opt->split_width)) != 0) { // to find all SMEM and some internal MEM
		int i;
		for (i = 0; i < a->n; ++i) { // go through each SMEM/MEM up to itr->start
			bwtintv_t *p = &a->a[i];
			int slen = (uint32_t)p->info - (p->info>>32); // seed length
			int64_t k;
			if (slen < opt->min_seed_len || p->x[2] > opt->max_occ) continue; // ignore if too short or too repetitive
			for (k = 0; k < p->x[2]; ++k) {
				mem_chain_t tmp, *lower, *upper;
				mem_seed_t s;
				int to_add = 0;
				s.rbeg = tmp.pos = bwt_sa(itr->bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
				s.qbeg = p->info>>32;
				s.len  = slen;
				if (s.rbeg < l_pac && l_pac < s.rbeg + s.len) continue; // bridging forward-reverse boundary; skip
				if (kb_size(tree)) {
					kb_intervalp(chn, tree, &tmp, &lower, &upper); // find the closest chain
					if (!lower || !test_and_merge(opt, l_pac, lower, &s)) to_add = 1;
				} else to_add = 1;
				if (to_add) { // add the seed as a new chain
					tmp.n = 1; tmp.m = 4;
					tmp.seeds = calloc(tmp.m, sizeof(mem_seed_t));
					tmp.seeds[0] = s;
					kb_putp(chn, tree, &tmp);
				}
			}
		}
	}
}

void mem_print_chain(const bntseq_t *bns, mem_chain_v *chn)
{
	int i, j;
	for (i = 0; i < chn->n; ++i) {
		mem_chain_t *p = &chn->a[i];
		printf("%d", p->n);
		for (j = 0; j < p->n; ++j) {
			bwtint_t pos;
			int is_rev, ref_id;
			pos = bns_depos(bns, p->seeds[j].rbeg, &is_rev);
			if (is_rev) pos -= p->seeds[j].len - 1;
			bns_cnt_ambi(bns, pos, p->seeds[j].len, &ref_id);
			printf("\t%d,%d,%ld(%s:%c%ld)", p->seeds[j].len, p->seeds[j].qbeg, (long)p->seeds[j].rbeg, bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
		}
		putchar('\n');
	}
}

mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int64_t l_pac, int len, const uint8_t *seq)
{
	mem_chain_v chain;
	smem_i *itr;
	kbtree_t(chn) *tree;

	kv_init(chain);
	if (len < opt->min_seed_len) return chain; // if the query is shorter than the seed length, no match
	tree = kb_init(chn, KB_DEFAULT_SIZE);
	itr = smem_itr_init(bwt);
	smem_set_query(itr, len, seq);
	mem_insert_seed(opt, l_pac, tree, itr);

	kv_resize(mem_chain_t, chain, kb_size(tree));

	#define traverse_func(p_) (chain.a[chain.n++] = *(p_))
	__kb_traverse(mem_chain_t, tree, traverse_func);
	#undef traverse_func

	smem_itr_destroy(itr);
	kb_destroy(chn, tree);
	return chain;
}

/********************
 * Filtering chains *
 ********************/

typedef struct {
	int beg, end, w;
	void *p, *p2;
} flt_aux_t;

#define flt_lt(a, b) ((a).w > (b).w)
KSORT_INIT(mem_flt, flt_aux_t, flt_lt)

int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains)
{
	flt_aux_t *a;
	int i, j, n;
	if (n_chn <= 1) return n_chn; // no need to filter
	a = malloc(sizeof(flt_aux_t) * n_chn);
	for (i = 0; i < n_chn; ++i) {
		mem_chain_t *c = &chains[i];
		int64_t end;
		int w = 0, tmp;
		for (j = 0, end = 0; j < c->n; ++j) {
			const mem_seed_t *s = &c->seeds[j];
			if (s->qbeg >= end) w += s->len;
			else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end;
			end = end > s->qbeg + s->len? end : s->qbeg + s->len;
		}
		tmp = w;
		for (j = 0, end = 0; j < c->n; ++j) {
			const mem_seed_t *s = &c->seeds[j];
			if (s->rbeg >= end) w += s->len;
			else if (s->rbeg + s->len > end) w += s->rbeg + s->len - end;
			end = end > s->qbeg + s->len? end : s->qbeg + s->len;
		}
		w = w < tmp? w : tmp;
		a[i].beg = c->seeds[0].qbeg;
		a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
		a[i].w = w; a[i].p = c; a[i].p2 = 0;
	}
	ks_introsort(mem_flt, n_chn, a);
	{ // reorder chains such that the best chain appears first
		mem_chain_t *swap;
		swap = malloc(sizeof(mem_chain_t) * n_chn);
		for (i = 0; i < n_chn; ++i) {
			swap[i] = *((mem_chain_t*)a[i].p);
			a[i].p = &chains[i]; // as we will memcpy() below, a[i].p is changed
		}
		memcpy(chains, swap, sizeof(mem_chain_t) * n_chn);
		free(swap);
	}
	for (i = 1, n = 1; i < n_chn; ++i) {
		for (j = 0; j < n; ++j) {
			int b_max = a[j].beg > a[i].beg? a[j].beg : a[i].beg;
			int e_min = a[j].end < a[i].end? a[j].end : a[i].end;
			if (e_min > b_max) { // have overlap
				int min_l = a[i].end - a[i].beg < a[j].end - a[j].beg? a[i].end - a[i].beg : a[j].end - a[j].beg;
				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
					if (a[j].p2 == 0) a[j].p2 = a[i].p;
					if (a[i].w < a[j].w * opt->chain_drop_ratio && a[j].w - a[i].w >= opt->min_seed_len<<1)
						break;
				}
			}
		}
		if (j == n) a[n++] = a[i]; // if have no significant overlap with better chains, keep it.
	}
	for (i = 0; i < n; ++i) { // mark chains to be kept
		mem_chain_t *c = (mem_chain_t*)a[i].p;
		if (c->n > 0) c->n = -c->n;
		c = (mem_chain_t*)a[i].p2;
		if (c && c->n > 0) c->n = -c->n;
	}
	free(a);
	for (i = 0; i < n_chn; ++i) { // free discarded chains
		mem_chain_t *c = &chains[i];
		if (c->n >= 0) {
			free(c->seeds);
			c->n = c->m = 0;
		} else c->n = -c->n;
	}
	for (i = n = 0; i < n_chn; ++i) { // squeeze out discarded chains
		if (chains[i].n > 0) {
			if (n != i) chains[n++] = chains[i];
			else ++n;
		}
	}
	return n;
}

/******************************
 * De-overlap single-end hits *
 ******************************/

#define alnreg_slt(a, b) ((a).score > (b).score || ((a).score == (b).score && ((a).rb < (b).rb || ((a).rb == (b).rb && (a).qb < (b).qb))))
KSORT_INIT(mem_ars, mem_alnreg_t, alnreg_slt)

int mem_sort_and_dedup(int n, mem_alnreg_t *a)
{
	int m, i;
	if (n <= 1) return n;
	ks_introsort(mem_ars, n, a);
	for (i = 1; i < n; ++i) { // mark identical hits
		if (a[i].score == a[i-1].score && a[i].rb == a[i-1].rb && a[i].qb == a[i-1].qb)
			a[i].qe = a[i].qb;
	}
	for (i = 1, m = 1; i < n; ++i) // exclude identical hits
		if (a[i].qe > a[i].qb) {
			if (m != i) a[m++] = a[i];
			else ++m;
		}
	return m;
}

void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a) // IMPORTANT: must run mem_sort_and_dedup() before calling this function
{ // similar to the loop in mem_chain_flt()
	int i, k, tmp;
	kvec_t(int) z;
	if (n == 0) return;
	kv_init(z);
	for (i = 0; i < n; ++i) a[i].sub = 0, a[i].secondary = -1;
	tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
	kv_push(int, z, 0);
	for (i = 1; i < n; ++i) {
		for (k = 0; k < z.n; ++k) {
			int j = z.a[k];
			int b_max = a[j].qb > a[i].qb? a[j].qb : a[i].qb;
			int e_min = a[j].qe < a[i].qe? a[j].qe : a[i].qe;
			if (e_min > b_max) { // have overlap
				int min_l = a[i].qe - a[i].qb < a[j].qe - a[j].qb? a[i].qe - a[i].qb : a[j].qe - a[j].qb;
				if (e_min - b_max >= min_l * opt->mask_level) { // significant overlap
					if (a[j].sub == 0) a[j].sub = a[i].score;
					if (a[j].score - a[i].score <= tmp) ++a[j].sub_n;
					break;
				}
			}
		}
		if (k == z.n) kv_push(int, z, i);
		else a[i].secondary = z.a[k];
	}
	free(z.a);
}

/****************************************
 * Construct the alignment from a chain *
 ****************************************/

/* mem_chain2aln() vs mem_chain2aln_short()
 *
 * mem_chain2aln() covers all the functionality of mem_chain2aln_short().
 * However, it may waste time on extracting the reference sequences given a
 * very long query. mem_chain2aln_short() is faster for very short chains in a
 * long query. It may fail when the matches are long or reach the end of the
 * query. In this case, mem_chain2aln() will be called again.
 * mem_chain2aln_short() is almost never used for short-read alignment.
 */

#define MEM_SHORT_EXT 50
#define MEM_SHORT_LEN 200
#define MAX_BAND_TRY  2

int mem_chain2aln_short(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
{
	int i, qb, qe, xtra;
	int64_t rb, re, rlen;
	uint8_t *rseq = 0;
	mem_alnreg_t a;
	kswr_t x;

	if (c->n == 0) return -1;
	qb = l_query;  qe = 0;
	rb = l_pac<<1; re = 0;
	memset(&a, 0, sizeof(mem_alnreg_t));
	for (i = 0; i < c->n; ++i) {
		const mem_seed_t *s = &c->seeds[i];
		qb = qb < s->qbeg? qb : s->qbeg;
		qe = qe > s->qbeg + s->len? qe : s->qbeg + s->len;
		rb = rb < s->rbeg? rb : s->rbeg;
		re = re > s->rbeg + s->len? re : s->rbeg + s->len;
		a.seedcov += s->len;
	}
	qb -= MEM_SHORT_EXT; qe += MEM_SHORT_EXT;
	if (qb <= 10 || qe >= l_query - 10) return 1; // because ksw_align() does not support end-to-end alignment
	rb -= MEM_SHORT_EXT; re += MEM_SHORT_EXT;
	rb = rb > 0? rb : 0;
	re = re < l_pac<<1? re : l_pac<<1;
	if (rb < l_pac && l_pac < re) {
		if (c->seeds[0].rbeg < l_pac) re = l_pac;
		else rb = l_pac;
	}
	if ((re - rb) - (qe - qb) > MEM_SHORT_EXT || (qe - qb) - (re - rb) > MEM_SHORT_EXT) return 1;
	if (qe - qb >= opt->w * 4 || re - rb >= opt->w * 4) return 1;
	if (qe - qb >= MEM_SHORT_LEN || re - rb >= MEM_SHORT_LEN) return 1;

	rseq = bns_get_seq(l_pac, pac, rb, re, &rlen);
	assert(rlen == re - rb);
	xtra = KSW_XSUBO | KSW_XSTART | ((qe - qb) * opt->a < 250? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
	x = ksw_align(qe - qb, (uint8_t*)query + qb, re - rb, rseq, 5, opt->mat, opt->q, opt->r, xtra, 0);
	free(rseq);
	if (x.tb < MEM_SHORT_EXT>>1 || x.te > re - rb - (MEM_SHORT_EXT>>1)) return 1;

	a.rb = rb + x.tb; a.re = rb + x.te + 1;
	a.qb = qb + x.qb; a.qe = qb + x.qe + 1;
	a.score = x.score;
	a.csub = x.score2;
	kv_push(mem_alnreg_t, *av, a);
	if (bwa_verbose >= 4) printf("SHORT: [%d,%d) <=> [%ld,%ld)\n", a.qb, a.qe, (long)a.rb, (long)a.re);
	return 0;
}

static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
{
	int l = (int)((double)(qlen * opt->a - opt->q) / opt->r + 1.);
	l = l > 1? l : 1;
	return l < opt->w<<1? l : opt->w<<1;
}

void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain_t *c, mem_alnreg_v *av)
{
	int i, k, max_off[2], aw[2]; // aw: actual bandwidth used in extension
	int64_t rlen, rmax[2], tmp, max = 0;
	const mem_seed_t *s;
	uint8_t *rseq = 0;
	uint64_t *srt;

	if (c->n == 0) return;
	// get the max possible span
	rmax[0] = l_pac<<1; rmax[1] = 0;
	for (i = 0; i < c->n; ++i) {
		int64_t b, e;
		const mem_seed_t *t = &c->seeds[i];
		b = t->rbeg - (t->qbeg + cal_max_gap(opt, t->qbeg));
		e = t->rbeg + t->len + ((l_query - t->qbeg - t->len) + cal_max_gap(opt, l_query - t->qbeg - t->len));
		rmax[0] = rmax[0] < b? rmax[0] : b;
		rmax[1] = rmax[1] > e? rmax[1] : e;
		if (t->len > max) max = t->len;
	}
	rmax[0] = rmax[0] > 0? rmax[0] : 0;
	rmax[1] = rmax[1] < l_pac<<1? rmax[1] : l_pac<<1;
	if (rmax[0] < l_pac && l_pac < rmax[1]) { // crossing the forward-reverse boundary; then choose one side
		if (c->seeds[0].rbeg < l_pac) rmax[1] = l_pac; // this works because all seeds are guaranteed to be on the same strand
		else rmax[0] = l_pac;
	}
	// retrieve the reference sequence
	rseq = bns_get_seq(l_pac, pac, rmax[0], rmax[1], &rlen);
	assert(rlen == rmax[1] - rmax[0]);

	srt = malloc(c->n * 8);
	for (i = 0; i < c->n; ++i)
		srt[i] = (uint64_t)c->seeds[i].len<<32 | i;
	ks_introsort_64(c->n, srt);

	for (k = c->n - 1; k >= 0; --k) {
		mem_alnreg_t *a;
		s = &c->seeds[(uint32_t)srt[k]];

		for (i = 0; i < av->n; ++i) { // test whether extension has been made before
			mem_alnreg_t *p = &av->a[i];
			int64_t rd;
			int qd, w, max_gap;
			if (s->rbeg < p->rb || s->rbeg + s->len > p->re || s->qbeg < p->qb || s->qbeg + s->len > p->qe) continue; // not fully contained
			// qd: distance ahead of the seed on query; rd: on reference
			qd = s->qbeg - p->qb; rd = s->rbeg - p->rb;
			max_gap = cal_max_gap(opt, qd < rd? qd : rd); // the maximal gap allowed in regions ahead of the seed
			w = max_gap < opt->w? max_gap : opt->w; // bounded by the band width
			if (qd - rd < w && rd - qd < w) break; // the seed is "around" a previous hit
			// similar to the previous four lines, but this time we look at the region behind
			qd = p->qe - (s->qbeg + s->len); rd = p->re - (s->rbeg + s->len);
			max_gap = cal_max_gap(opt, qd < rd? qd : rd);
			w = max_gap < opt->w? max_gap : opt->w;
			if (qd - rd < w && rd - qd < w) break;
		}
		if (i < av->n) continue;

		a = kv_pushp(mem_alnreg_t, *av);
		memset(a, 0, sizeof(mem_alnreg_t));
		a->w = aw[0] = aw[1] = opt->w;
		a->score = a->truesc = -1;

		if (s->qbeg) { // left extension
			uint8_t *rs, *qs;
			int qle, tle, gtle, gscore;
			qs = malloc(s->qbeg);
			for (i = 0; i < s->qbeg; ++i) qs[i] = query[s->qbeg - 1 - i];
			tmp = s->rbeg - rmax[0];
			rs = malloc(tmp);
			for (i = 0; i < tmp; ++i) rs[i] = rseq[tmp - 1 - i];
			for (i = 0; i < MAX_BAND_TRY; ++i) {
				int prev = a->score;
				aw[0] = opt->w << i;
				a->score = ksw_extend(s->qbeg, qs, tmp, rs, 5, opt->mat, opt->q, opt->r, aw[0], opt->zdrop, s->len * opt->a, &qle, &tle, &gtle, &gscore, &max_off[0]);
				if (bwa_verbose >= 4) { printf("L\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); }
				if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break;
			}
			// check whether we prefer to reach the end of the query
			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
				a->qb = s->qbeg - qle, a->rb = s->rbeg - tle;
				a->truesc = a->score;
			} else { // to-end extension
				a->qb = 0, a->rb = s->rbeg - gtle;
				a->truesc = gscore;
			}
			free(qs); free(rs);
		} else a->score = a->truesc = s->len * opt->a, a->qb = 0, a->rb = s->rbeg;

		if (s->qbeg + s->len != l_query) { // right extension
			int qle, tle, qe, re, gtle, gscore, sc0 = a->score;
			qe = s->qbeg + s->len;
			re = s->rbeg + s->len - rmax[0];
			assert(re >= 0);
			for (i = 0; i < MAX_BAND_TRY; ++i) {
				int prev = a->score;
				aw[1] = opt->w << i;
				a->score = ksw_extend(l_query - qe, query + qe, rmax[1] - rmax[0] - re, rseq + re, 5, opt->mat, opt->q, opt->r, aw[1], opt->zdrop, sc0, &qle, &tle, &gtle, &gscore, &max_off[1]);
				if (bwa_verbose >= 4) { printf("R\t%d < %d; w=%d; max_off=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); }
				if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break;
			}
			// similar to the above
			if (gscore <= 0 || gscore <= a->score - opt->pen_clip) { // local extension
				a->qe = qe + qle, a->re = rmax[0] + re + tle;
				a->truesc += a->score - sc0;
			} else { // to-end extension
				a->qe = l_query, a->re = rmax[0] + re + gtle;
				a->truesc += gscore - sc0;
			}
		} else a->qe = l_query, a->re = s->rbeg + s->len;
		if (bwa_verbose >= 4) { printf("[%d]\taw={%d,%d}\tscore=%d\t[%d,%d) <=> [%ld,%ld)\n", k, aw[0], aw[1], a->score, a->qb, a->qe, (long)a->rb, (long)a->re); fflush(stdout); }

		// compute seedcov
		for (i = 0, a->seedcov = 0; i < c->n; ++i) {
			const mem_seed_t *t = &c->seeds[i];
			if (t->qbeg >= a->qb && t->qbeg + t->len <= a->qe && t->rbeg >= a->rb && t->rbeg + t->len <= a->re) // seed fully contained
				a->seedcov += t->len; // this is not very accurate, but for approx. mapQ, this is good enough
		}
		a->w = aw[0] > aw[1]? aw[0] : aw[1];
	}
	free(srt); free(rseq);
}

/*****************************
 * Basic hit->SAM conversion *
 *****************************/

static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
{
	int w;
	if (l1 == l2 && l1 * a - score < (q + r - a)<<1) return 0; // to get equal alignment length, we need at least two gaps
	w = ((double)((l1 < l2? l1 : l2) * a - score - q) / r + 1.);
	if (w < abs(l1 - l2)) w = abs(l1 - l2);
	return w;
}

static inline int get_rlen(int n_cigar, const uint32_t *cigar)
{
	int k, l;
	for (k = l = 0; k < n_cigar; ++k) {
		int op = cigar[k]&0xf;
		if (op == 0 || op == 2)
			l += cigar[k]>>4;
	}
	return l;
}

void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_)
{
	int i;
	mem_aln_t ptmp = list[which], *p = &ptmp, mtmp, *m = 0; // make a copy of the alignment to convert

	if (m_) mtmp = *m_, m = &mtmp;
	// set flag
	p->flag |= m? 0x1 : 0; // is paired in sequencing
	p->flag |= p->rid < 0? 0x4 : 0; // is mapped
	p->flag |= m && m->rid < 0? 0x8 : 0; // is mate mapped
	if (p->rid < 0 && m && m->rid >= 0) // copy mate to alignment
		p->rid = m->rid, p->pos = m->pos, p->is_rev = m->is_rev, p->n_cigar = 0;
	if (m && m->rid < 0 && p->rid >= 0) // copy alignment to mate
		m->rid = p->rid, m->pos = p->pos, m->is_rev = p->is_rev, m->n_cigar = 0;
	p->flag |= p->is_rev? 0x10 : 0; // is on the reverse strand
	p->flag |= m && m->is_rev? 0x20 : 0; // is mate on the reverse strand

	// print up to CIGAR
	kputs(s->name, str); kputc('\t', str); // QNAME
	kputw((p->flag&0xffff) | (p->flag&0x10000? 0x100 : 0), str); kputc('\t', str); // FLAG
	if (p->rid >= 0) { // with coordinate
		kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
		kputl(p->pos + 1, str); kputc('\t', str); // POS
		kputw(p->mapq, str); kputc('\t', str); // MAPQ
		if (p->n_cigar) { // aligned
			for (i = 0; i < p->n_cigar; ++i) {
				kputw(p->cigar[i]>>4, str); kputc("MIDSH"[p->cigar[i]&0xf], str);
			}
		} else kputc('*', str); // having a coordinate but unaligned (e.g. when copy_mate is true)
	} else kputsn("*\t0\t0\t*", 7, str); // without coordinte
	kputc('\t', str);

	// print the mate position if applicable
	if (m && m->rid >= 0) {
		if (p->rid == m->rid) kputc('=', str);
		else kputs(bns->anns[m->rid].name, str);
		kputc('\t', str);
		kputl(m->pos + 1, str); kputc('\t', str);
		if (p->rid == m->rid) {
			int64_t p0 = p->pos + (p->is_rev? get_rlen(p->n_cigar, p->cigar) - 1 : 0);
			int64_t p1 = m->pos + (m->is_rev? get_rlen(m->n_cigar, m->cigar) - 1 : 0);
			if (m->n_cigar == 0 || p->n_cigar == 0) kputc('0', str);
			else kputl(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
		} else kputc('0', str);
	} else kputsn("*\t0\t0", 5, str);
	kputc('\t', str);

	// print SEQ and QUAL
	if (p->flag & 0x100) { // for secondary alignments, don't write SEQ and QUAL
		kputsn("*\t*", 3, str);
	} else if (!p->is_rev) { // the forward strand
		int i, qb = 0, qe = s->l_seq;
		if (p->n_cigar) {
			if ((p->cigar[0]&0xf) == 4) qb += p->cigar[0]>>4;
			if ((p->cigar[p->n_cigar-1]&0xf) == 4) qe -= p->cigar[p->n_cigar-1]>>4;
		}
		ks_resize(str, str->l + (qe - qb) + 1);
		for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
		kputc('\t', str);
		if (s->qual) { // printf qual
			ks_resize(str, str->l + (qe - qb) + 1);
			for (i = qb; i < qe; ++i) str->s[str->l++] = s->qual[i];
			str->s[str->l] = 0;
		} else kputc('*', str);
	} else { // the reverse strand
		int i, qb = 0, qe = s->l_seq;
		if (p->n_cigar) {
			if ((p->cigar[0]&0xf) == 4) qe -= p->cigar[0]>>4;
			if ((p->cigar[p->n_cigar-1]&0xf) == 4) qb += p->cigar[p->n_cigar-1]>>4;
		}
		ks_resize(str, str->l + (qe - qb) + 1);
		for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
		kputc('\t', str);
		if (s->qual) { // printf qual
			ks_resize(str, str->l + (qe - qb) + 1);
			for (i = qe-1; i >= qb; --i) str->s[str->l++] = s->qual[i];
			str->s[str->l] = 0;
		} else kputc('*', str);
	}

	// print optional tags
	if (p->n_cigar) { kputsn("\tNM:i:", 6, str); kputw(p->NM, str); }
	if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
	if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
	if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
	for (i = 0; i < n; ++i)
		if (i != which && !(list[i].flag&0x20000)) break; // 0x20000: shadowed multi hit
	if (i < n) { // there are other primary hits; output them
		kputsn("\tXP:Z:", 6, str);
		for (i = 0; i < n; ++i) {
			const mem_aln_t *r = &list[i];
			int k;
			if (i == which || (list[i].flag&0x20000)) continue; // proceed if: 1) different from the current; 2) not shadowed multi hit
			kputs(bns->anns[r->rid].name, str); kputc(',', str);
			kputc("+-"[r->is_rev], str);
			kputl(r->pos+1, str); kputc(',', str);
			for (k = 0; k < r->n_cigar; ++k) {
				kputw(r->cigar[k]>>4, str); kputc("MIDSH"[r->cigar[k]&0xf], str);
			}
			kputc(',', str); kputw(r->mapq, str);
			kputc(',', str); kputw(r->NM, str);
			kputc(';', str);
		}
	}
	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
	kputc('\n', str);
}

/************************
 * Integrated interface *
 ************************/

int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
{
	int mapq, l, sub = a->sub? a->sub : opt->min_seed_len * opt->a;
	double identity;
	sub = a->csub > sub? a->csub : sub;
	if (sub >= a->score) return 0;
	l = a->qe - a->qb > a->re - a->rb? a->qe - a->qb : a->re - a->rb;
	mapq = a->score? (int)(MEM_MAPQ_COEF * (1. - (double)sub / a->score) * log(a->seedcov) + .499) : 0;
	identity = 1. - (double)(l * opt->a - a->score) / (opt->a + opt->b) / l;
	mapq = identity < 0.95? (int)(mapq * identity * identity + .499) : mapq;
	if (a->sub_n > 0) mapq -= (int)(4.343 * log(a->sub_n+1) + .499);
	if (mapq > 60) mapq = 60;
	if (mapq < 0) mapq = 0;
	return mapq;
}

void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
{
	kstring_t str;
	str.l = str.m = 0; str.s = 0;
	if (a->n > 0 && a->a[0].score >= opt->T) {
		int k;
		kvec_t(mem_aln_t) aa;
		kv_init(aa);
		for (k = 0; k < a->n; ++k) {
			mem_alnreg_t *p = &a->a[k];
			mem_aln_t *q;
			if (p->score < opt->T) continue;
			if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
			if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
			q = kv_pushp(mem_aln_t, aa);
			*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
			q->flag |= extra_flag | (p->secondary >= 0? 0x100 : 0); // flag secondary
			if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
			if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) q->flag |= 0x10000;
			if (k && q->mapq > aa.a[0].mapq) q->mapq = aa.a[0].mapq;
		}
		for (k = 0; k < aa.n; ++k)
			mem_aln2sam(bns, &str, s, aa.n, aa.a, k, m);
		for (k = 0; k < aa.n; ++k) free(aa.a[k].cigar);
		free(aa.a);
	} else {
		mem_aln_t t;
		t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
		t.flag |= extra_flag;
		mem_aln2sam(bns, &str, s, 1, &t, 0, m);
	}
	s->sam = str.s;
}

mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
{
	int i;
	mem_chain_v chn;
	mem_alnreg_v regs;

	for (i = 0; i < l_seq; ++i) // convert to 2-bit encoding if we have not done so
		seq[i] = seq[i] < 4? seq[i] : nst_nt4_table[(int)seq[i]];

	chn = mem_chain(opt, bwt, bns->l_pac, l_seq, (uint8_t*)seq);
	chn.n = mem_chain_flt(opt, chn.n, chn.a);
	if (bwa_verbose >= 4) mem_print_chain(bns, &chn);

	kv_init(regs);
	for (i = 0; i < chn.n; ++i) {
		mem_chain_t *p = &chn.a[i];
		int ret;
		ret = mem_chain2aln_short(opt, bns->l_pac, pac, l_seq, (uint8_t*)seq, p, &regs);
		if (ret > 0) mem_chain2aln(opt, bns->l_pac, pac, l_seq, (uint8_t*)seq, p, &regs);
		free(chn.a[i].seeds);
	}
	free(chn.a);
	regs.n = mem_sort_and_dedup(regs.n, regs.a);
	return regs;
}

mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq_)
{ // the difference from mem_align1_core() is that this routine: 1) calls mem_mark_primary_se(); 2) does not modify the input sequence
	mem_alnreg_v ar;
	char *seq;
	seq = malloc(l_seq);
	memcpy(seq, seq_, l_seq); // makes a copy of seq_
	ar = mem_align1_core(opt, bwt, bns, pac, l_seq, seq);
	mem_mark_primary_se(opt, ar.n, ar.a);
	free(seq);
	return ar;
}

// This routine is only used for the API purpose
mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar)
{
	mem_aln_t a;
	int i, w2, qb, qe, NM, score, is_rev;
	int64_t pos, rb, re;
	uint8_t *query;

	memset(&a, 0, sizeof(mem_aln_t));
	if (ar == 0 || ar->rb < 0 || ar->re < 0) { // generate an unmapped record
		a.rid = -1; a.pos = -1; a.flag |= 0x4;
		return a;
	}
	qb = ar->qb, qe = ar->qe;
	rb = ar->rb, re = ar->re;
	query = malloc(l_query);
	for (i = 0; i < l_query; ++i) // convert to the nt4 encoding
		query[i] = query_[i] < 5? query_[i] : nst_nt4_table[(int)query_[i]];
	a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
	if (ar->secondary >= 0) a.flag |= 0x20000;
	bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re);
	w2 = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->q, opt->r);
	w2 = w2 < opt->w? w2 : opt->w;
	a.cigar = bwa_gen_cigar(opt->mat, opt->q, opt->r, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
	a.NM = NM;
	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
	a.is_rev = is_rev;
	if (qb != 0 || qe != l_query) { // add clipping to CIGAR
		int clip5, clip3;
		clip5 = is_rev? l_query - qe : qb;
		clip3 = is_rev? qb : l_query - qe;
		a.cigar = realloc(a.cigar, 4 * (a.n_cigar + 2));
		if (clip5) {
			memmove(a.cigar+1, a.cigar, a.n_cigar * 4);
			a.cigar[0] = clip5<<4 | (opt->flag&MEM_F_HARDCLIP? 4 : 3);
			++a.n_cigar;
		}
		if (clip3) a.cigar[a.n_cigar++] = clip3<<4 | (opt->flag&MEM_F_HARDCLIP? 4 : 3);
	}
	a.rid = bns_pos2rid(bns, pos);
	a.pos = pos - bns->anns[a.rid].offset;
	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
	free(query);
	return a;
}

typedef struct {
	int start, step, n;
	const mem_opt_t *opt;
	const bwt_t *bwt;
	const bntseq_t *bns;
	const uint8_t *pac;
	const mem_pestat_t *pes;
	bseq1_t *seqs;
	mem_alnreg_v *regs;
} worker_t;

static void *worker1(void *data)
{
	worker_t *w = (worker_t*)data;
	int i;
	if (!(w->opt->flag&MEM_F_PE)) {
		for (i = w->start; i < w->n; i += w->step)
			w->regs[i] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i].l_seq, w->seqs[i].seq);
	} else { // for PE we align the two ends in the same thread in case the 2nd read is of worse quality, in which case some threads may be faster/slower
		for (i = w->start; i < w->n>>1; i += w->step) {
			w->regs[i<<1|0] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|0].l_seq, w->seqs[i<<1|0].seq);
			w->regs[i<<1|1] = mem_align1_core(w->opt, w->bwt, w->bns, w->pac, w->seqs[i<<1|1].l_seq, w->seqs[i<<1|1].seq);
		}
	}
	return 0;
}

static void *worker2(void *data)
{
	extern int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2]);
	worker_t *w = (worker_t*)data;
	int i;
	if (!(w->opt->flag&MEM_F_PE)) {
		for (i = w->start; i < w->n; i += w->step) {
			mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
			mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
			free(w->regs[i].a);
		}
	} else {
		int n = 0;
		for (i = w->start; i < w->n>>1; i += w->step) { // not implemented yet
			n += mem_sam_pe(w->opt, w->bns, w->pac, w->pes, i, &w->seqs[i<<1], &w->regs[i<<1]);
			free(w->regs[i<<1|0].a); free(w->regs[i<<1|1].a);
		}
		fprintf(stderr, "[M::%s@%d] performed mate-SW for %d reads\n", __func__, w->start, n);
	}
	return 0;
}

void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs)
{
	int i;
	worker_t *w;
	mem_alnreg_v *regs;
	mem_pestat_t pes[4];

	w = calloc(opt->n_threads, sizeof(worker_t));
	regs = malloc(n * sizeof(mem_alnreg_v));
	for (i = 0; i < opt->n_threads; ++i) {
		worker_t *p = &w[i];
		p->start = i; p->step = opt->n_threads; p->n = n;
		p->opt = opt; p->bwt = bwt; p->bns = bns; p->pac = pac;
		p->seqs = seqs; p->regs = regs;
		p->pes = &pes[0];
	}
#ifdef HAVE_PTHREAD
	if (opt->n_threads == 1) {
		worker1(w);
		if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
		worker2(w);
	} else {
		pthread_t *tid;
		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker1, &w[i]);
		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
		if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker2, &w[i]);
		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
		free(tid);
	}
#else
	worker1(w);
	if (opt->flag&MEM_F_PE) mem_pestat(opt, bns->l_pac, n, regs, pes);
	worker2(w);
#endif
	for (i = 0; i < n; ++i) {
		fputs(seqs[i].sam, stdout);
		free(seqs[i].name); free(seqs[i].comment); free(seqs[i].seq); free(seqs[i].qual); free(seqs[i].sam);
	}
	free(regs); free(w);
}
bwa-0.7.3a/bwamem.h000644 000767 000024 00000014572 12120745361 013721 0ustar00lh3staff000000 000000 #ifndef BWAMEM_H_
#define BWAMEM_H_

#include "bwt.h"
#include "bntseq.h"
#include "bwa.h"

#define MEM_MAPQ_COEF 30.0
#define MEM_MAPQ_MAX  60

struct __smem_i;
typedef struct __smem_i smem_i;

#define MEM_F_HARDCLIP  0x1
#define MEM_F_PE        0x2
#define MEM_F_NOPAIRING 0x4
#define MEM_F_ALL       0x8
#define MEM_F_NO_MULTI  0x10

typedef struct {
	int a, b, q, r;         // match score, mismatch penalty and gap open/extension penalty. A gap of size k costs q+k*r
	int pen_unpaired;       // phred-scaled penalty for unpaired reads
	int pen_clip;           // clipping penalty. This score is not deducted from the DP score.
	int w;                  // band width
	int zdrop;              // Z-dropoff

	int T;                  // output score threshold; only affecting output
	int flag;               // see MEM_F_* macros
	int min_seed_len;       // minimum seed length
	float split_factor;     // split into a seed if MEM is longer than min_seed_len*split_factor
	int split_width;        // split into a seed if its occurence is smaller than this value
	int max_occ;            // skip a seed if its occurence is larger than this value
	int max_chain_gap;      // do not chain seed if it is max_chain_gap-bp away from the closest seed
	int n_threads;          // number of threads
	int chunk_size;         // process chunk_size-bp sequences in a batch
	float mask_level;       // regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
	float chain_drop_ratio; // drop a chain if its seed coverage is below chain_drop_ratio times the seed coverage of a better chain overlapping with the small chain
	int max_ins;            // when estimating insert size distribution, skip pairs with insert longer than this value
	int max_matesw;         // perform maximally max_matesw rounds of mate-SW for each end
	int8_t mat[25];         // scoring matrix; mat[0] == 0 if unset
} mem_opt_t;

typedef struct {
	int64_t rb, re; // [rb,re): reference sequence in the alignment
	int qb, qe;     // [qb,qe): query sequence in the alignment
	int score;      // best local SW score
	int truesc;     // actual score corresponding to the aligned region; possibly smaller than $score
	int sub;        // 2nd best SW score
	int csub;       // SW score of a tandem hit
	int sub_n;      // approximate number of suboptimal hits
	int w;          // actual band width used in extension
	int seedcov;    // length of regions coverged by seeds
	int secondary;  // index of the parent hit shadowing the current hit; <0 if primary
} mem_alnreg_t;

typedef struct { size_t n, m; mem_alnreg_t *a; } mem_alnreg_v;

typedef struct {
	int low, high, failed;
	double avg, std;
} mem_pestat_t;

typedef struct { // This struct is only used for the convenience of API.
	int64_t pos;     // forward strand 5'-end mapping position
	int rid;         // reference sequence index in bntseq_t; <0 for unmapped
	int flag;        // extra flag
	uint32_t is_rev:1, mapq:8, NM:23; // is_rev: whether on the reverse strand; mapq: mapping quality; NM: edit distance
	int n_cigar;     // number of CIGAR operations
	uint32_t *cigar; // CIGAR in the BAM encoding: opLen<<4|op; op to integer mapping: MIDSH=>01234

	int score, sub;
} mem_aln_t;

#ifdef __cplusplus
extern "C" {
#endif

	smem_i *smem_itr_init(const bwt_t *bwt);
	void smem_itr_destroy(smem_i *itr);
	void smem_set_query(smem_i *itr, int len, const uint8_t *query);
	const bwtintv_v *smem_next(smem_i *itr, int split_len, int split_width);

	mem_opt_t *mem_opt_init(void);
	void mem_fill_scmat(int a, int b, int8_t mat[25]);

	/**
	 * Align a batch of sequences and generate the alignments in the SAM format
	 *
	 * This routine requires $seqs[i].{l_seq,seq,name} and write $seqs[i].sam.
	 * Note that $seqs[i].sam may consist of several SAM lines if the
	 * corresponding sequence has multiple primary hits.
	 *
	 * In the paired-end mode (i.e. MEM_F_PE is set in $opt->flag), query
	 * sequences must be interleaved: $n must be an even number and the 2i-th
	 * sequence and the (2i+1)-th sequence constitute a read pair. In this
	 * mode, there should be enough (typically >50) unique pairs for the
	 * routine to infer the orientation and insert size.
	 *
	 * @param opt    alignment parameters
	 * @param bwt    FM-index of the reference sequence
	 * @param bns    Information of the reference
	 * @param pac    2-bit encoded reference
	 * @param n      number of query sequences
	 * @param seqs   query sequences; $seqs[i].seq/sam to be modified after the call
	 */
	void mem_process_seqs(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int n, bseq1_t *seqs);

	/**
	 * Find the aligned regions for one query sequence
	 *
	 * Note that this routine does not generate CIGAR. CIGAR should be
	 * generated later by mem_reg2aln() below.
	 *
	 * @param opt    alignment parameters
	 * @param bwt    FM-index of the reference sequence
	 * @param bns    Information of the reference
	 * @param pac    2-bit encoded reference
	 * @param l_seq  length of query sequence
	 * @param seq    query sequence
	 *
	 * @return       list of aligned regions.
	 */
	mem_alnreg_v mem_align1(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq);

	/**
	 * Generate CIGAR and forward-strand position from alignment region
	 *
	 * @param opt    alignment parameters
	 * @param bns    Information of the reference
	 * @param pac    2-bit encoded reference
	 * @param l_seq  length of query sequence
	 * @param seq    query sequence
	 * @param ar     one alignment region
	 *
	 * @return       CIGAR, strand, mapping quality and forward-strand position
	 */
	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq, const mem_alnreg_t *ar);

	/**
	 * Infer the insert size distribution from interleaved alignment regions
	 *
	 * This function can be called after mem_align1(), as long as paired-end
	 * reads are properly interleaved.
	 *
	 * @param opt    alignment parameters
	 * @param l_pac  length of concatenated reference sequence
	 * @param n      number of query sequences; must be an even number
	 * @param regs   region array of size $n; 2i-th and (2i+1)-th elements constitute a pair
	 * @param pes    inferred insert size distribution (output)
	 */
	void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwamem_pair.c000644 000767 000024 00000033547 12120745361 014732 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <math.h>
#include "kstring.h"
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"
#include "ksw.h"

#define MIN_RATIO     0.8
#define MIN_DIR_CNT   10
#define MIN_DIR_RATIO 0.05
#define OUTLIER_BOUND 2.0
#define MAPPING_BOUND 3.0
#define MAX_STDDEV    4.0

static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t *dist)
{
	int64_t p2;
	int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
	p2 = r1 == r2? b2 : (l_pac<<1) - 1 - b2; // p2 is the coordinate of read 2 on the read 1 strand
	*dist = p2 > b1? p2 - b1 : b1 - p2;
	return (r1 == r2? 0 : 1) ^ (p2 > b1? 0 : 3);
}

static int cal_sub(const mem_opt_t *opt, mem_alnreg_v *r)
{
	int j;
	for (j = 1; j < r->n; ++j) { // choose unique alignment
		int b_max = r->a[j].qb > r->a[0].qb? r->a[j].qb : r->a[0].qb;
		int e_min = r->a[j].qe < r->a[0].qe? r->a[j].qe : r->a[0].qe;
		if (e_min > b_max) { // have overlap
			int min_l = r->a[j].qe - r->a[j].qb < r->a[0].qe - r->a[0].qb? r->a[j].qe - r->a[j].qb : r->a[0].qe - r->a[0].qb;
			if (e_min - b_max >= min_l * opt->mask_level) break; // significant overlap
		}
	}
	return j < r->n? r->a[j].score : opt->min_seed_len * opt->a;
}

void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4])
{
	int i, d, max;
	uint64_v isize[4];
	memset(pes, 0, 4 * sizeof(mem_pestat_t));
	memset(isize, 0, sizeof(kvec_t(int)) * 4);
	for (i = 0; i < n>>1; ++i) {
		int dir;
		int64_t is;
		mem_alnreg_v *r[2];
		r[0] = (mem_alnreg_v*)&regs[i<<1|0];
		r[1] = (mem_alnreg_v*)&regs[i<<1|1];
		if (r[0]->n == 0 || r[1]->n == 0) continue;
		if (cal_sub(opt, r[0]) > MIN_RATIO * r[0]->a[0].score) continue;
		if (cal_sub(opt, r[1]) > MIN_RATIO * r[1]->a[0].score) continue;
		dir = mem_infer_dir(l_pac, r[0]->a[0].rb, r[1]->a[0].rb, &is);
		if (is && is <= opt->max_ins) kv_push(uint64_t, isize[dir], is);
	}
	if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
	for (d = 0; d < 4; ++d) { // TODO: this block is nearly identical to the one in bwtsw2_pair.c. It would be better to merge these two.
		mem_pestat_t *r = &pes[d];
		uint64_v *q = &isize[d];
		int p25, p50, p75, x;
		if (q->n < MIN_DIR_CNT) {
			fprintf(stderr, "[M::%s] skip orientation %c%c as there are not enough pairs\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
			r->failed = 1;
			continue;
		} else fprintf(stderr, "[M::%s] analyzing insert size distribution for orientation %c%c...\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
		ks_introsort_64(q->n, q->a);
		p25 = q->a[(int)(.25 * q->n + .499)];
		p50 = q->a[(int)(.50 * q->n + .499)];
		p75 = q->a[(int)(.75 * q->n + .499)];
		r->low  = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
		if (r->low < 1) r->low = 1;
		r->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
		fprintf(stderr, "[M::%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
		fprintf(stderr, "[M::%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r->low, r->high);
		for (i = x = 0, r->avg = 0; i < q->n; ++i)
			if (q->a[i] >= r->low && q->a[i] <= r->high)
				r->avg += q->a[i], ++x;
		r->avg /= x;
		for (i = 0, r->std = 0; i < q->n; ++i)
			if (q->a[i] >= r->low && q->a[i] <= r->high)
				r->std += (q->a[i] - r->avg) * (q->a[i] - r->avg);
		r->std = sqrt(r->std / x);
		fprintf(stderr, "[M::%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r->avg, r->std);
		r->low  = (int)(p25 - MAPPING_BOUND * (p75 - p25) + .499);
		r->high = (int)(p75 + MAPPING_BOUND * (p75 - p25) + .499);
		if (r->low  > r->avg - MAX_STDDEV * r->std) r->low  = (int)(r->avg - MAX_STDDEV * r->std + .499);
		if (r->high < r->avg - MAX_STDDEV * r->std) r->high = (int)(r->avg + MAX_STDDEV * r->std + .499);
		if (r->low < 1) r->low = 1;
		fprintf(stderr, "[M::%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r->low, r->high);
		free(q->a);
	}
	for (d = 0, max = 0; d < 4; ++d)
		max = max > isize[d].n? max : isize[d].n;
	for (d = 0; d < 4; ++d)
		if (pes[d].failed == 0 && isize[d].n < max * MIN_DIR_RATIO) {
			pes[d].failed = 1;
			fprintf(stderr, "[M::%s] skip orientation %c%c\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
		}
}

int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], const mem_alnreg_t *a, int l_ms, const uint8_t *ms, mem_alnreg_v *ma)
{
	int i, r, skip[4], n = 0;
	for (r = 0; r < 4; ++r)
		skip[r] = pes[r].failed? 1 : 0;
	for (i = 0; i < ma->n; ++i) { // check which orinentation has been found
		int64_t dist;
		r = mem_infer_dir(l_pac, a->rb, ma->a[i].rb, &dist);
		if (dist >= pes[r].low && dist <= pes[r].high)
			skip[r] = 1;
	}
	if (skip[0] + skip[1] + skip[2] + skip[3] == 4) return 0; // consistent pair exist; no need to perform SW
	for (r = 0; r < 4; ++r) {
		int is_rev, is_larger;
		uint8_t *seq, *rev = 0, *ref;
		int64_t rb, re, len;
		if (skip[r]) continue;
		is_rev = (r>>1 != (r&1)); // whether to reverse complement the mate
		is_larger = !(r>>1); // whether the mate has larger coordinate
		if (is_rev) {
			rev = malloc(l_ms); // this is the reverse complement of $ms
			for (i = 0; i < l_ms; ++i) rev[l_ms - 1 - i] = ms[i] < 4? 3 - ms[i] : 4;
			seq = rev;
		} else seq = (uint8_t*)ms;
		if (!is_rev) {
			rb = is_larger? a->rb + pes[r].low : a->rb - pes[r].high;
			re = (is_larger? a->rb + pes[r].high: a->rb - pes[r].low) + l_ms; // if on the same strand, end position should be larger to make room for the seq length
		} else {
			rb = (is_larger? a->rb + pes[r].low : a->rb - pes[r].high) - l_ms; // similarly on opposite strands
			re = is_larger? a->rb + pes[r].high: a->rb - pes[r].low;
		}
		if (rb < 0) rb = 0;
		if (re > l_pac<<1) re = l_pac<<1;
		ref = bns_get_seq(l_pac, pac, rb, re, &len);
		if (len == re - rb) { // no funny things happening
			kswr_t aln;
			mem_alnreg_t b;
			int tmp, xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250? KSW_XBYTE : 0) | opt->min_seed_len;
			aln = ksw_align(l_ms, seq, len, ref, 5, opt->mat, opt->q, opt->r, xtra, 0);
			memset(&b, 0, sizeof(mem_alnreg_t));
			if (aln.score >= opt->min_seed_len) {
				b.qb = is_rev? l_ms - (aln.qe + 1) : aln.qb;                                                                                                                                                                              
				b.qe = is_rev? l_ms - aln.qb : aln.qe + 1; 
				b.rb = is_rev? (l_pac<<1) - (rb + aln.te + 1) : rb + aln.tb;
				b.re = is_rev? (l_pac<<1) - (rb + aln.tb) : rb + aln.te + 1;
				b.score = aln.score;
				b.csub = aln.score2;
				b.secondary = -1;
				b.seedcov = (b.re - b.rb < b.qe - b.qb? b.re - b.rb : b.qe - b.qb) >> 1;
//				printf("*** %d, [%lld,%lld], %d:%d, (%lld,%lld), (%lld,%lld) == (%lld,%lld)\n", aln.score, rb, re, is_rev, is_larger, a->rb, a->re, ma->a[0].rb, ma->a[0].re, b.rb, b.re);
				kv_push(mem_alnreg_t, *ma, b); // make room for a new element
				// move b s.t. ma is sorted
				for (i = 0; i < ma->n - 1; ++i) // find the insertion point
					if (ma->a[i].score < b.score) break;
				tmp = i;
				for (i = ma->n - 1; i > tmp; --i) ma->a[i] = ma->a[i-1];
				ma->a[i] = b;
			}
			++n;
		}
		if (rev) free(rev);
		free(ref);
	}
	return n;
}

int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id, int *sub, int *n_sub, int z[2])
{
	pair64_v v, u;
	int r, i, k, y[4], ret; // y[] keeps the last hit
	kv_init(v); kv_init(u);
	for (r = 0; r < 2; ++r) { // loop through read number
		for (i = 0; i < a[r].n; ++i) {
			pair64_t key;
			mem_alnreg_t *e = &a[r].a[i];
			key.x = e->rb < l_pac? e->rb : (l_pac<<1) - 1 - e->rb; // forward position
			key.y = (uint64_t)e->score << 32 | i << 2 | (e->rb >= l_pac)<<1 | r;
			kv_push(pair64_t, v, key);
		}
	}
	ks_introsort_128(v.n, v.a);
	y[0] = y[1] = y[2] = y[3] = -1;
	//for (i = 0; i < v.n; ++i) printf("[%d]\t%d\t%c%ld\n", i, (int)(v.a[i].y&1)+1, "+-"[v.a[i].y>>1&1], (long)v.a[i].x);
	for (i = 0; i < v.n; ++i) {
		for (r = 0; r < 2; ++r) { // loop through direction
			int dir = r<<1 | (v.a[i].y>>1&1), which;
			if (pes[dir].failed) continue; // invalid orientation
			which = r<<1 | ((v.a[i].y&1)^1);
			if (y[which] < 0) continue; // no previous hits
			for (k = y[which]; k >= 0; --k) { // TODO: this is a O(n^2) solution in the worst case; remember to check if this loop takes a lot of time (I doubt)
				int64_t dist;
				int q;
				double ns;
				pair64_t *p;
				if ((v.a[k].y&3) != which) continue;
				dist = (int64_t)v.a[i].x - v.a[k].x;
				//printf("%d: %lld\n", k, dist);
				if (dist > pes[dir].high) break;
				if (dist < pes[dir].low)  continue;
				ns = (dist - pes[dir].avg) / pes[dir].std;
				q = (int)((v.a[i].y>>32) + (v.a[k].y>>32) + .721 * log(2. * erfc(fabs(ns) * M_SQRT1_2)) * opt->a + .499); // .721 = 1/log(4)
				if (q < 0) q = 0;
				p = kv_pushp(pair64_t, u);
				p->y = (uint64_t)k<<32 | i;
				p->x = (uint64_t)q<<32 | (hash_64(p->y ^ id<<8) & 0xffffffffU);
				//printf("[%lld,%lld]\t%d\tdist=%ld\n", v.a[k].x, v.a[i].x, q, (long)dist);
			}
		}
		y[v.a[i].y&3] = i;
	}
	if (u.n) { // found at least one proper pair
		int tmp = opt->a + opt->b > opt->q + opt->r? opt->a + opt->b : opt->q + opt->r;
		ks_introsort_128(u.n, u.a);
		i = u.a[u.n-1].y >> 32; k = u.a[u.n-1].y << 32 >> 32;
		z[v.a[i].y&1] = v.a[i].y<<32>>34; // index of the best pair
		z[v.a[k].y&1] = v.a[k].y<<32>>34;
		ret = u.a[u.n-1].x >> 32;
		*sub = u.n > 1? u.a[u.n-2].x>>32 : 0;
		for (i = (long)u.n - 2, *n_sub = 0; i >= 0; --i)
			if (*sub - (int)(u.a[i].x>>32) <= tmp) ++*n_sub;
	} else ret = 0, *sub = 0, *n_sub = 0;
	free(u.a); free(v.a);
	return ret;
}

int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
{
	extern void mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a);
	extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
	extern void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
	extern void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);

	int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
	kstring_t str;
	mem_alnreg_v b[2];
	mem_aln_t h[2];

	str.l = str.m = 0; str.s = 0;
	// perform SW for the best alignment
	kv_init(b[0]); kv_init(b[1]);
	for (i = 0; i < 2; ++i)
		for (j = 0; j < a[i].n; ++j)
			if (a[i].a[j].score >= a[i].a[0].score  - opt->pen_unpaired)
				kv_push(mem_alnreg_t, b[i], a[i].a[j]);
	for (i = 0; i < 2; ++i)
		for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
			n += mem_matesw(opt, bns->l_pac, pac, pes, &b[i].a[j], s[!i].l_seq, (uint8_t*)s[!i].seq, &a[!i]);
	free(b[0].a); free(b[1].a);
	mem_mark_primary_se(opt, a[0].n, a[0].a);
	mem_mark_primary_se(opt, a[1].n, a[1].a);
	if (opt->flag&MEM_F_NOPAIRING) goto no_pairing;
	// pairing single-end hits
	if (a[0].n && a[1].n && (o = mem_pair(opt, bns->l_pac, pac, pes, s, a, id, &subo, &n_sub, z)) > 0) {
		int is_multi[2], q_pe, score_un, q_se[2];
		// check if an end has multiple hits even after mate-SW
		for (i = 0; i < 2; ++i) {
			for (j = 1; j < a[i].n; ++j)
				if (a[i].a[j].secondary < 0 && a[i].a[j].score >= opt->T) break;
			is_multi[i] = j < a[i].n? 1 : 0;
		}
		if (is_multi[0] || is_multi[1]) goto no_pairing; // TODO: in rare cases, the true hit may be long but with low score
		// compute mapQ for the best SE hit
		score_un = a[0].a[0].score + a[1].a[0].score - opt->pen_unpaired;
		//q_pe = o && subo < o? (int)(MEM_MAPQ_COEF * (1. - (double)subo / o) * log(a[0].a[z[0]].seedcov + a[1].a[z[1]].seedcov) + .499) : 0;
		subo = subo > score_un? subo : score_un;
		q_pe = (o - subo) * 6;
		if (n_sub > 0) q_pe -= (int)(4.343 * log(n_sub+1) + .499);
		if (q_pe < 0) q_pe = 0;
		if (q_pe > 60) q_pe = 60;
		// the following assumes no split hits
		if (o > score_un) { // paired alignment is preferred
			mem_alnreg_t *c[2];
			c[0] = &a[0].a[z[0]]; c[1] = &a[1].a[z[1]];
			for (i = 0; i < 2; ++i) {
				if (c[i]->secondary >= 0)
					c[i]->sub = a[i].a[c[i]->secondary].score, c[i]->secondary = -2;
				q_se[i] = mem_approx_mapq_se(opt, c[i]);
			}
			q_se[0] = q_se[0] > q_pe? q_se[0] : q_pe < q_se[0] + 40? q_pe : q_se[0] + 40;
			q_se[1] = q_se[1] > q_pe? q_se[1] : q_pe < q_se[1] + 40? q_pe : q_se[1] + 40;
			extra_flag |= 2;
			// cap at the tandem repeat score
			q_se[0] = q_se[0] < (c[0]->score - c[0]->csub) * 6? q_se[0] : (c[0]->score - c[0]->csub) * 6;
			q_se[1] = q_se[1] < (c[1]->score - c[1]->csub) * 6? q_se[1] : (c[1]->score - c[1]->csub) * 6;
		} else { // the unpaired alignment is preferred
			z[0] = z[1] = 0;
			q_se[0] = mem_approx_mapq_se(opt, &a[0].a[0]);
			q_se[1] = mem_approx_mapq_se(opt, &a[1].a[0]);
		}
		// write SAM
		h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag;
		h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
		mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
		mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
		free(h[0].cigar); free(h[1].cigar);
	} else goto no_pairing;
	return n;

no_pairing:
	for (i = 0; i < 2; ++i) {
		if (a[i].n && a[i].a[0].score >= opt->T)
			h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[0]);
		else h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, 0);
	}
	if (h[0].rid == h[1].rid && h[0].rid >= 0) { // if the top hits from the two ends constitute a proper pair, flag it.
		int64_t dist;
		int d;
		d = mem_infer_dir(bns->l_pac, a[0].a[0].rb, a[1].a[0].rb, &dist);
		if (!pes[d].failed && dist >= pes[d].low && dist <= pes[d].high) extra_flag |= 2;
	}
	mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
	mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
	free(h[0].cigar); free(h[1].cigar);
	return n;
}
bwa-0.7.3a/bwape.c000644 000767 000024 00000067447 12120745361 013553 0ustar00lh3staff000000 000000 #include <unistd.h>
#include <math.h>
#include <stdlib.h>
#include <time.h>
#include <stdio.h>
#include <string.h>
#include "bwtaln.h"
#include "kvec.h"
#include "bntseq.h"
#include "utils.h"
#include "bwase.h"
#include "bwa.h"
#include "ksw.h"

typedef struct {
	int n;
	bwtint_t *a;
} poslist_t;

typedef struct {
	double avg, std, ap_prior;
	bwtint_t low, high, high_bayesian;
} isize_info_t;

#define b128_eq(a, b) ((a).x == (b).x && (a).y == (b).y)
#define b128_hash(a) ((uint32_t)(a).x)

#include "khash.h"
KHASH_INIT(b128, pair64_t, poslist_t, 1, b128_hash, b128_eq)

typedef struct {
	pair64_v arr;
	pair64_v pos[2];
	kvec_t(bwt_aln1_t) aln[2];
} pe_data_t;

#define MIN_HASH_WIDTH 1000

extern int g_log_n[256]; // in bwase.c
static kh_b128_t *g_hash;

void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi);
void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
int bwa_approx_mapQ(const bwa_seq_t *p, int mm);
void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2);
bntseq_t *bwa_open_nt(const char *prefix);
void bwa_print_sam_SQ(const bntseq_t *bns);
void bwa_print_sam_PG();

pe_opt_t *bwa_init_pe_opt()
{
	pe_opt_t *po;
	po = (pe_opt_t*)calloc(1, sizeof(pe_opt_t));
	po->max_isize = 500;
	po->force_isize = 0;
	po->max_occ = 100000;
	po->n_multi = 3;
	po->N_multi = 10;
	po->type = BWA_PET_STD;
	po->is_sw = 1;
	po->ap_prior = 1e-5;
	return po;
}
/*
static double ierfc(double x) // inverse erfc(); iphi(x) = M_SQRT2 *ierfc(2 * x);
{
	const double a = 0.140012;
	double b, c;
	b = log(x * (2 - x));
	c = 2./M_PI/a + b / 2.;
	return sqrt(sqrt(c * c - b / a) - c);
}
*/

// for normal distribution, this is about 3std
#define OUTLIER_BOUND 2.0

static int infer_isize(int n_seqs, bwa_seq_t *seqs[2], isize_info_t *ii, double ap_prior, int64_t L)
{
	uint64_t x, *isizes, n_ap = 0;
	int n, i, tot, p25, p75, p50, max_len = 1, tmp;
	double skewness = 0.0, kurtosis = 0.0, y;

	ii->avg = ii->std = -1.0;
	ii->low = ii->high = ii->high_bayesian = 0;
	isizes = (uint64_t*)calloc(n_seqs, 8);
	for (i = 0, tot = 0; i != n_seqs; ++i) {
		bwa_seq_t *p[2];
		p[0] = seqs[0] + i; p[1] = seqs[1] + i;
		if (p[0]->mapQ >= 20 && p[1]->mapQ >= 20) {
			x = (p[0]->pos < p[1]->pos)? p[1]->pos + p[1]->len - p[0]->pos : p[0]->pos + p[0]->len - p[1]->pos;
			if (x < 100000) isizes[tot++] = x;
		}
		if (p[0]->len > max_len) max_len = p[0]->len;
		if (p[1]->len > max_len) max_len = p[1]->len;
	}
	if (tot < 20) {
		fprintf(stderr, "[infer_isize] fail to infer insert size: too few good pairs\n");
		free(isizes);
		return -1;
	}
	ks_introsort_64(tot, isizes);
	p25 = isizes[(int)(tot*0.25 + 0.5)];
	p50 = isizes[(int)(tot*0.50 + 0.5)];
	p75 = isizes[(int)(tot*0.75 + 0.5)];
	tmp  = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
	ii->low = tmp > max_len? tmp : max_len; // ii->low is unsigned
	ii->high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
	for (i = 0, x = n = 0; i < tot; ++i)
		if (isizes[i] >= ii->low && isizes[i] <= ii->high)
			++n, x += isizes[i];
	ii->avg = (double)x / n;
	for (i = 0; i < tot; ++i) {
		if (isizes[i] >= ii->low && isizes[i] <= ii->high) {
			double tmp = (isizes[i] - ii->avg) * (isizes[i] - ii->avg);
			ii->std += tmp;
			skewness += tmp * (isizes[i] - ii->avg);
			kurtosis += tmp * tmp;
		}
	}
	kurtosis = kurtosis/n / (ii->std / n * ii->std / n) - 3;
	ii->std = sqrt(ii->std / n); // it would be better as n-1, but n is usually very large
	skewness = skewness / n / (ii->std * ii->std * ii->std);
	for (y = 1.0; y < 10.0; y += 0.01)
		if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
	ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
	for (i = 0; i < tot; ++i)
		if (isizes[i] > ii->high_bayesian) ++n_ap;
	ii->ap_prior = .01 * (n_ap + .01) / tot;
	if (ii->ap_prior < ap_prior) ii->ap_prior = ap_prior;
	free(isizes);
	fprintf(stderr, "[infer_isize] (25, 50, 75) percentile: (%d, %d, %d)\n", p25, p50, p75);
	if (isnan(ii->std) || p75 > 100000) {
		ii->low = ii->high = ii->high_bayesian = 0; ii->avg = ii->std = -1.0;
		fprintf(stderr, "[infer_isize] fail to infer insert size: weird pairing\n");
		return -1;
	}
	for (y = 1.0; y < 10.0; y += 0.01)
		if (.5 * erfc(y / M_SQRT2) < ap_prior / L * (y * ii->std + ii->avg)) break;
	ii->high_bayesian = (bwtint_t)(y * ii->std + ii->avg + .499);
	fprintf(stderr, "[infer_isize] low and high boundaries: %ld and %ld for estimating avg and std\n", (long)ii->low, (long)ii->high);
	fprintf(stderr, "[infer_isize] inferred external isize from %d pairs: %.3lf +/- %.3lf\n", n, ii->avg, ii->std);
	fprintf(stderr, "[infer_isize] skewness: %.3lf; kurtosis: %.3lf; ap_prior: %.2e\n", skewness, kurtosis, ii->ap_prior);
	fprintf(stderr, "[infer_isize] inferred maximum insert size: %ld (%.2lf sigma)\n", (long)ii->high_bayesian, y);
	return 0;
}

static int pairing(bwa_seq_t *p[2], pe_data_t *d, const pe_opt_t *opt, int s_mm, const isize_info_t *ii)
{
	int i, j, o_n, subo_n, cnt_chg = 0, low_bound = ii->low, max_len;
	uint64_t o_score, subo_score;
	pair64_t last_pos[2][2], o_pos[2];
	max_len = p[0]->full_len;
	if (max_len < p[1]->full_len) max_len = p[1]->full_len;
	if (low_bound < max_len) low_bound = max_len;

	// here v>=u. When ii is set, we check insert size with ii; otherwise with opt->max_isize
#define __pairing_aux(u,v) do { \
		bwtint_t l = (v).x + p[(v).y&1]->len - ((u).x); \
		if ((u).x != (uint64_t)-1 && (v).x > (u).x && l >= max_len \
			&& ((ii->high && l <= ii->high_bayesian) || (ii->high == 0 && l <= opt->max_isize))) \
		{ \
			uint64_t s = d->aln[(v).y&1].a[(v).y>>2].score + d->aln[(u).y&1].a[(u).y>>2].score; \
			s *= 10; \
			if (ii->high) s += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * fabs(l - ii->avg) / ii->std)) + .499); \
			s = s<<32 | (uint32_t)hash_64((u).x<<32 | (v).x); \
			if (s>>32 == o_score>>32) ++o_n; \
			else if (s>>32 < o_score>>32) { subo_n += o_n; o_n = 1; } \
			else ++subo_n; \
			if (s < o_score) subo_score = o_score, o_score = s, o_pos[(u).y&1] = (u), o_pos[(v).y&1] = (v); \
			else if (s < subo_score) subo_score = s; \
		} \
	} while (0)

#define __pairing_aux2(q, w) do { \
		const bwt_aln1_t *r = d->aln[(w).y&1].a + ((w).y>>2); \
		(q)->extra_flag |= SAM_FPP; \
		if ((q)->pos != (w).x || (q)->strand != ((w).y>>1&1)) { \
			(q)->n_mm = r->n_mm; (q)->n_gapo = r->n_gapo; (q)->n_gape = r->n_gape; (q)->strand = (w).y>>1&1; \
			(q)->score = r->score; \
			(q)->pos = (w).x; \
			if ((q)->mapQ > 0) ++cnt_chg; \
		} \
	} while (0)

	o_score = subo_score = (uint64_t)-1;
	o_n = subo_n = 0;
	ks_introsort_128(d->arr.n, d->arr.a);
	for (j = 0; j < 2; ++j) last_pos[j][0].x = last_pos[j][0].y = last_pos[j][1].x = last_pos[j][1].y = (uint64_t)-1;
	if (opt->type == BWA_PET_STD) {
		for (i = 0; i < d->arr.n; ++i) {
			pair64_t x = d->arr.a[i];
			int strand = x.y>>1&1;
			if (strand == 1) { // reverse strand, then check
				int y = 1 - (x.y&1);
				__pairing_aux(last_pos[y][1], x);
				__pairing_aux(last_pos[y][0], x);
			} else { // forward strand, then push
				last_pos[x.y&1][0] = last_pos[x.y&1][1];
				last_pos[x.y&1][1] = x;
			}
		}
	} else {
		fprintf(stderr, "[paring] not implemented yet!\n");
		exit(1);
	}
	// set pairing
	//fprintf(stderr, "[%ld, %d, %d, %d]\n", d->arr.n, (int)(o_score>>32), (int)(subo_score>>32), o_n);
	if (o_score != (uint64_t)-1) {
		int mapQ_p = 0; // this is the maximum mapping quality when one end is moved
		//fprintf(stderr, "%d, %d\n", o_n, subo_n);
		if (o_n == 1) {
			if (subo_score == (uint64_t)-1) mapQ_p = 29; // no sub-optimal pair
			else if ((subo_score>>32) - (o_score>>32) > s_mm * 10) mapQ_p = 23; // poor sub-optimal pair
			else {
				int n = subo_n > 255? 255 : subo_n;
				mapQ_p = ((subo_score>>32) - (o_score>>32)) / 2 - g_log_n[n];
				if (mapQ_p < 0) mapQ_p = 0;
			}
		}
		if ((p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) && (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1))) { // both ends not moved
			if (p[0]->mapQ > 0 && p[1]->mapQ > 0) {
				int mapQ = p[0]->mapQ + p[1]->mapQ;
				if (mapQ > 60) mapQ = 60;
				p[0]->mapQ = p[1]->mapQ = mapQ;
			} else {
				if (p[0]->mapQ == 0) p[0]->mapQ = (mapQ_p + 7 < p[1]->mapQ)? mapQ_p + 7 : p[1]->mapQ;
				if (p[1]->mapQ == 0) p[1]->mapQ = (mapQ_p + 7 < p[0]->mapQ)? mapQ_p + 7 : p[0]->mapQ;
			}
		} else if (p[0]->pos == o_pos[0].x && p[0]->strand == (o_pos[0].y>>1&1)) { // [1] moved
			p[1]->seQ = 0; p[1]->mapQ = p[0]->mapQ;
			if (p[1]->mapQ > mapQ_p) p[1]->mapQ = mapQ_p;
		} else if (p[1]->pos == o_pos[1].x && p[1]->strand == (o_pos[1].y>>1&1)) { // [0] moved
			p[0]->seQ = 0; p[0]->mapQ = p[1]->mapQ;
			if (p[0]->mapQ > mapQ_p) p[0]->mapQ = mapQ_p;
		} else { // both ends moved
			p[0]->seQ = p[1]->seQ = 0;
			mapQ_p -= 20;
			if (mapQ_p < 0) mapQ_p = 0;
			p[0]->mapQ = p[1]->mapQ = mapQ_p;
		}
		__pairing_aux2(p[0], o_pos[0]);
		__pairing_aux2(p[1], o_pos[1]);
	}
	return cnt_chg;
}

typedef struct {
	kvec_t(bwt_aln1_t) aln;
} aln_buf_t;

int bwa_cal_pac_pos_pe(const bntseq_t *bns, const char *prefix, bwt_t *const _bwt, int n_seqs, bwa_seq_t *seqs[2], FILE *fp_sa[2], isize_info_t *ii,
					   const pe_opt_t *opt, const gap_opt_t *gopt, const isize_info_t *last_ii)
{
	int i, j, cnt_chg = 0;
	char str[1024];
	bwt_t *bwt;
	pe_data_t *d;
	aln_buf_t *buf[2];

	d = (pe_data_t*)calloc(1, sizeof(pe_data_t));
	buf[0] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));
	buf[1] = (aln_buf_t*)calloc(n_seqs, sizeof(aln_buf_t));

	if (_bwt == 0) { // load forward SA
		strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
		strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
	} else bwt = _bwt;

	// SE
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p[2];
		for (j = 0; j < 2; ++j) {
			int n_aln;
			p[j] = seqs[j] + i;
			p[j]->n_multi = 0;
			p[j]->extra_flag |= SAM_FPD | (j == 0? SAM_FR1 : SAM_FR2);
			fread(&n_aln, 4, 1, fp_sa[j]);
			if (n_aln > kv_max(d->aln[j]))
				kv_resize(bwt_aln1_t, d->aln[j], n_aln);
			d->aln[j].n = n_aln;
			fread(d->aln[j].a, sizeof(bwt_aln1_t), n_aln, fp_sa[j]);
			kv_copy(bwt_aln1_t, buf[j][i].aln, d->aln[j]); // backup d->aln[j]
			// generate SE alignment and mapping quality
			bwa_aln2seq(n_aln, d->aln[j].a, p[j]);
			if (p[j]->type == BWA_TYPE_UNIQUE || p[j]->type == BWA_TYPE_REPEAT) {
				int strand;
				int max_diff = gopt->fnr > 0.0? bwa_cal_maxdiff(p[j]->len, BWA_AVG_ERR, gopt->fnr) : gopt->max_diff;
				p[j]->seQ = p[j]->mapQ = bwa_approx_mapQ(p[j], max_diff);
				p[j]->pos = bwa_sa2pos(bns, bwt, p[j]->sa, p[j]->len, &strand);
				p[j]->strand = strand;
			}
		}
	}

	// infer isize
	infer_isize(n_seqs, seqs, ii, opt->ap_prior, bwt->seq_len/2);
	if (ii->avg < 0.0 && last_ii->avg > 0.0) *ii = *last_ii;
	if (opt->force_isize) {
		fprintf(stderr, "[%s] discard insert size estimate as user's request.\n", __func__);
		ii->low = ii->high = 0; ii->avg = ii->std = -1.0;
	}

	// PE
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p[2];
		for (j = 0; j < 2; ++j) {
			p[j] = seqs[j] + i;
			kv_copy(bwt_aln1_t, d->aln[j], buf[j][i].aln);
		}
		if ((p[0]->type == BWA_TYPE_UNIQUE || p[0]->type == BWA_TYPE_REPEAT)
			&& (p[1]->type == BWA_TYPE_UNIQUE || p[1]->type == BWA_TYPE_REPEAT))
		{ // only when both ends mapped
			pair64_t x;
			int j, k;
			long long n_occ[2];
			for (j = 0; j < 2; ++j) {
				n_occ[j] = 0;
				for (k = 0; k < d->aln[j].n; ++k)
					n_occ[j] += d->aln[j].a[k].l - d->aln[j].a[k].k + 1;
			}
			if (n_occ[0] > opt->max_occ || n_occ[1] > opt->max_occ) continue;
			d->arr.n = 0;
			for (j = 0; j < 2; ++j) {
				for (k = 0; k < d->aln[j].n; ++k) {
					bwt_aln1_t *r = d->aln[j].a + k;
					bwtint_t l;
					if (0 && r->l - r->k + 1 >= MIN_HASH_WIDTH) { // then check hash table
						pair64_t key;
						int ret;
						key.x = r->k; key.y = r->l;
						khint_t iter = kh_put(b128, g_hash, key, &ret);
						if (ret) { // not in the hash table; ret must equal 1 as we never remove elements
							poslist_t *z = &kh_val(g_hash, iter);
							z->n = r->l - r->k + 1;
							z->a = (bwtint_t*)malloc(sizeof(bwtint_t) * z->n);
							for (l = r->k; l <= r->l; ++l) {
								int strand;
								z->a[l - r->k] = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand)<<1;
								z->a[l - r->k] |= strand;
							}
						}
						for (l = 0; l < kh_val(g_hash, iter).n; ++l) {
							x.x = kh_val(g_hash, iter).a[l]>>1;
							x.y = k<<2 | (kh_val(g_hash, iter).a[l]&1)<<1 | j;
							kv_push(pair64_t, d->arr, x);
						}
					} else { // then calculate on the fly
						for (l = r->k; l <= r->l; ++l) {
							int strand;
							x.x = bwa_sa2pos(bns, bwt, l, p[j]->len, &strand);
							x.y = k<<2 | strand<<1 | j;
							kv_push(pair64_t, d->arr, x);
						}
					}
				}
			}
			cnt_chg += pairing(p, d, opt, gopt->s_mm, ii);
		}

		if (opt->N_multi || opt->n_multi) {
			for (j = 0; j < 2; ++j) {
				if (p[j]->type != BWA_TYPE_NO_MATCH) {
					int k, n_multi;
					if (!(p[j]->extra_flag&SAM_FPP) && p[1-j]->type != BWA_TYPE_NO_MATCH) {
						bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, p[j]->c1+p[j]->c2-1 > opt->N_multi? opt->n_multi : opt->N_multi);
					} else bwa_aln2seq_core(d->aln[j].n, d->aln[j].a, p[j], 0, opt->n_multi);
					for (k = 0, n_multi = 0; k < p[j]->n_multi; ++k) {
						int strand;
						bwt_multi1_t *q = p[j]->multi + k;
						q->pos = bwa_sa2pos(bns, bwt, q->pos, p[j]->len, &strand);
						q->strand = strand;
						if (q->pos != p[j]->pos)
							p[j]->multi[n_multi++] = *q;
					}
					p[j]->n_multi = n_multi;
				}
			}
		}
	}

	// free
	for (i = 0; i < n_seqs; ++i) {
		kv_destroy(buf[0][i].aln);
		kv_destroy(buf[1][i].aln);
	}
	free(buf[0]); free(buf[1]);
	if (_bwt == 0) bwt_destroy(bwt);
	kv_destroy(d->arr);
	kv_destroy(d->pos[0]); kv_destroy(d->pos[1]);
	kv_destroy(d->aln[0]); kv_destroy(d->aln[1]);
	free(d);
	return cnt_chg;
}

#define SW_MIN_MATCH_LEN 20
#define SW_MIN_MAPQ 17

// cnt = n_mm<<16 | n_gapo<<8 | n_gape
bwa_cigar_t *bwa_sw_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, const ubyte_t *seq, int64_t *beg, int reglen, int *n_cigar, uint32_t *_cnt)
{
	kswr_t r;
	uint32_t *cigar32 = 0;
	bwa_cigar_t *cigar = 0;
	ubyte_t *ref_seq;
	bwtint_t k, x, y, l;
	int xtra;
	int8_t mat[25];

	bwa_fill_scmat(1, 3, mat);
	// check whether there are too many N's
	if (reglen < SW_MIN_MATCH_LEN || (int64_t)l_pac - *beg < len) return 0;
	for (k = 0, x = 0; k < len; ++k)
		if (seq[k] >= 4) ++x;
	if ((float)x/len >= 0.25 || len - x < SW_MIN_MATCH_LEN) return 0;

	// get reference subsequence
	ref_seq = (ubyte_t*)calloc(reglen, 1);
	for (k = *beg, l = 0; l < reglen && k < l_pac; ++k)
		ref_seq[l++] = pacseq[k>>2] >> ((~k&3)<<1) & 3;

	// do alignment
	xtra = KSW_XSUBO | KSW_XSTART | (len < 250? KSW_XBYTE : 0);
	r = ksw_align(len, (uint8_t*)seq, l, ref_seq, 5, mat, 5, 1, xtra, 0);
	ksw_global(r.qe - r.qb + 1, &seq[r.qb], r.te - r.tb + 1, &ref_seq[r.tb], 5, mat, 5, 1, 50, n_cigar, &cigar32);
	cigar = (bwa_cigar_t*)cigar32;
	for (k = 0; k < *n_cigar; ++k)
		cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));

	if (r.score < SW_MIN_MATCH_LEN || r.score2 == r.score) { // poor hit or tandem hits
		free(cigar); free(ref_seq); *n_cigar = 0;
		return 0;
	}

	// check whether the alignment is good enough
	for (k = 0, x = y = 0; k < *n_cigar; ++k) {
		bwa_cigar_t c = cigar[k];
		if (__cigar_op(c) == FROM_M) x += __cigar_len(c), y += __cigar_len(c);
		else if (__cigar_op(c) == FROM_D) x += __cigar_len(c);
		else y += __cigar_len(c);
	}
	if (x < SW_MIN_MATCH_LEN || y < SW_MIN_MATCH_LEN) { // not good enough
		free(cigar); free(ref_seq);
		*n_cigar = 0;
		return 0;
	}

	{ // update cigar and coordinate;
		int start = r.qb, end = r.qe + 1;
		*beg += r.tb;
		cigar = (bwa_cigar_t*)realloc(cigar, sizeof(bwa_cigar_t) * (*n_cigar + 2));
		if (start) {
			memmove(cigar + 1, cigar, sizeof(bwa_cigar_t) * (*n_cigar));
			cigar[0] = __cigar_create(3, start);
			++(*n_cigar);
		}
		if (end < len) {
			/*cigar[*n_cigar] = 3<<14 | (len - end);*/
			cigar[*n_cigar] = __cigar_create(3, (len - end));
			++(*n_cigar);
		}
	}

	{ // set *cnt
		int n_mm, n_gapo, n_gape;
		n_mm = n_gapo = n_gape = 0;
		x = r.tb; y = r.qb;
		for (k = 0; k < *n_cigar; ++k) {
			bwa_cigar_t c = cigar[k];
			if (__cigar_op(c) == FROM_M) {
				for (l = 0; l < (__cigar_len(c)); ++l)
					if (ref_seq[x+l] < 4 && seq[y+l] < 4 && ref_seq[x+l] != seq[y+l]) ++n_mm;
				x += __cigar_len(c), y += __cigar_len(c);
			} else if (__cigar_op(c) == FROM_D) {
				x += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
			} else if (__cigar_op(c) == FROM_I) {
				y += __cigar_len(c), ++n_gapo, n_gape += (__cigar_len(c)) - 1;
			}
		}
		*_cnt = (uint32_t)n_mm<<16 | n_gapo<<8 | n_gape;
	}
	
	free(ref_seq);
	return cigar;
}

ubyte_t *bwa_paired_sw(const bntseq_t *bns, const ubyte_t *_pacseq, int n_seqs, bwa_seq_t *seqs[2], const pe_opt_t *popt, const isize_info_t *ii)
{
	ubyte_t *pacseq;
	int i;
	uint64_t n_tot[2], n_mapped[2];

	// load reference sequence
	if (_pacseq == 0) {
		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
		rewind(bns->fp_pac);
		fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
	} else pacseq = (ubyte_t*)_pacseq;
	if (!popt->is_sw || ii->avg < 0.0) return pacseq;

	// perform mate alignment
	n_tot[0] = n_tot[1] = n_mapped[0] = n_mapped[1] = 0;
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p[2];
		p[0] = seqs[0] + i; p[1] = seqs[1] + i;
		if ((p[0]->mapQ >= SW_MIN_MAPQ || p[1]->mapQ >= SW_MIN_MAPQ) && (p[0]->extra_flag&SAM_FPP) == 0) { // unpaired and one read has high mapQ
			int k, n_cigar[2], is_singleton, mapQ = 0, mq_adjust[2];
			int64_t beg[2], end[2];
			bwa_cigar_t *cigar[2];
			uint32_t cnt[2];

			/* In the following, _pref points to the reference read
			 * which must be aligned; _pmate points to its mate which is
			 * considered to be modified. */

#define __set_rght_coor(_a, _b, _pref, _pmate) do {						\
				(_a) = (int64_t)_pref->pos + ii->avg - 3 * ii->std - _pmate->len * 1.5; \
				(_b) = (_a) + 6 * ii->std + 2 * _pmate->len;			\
				if ((_a) < (int64_t)_pref->pos + _pref->len) (_a) = _pref->pos + _pref->len; \
				if ((_b) > bns->l_pac) (_b) = bns->l_pac;				\
			} while (0)

#define __set_left_coor(_a, _b, _pref, _pmate) do {						\
				(_a) = (int64_t)_pref->pos + _pref->len - ii->avg - 3 * ii->std - _pmate->len * 0.5; \
				(_b) = (_a) + 6 * ii->std + 2 * _pmate->len;			\
				if ((_a) < 0) (_a) = 0;									\
				if ((_b) > _pref->pos) (_b) = _pref->pos;				\
			} while (0)
			
#define __set_fixed(_pref, _pmate, _beg, _cnt) do {						\
				_pmate->type = BWA_TYPE_MATESW;							\
				_pmate->pos = _beg;										\
				_pmate->seQ = _pref->seQ;								\
				_pmate->strand = (popt->type == BWA_PET_STD)? 1 - _pref->strand : _pref->strand; \
				_pmate->n_mm = _cnt>>16; _pmate->n_gapo = _cnt>>8&0xff; _pmate->n_gape = _cnt&0xff; \
				_pmate->extra_flag |= SAM_FPP;							\
				_pref->extra_flag |= SAM_FPP;							\
			} while (0)

			mq_adjust[0] = mq_adjust[1] = 255; // not effective
			is_singleton = (p[0]->type == BWA_TYPE_NO_MATCH || p[1]->type == BWA_TYPE_NO_MATCH)? 1 : 0;

			++n_tot[is_singleton];
			cigar[0] = cigar[1] = 0;
			n_cigar[0] = n_cigar[1] = 0;
			if (popt->type != BWA_PET_STD) continue; // other types of pairing is not considered
			for (k = 0; k < 2; ++k) { // p[1-k] is the reference read and p[k] is the read considered to be modified
				ubyte_t *seq;
				if (p[1-k]->type == BWA_TYPE_NO_MATCH) continue; // if p[1-k] is unmapped, skip
				{ // note that popt->type == BWA_PET_STD always true; in older versions, there was a branch for color-space FF/RR reads
					if (p[1-k]->strand == 0) { // then the mate is on the reverse strand and has larger coordinate
						__set_rght_coor(beg[k], end[k], p[1-k], p[k]);
						seq = p[k]->rseq;
					} else { // then the mate is on forward stand and has smaller coordinate
						__set_left_coor(beg[k], end[k], p[1-k], p[k]);
						seq = p[k]->seq;
						seq_reverse(p[k]->len, seq, 0); // because ->seq is reversed; this will reversed back shortly
					}
				}
				// perform SW alignment
				cigar[k] = bwa_sw_core(bns->l_pac, pacseq, p[k]->len, seq, &beg[k], end[k] - beg[k], &n_cigar[k], &cnt[k]);
				if (cigar[k] && p[k]->type != BWA_TYPE_NO_MATCH) { // re-evaluate cigar[k]
					int s_old, clip = 0, s_new;
					if (__cigar_op(cigar[k][0]) == 3) clip += __cigar_len(cigar[k][0]);
					if (__cigar_op(cigar[k][n_cigar[k]-1]) == 3) clip += __cigar_len(cigar[k][n_cigar[k]-1]);
					s_old = (int)((p[k]->n_mm * 9 + p[k]->n_gapo * 13 + p[k]->n_gape * 2) / 3. * 8. + .499);
					s_new = (int)(((cnt[k]>>16) * 9 + (cnt[k]>>8&0xff) * 13 + (cnt[k]&0xff) * 2 + clip * 3) / 3. * 8. + .499);
					s_old += -4.343 * log(ii->ap_prior / bns->l_pac);
					s_new += (int)(-4.343 * log(.5 * erfc(M_SQRT1_2 * 1.5) + .499)); // assume the mapped isize is 1.5\sigma
					if (s_old < s_new) { // reject SW alignment
						mq_adjust[k] = s_new - s_old;
						free(cigar[k]); cigar[k] = 0; n_cigar[k] = 0;
					} else mq_adjust[k] = s_old - s_new;
				}
				// now revserse sequence back such that p[*]->seq looks untouched
				if (popt->type == BWA_PET_STD) {
					if (p[1-k]->strand == 1) seq_reverse(p[k]->len, seq, 0);
				} else {
					if (p[1-k]->strand == 0) seq_reverse(p[k]->len, seq, 0);
				}
			}
			k = -1; // no read to be changed
			if (cigar[0] && cigar[1]) {
				k = p[0]->mapQ < p[1]->mapQ? 0 : 1; // p[k] to be fixed
				mapQ = abs(p[1]->mapQ - p[0]->mapQ);
			} else if (cigar[0]) k = 0, mapQ = p[1]->mapQ;
			else if (cigar[1]) k = 1, mapQ = p[0]->mapQ;
			if (k >= 0 && p[k]->pos != beg[k]) {
				++n_mapped[is_singleton];
				{ // recalculate mapping quality
					int tmp = (int)p[1-k]->mapQ - p[k]->mapQ/2 - 8;
					if (tmp <= 0) tmp = 1;
					if (mapQ > tmp) mapQ = tmp;
					p[k]->mapQ = p[1-k]->mapQ = mapQ;
					p[k]->seQ = p[1-k]->seQ = p[1-k]->seQ < mapQ? p[1-k]->seQ : mapQ;
					if (p[k]->mapQ > mq_adjust[k]) p[k]->mapQ = mq_adjust[k];
					if (p[k]->seQ > mq_adjust[k]) p[k]->seQ = mq_adjust[k];
				}
				// update CIGAR
				free(p[k]->cigar); p[k]->cigar = cigar[k]; cigar[k] = 0;
				p[k]->n_cigar = n_cigar[k];
				// update the rest of information
				__set_fixed(p[1-k], p[k], beg[k], cnt[k]);
			}
			free(cigar[0]); free(cigar[1]);
		}
	}
	fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d singletons are mated.\n",
			(long long)n_mapped[1], (long long)n_tot[1], SW_MIN_MAPQ);
	fprintf(stderr, "[bwa_paired_sw] %lld out of %lld Q%d discordant pairs are fixed.\n",
			(long long)n_mapped[0], (long long)n_tot[0], SW_MIN_MAPQ);
	return pacseq;
}

void bwa_sai2sam_pe_core(const char *prefix, char *const fn_sa[2], char *const fn_fa[2], pe_opt_t *popt, const char *rg_line)
{
	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
	int i, j, n_seqs, tot_seqs = 0;
	bwa_seq_t *seqs[2];
	bwa_seqio_t *ks[2];
	clock_t t;
	bntseq_t *bns;
	FILE *fp_sa[2];
	gap_opt_t opt, opt0;
	khint_t iter;
	isize_info_t last_ii; // this is for the last batch of reads
	char str[1024];
	bwt_t *bwt;
	uint8_t *pac;

	// initialization
	bwase_initialize(); // initialize g_log_n[] in bwase.c
	pac = 0; bwt = 0;
	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
	bns = bns_restore(prefix);
	srand48(bns->seed);
	fp_sa[0] = xopen(fn_sa[0], "r");
	fp_sa[1] = xopen(fn_sa[1], "r");
	g_hash = kh_init(b128);
	last_ii.avg = -1.0;

	fread(&opt, sizeof(gap_opt_t), 1, fp_sa[0]);
	ks[0] = bwa_open_reads(opt.mode, fn_fa[0]);
	opt0 = opt;
	fread(&opt, sizeof(gap_opt_t), 1, fp_sa[1]); // overwritten!
	ks[1] = bwa_open_reads(opt.mode, fn_fa[1]);
	{ // for Illumina alignment only
		if (popt->is_preload) {
			strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
			strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
			pac = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
			rewind(bns->fp_pac);
			fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
		}
	}

	// core loop
	bwa_print_sam_hdr(bns, rg_line);
	bwa_print_sam_PG();
	while ((seqs[0] = bwa_read_seq(ks[0], 0x40000, &n_seqs, opt0.mode, opt0.trim_qual)) != 0) {
		int cnt_chg;
		isize_info_t ii;
		ubyte_t *pacseq;

		seqs[1] = bwa_read_seq(ks[1], 0x40000, &n_seqs, opt.mode, opt.trim_qual);
		tot_seqs += n_seqs;
		t = clock();

		fprintf(stderr, "[bwa_sai2sam_pe_core] convert to sequence coordinate... \n");
		cnt_chg = bwa_cal_pac_pos_pe(bns, prefix, bwt, n_seqs, seqs, fp_sa, &ii, popt, &opt, &last_ii);
		fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
		fprintf(stderr, "[bwa_sai2sam_pe_core] changing coordinates of %d alignments.\n", cnt_chg);

		fprintf(stderr, "[bwa_sai2sam_pe_core] align unmapped mate...\n");
		pacseq = bwa_paired_sw(bns, pac, n_seqs, seqs, popt, &ii);
		fprintf(stderr, "[bwa_sai2sam_pe_core] time elapses: %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		fprintf(stderr, "[bwa_sai2sam_pe_core] refine gapped alignments... ");
		for (j = 0; j < 2; ++j)
			bwa_refine_gapped(bns, n_seqs, seqs[j], pacseq);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
		if (pac == 0) free(pacseq);

		fprintf(stderr, "[bwa_sai2sam_pe_core] print alignments... ");
		for (i = 0; i < n_seqs; ++i) {
			bwa_seq_t *p[2];
			p[0] = seqs[0] + i; p[1] = seqs[1] + i;
			if (p[0]->bc[0] || p[1]->bc[0]) {
				strcat(p[0]->bc, p[1]->bc);
				strcpy(p[1]->bc, p[0]->bc);
			}
			bwa_print_sam1(bns, p[0], p[1], opt.mode, opt.max_top2);
			bwa_print_sam1(bns, p[1], p[0], opt.mode, opt.max_top2);
		}
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		for (j = 0; j < 2; ++j)
			bwa_free_read_seq(n_seqs, seqs[j]);
		fprintf(stderr, "[bwa_sai2sam_pe_core] %d sequences have been processed.\n", tot_seqs);
		last_ii = ii;
	}

	// destroy
	bns_destroy(bns);
	for (i = 0; i < 2; ++i) {
		bwa_seq_close(ks[i]);
		fclose(fp_sa[i]);
	}
	for (iter = kh_begin(g_hash); iter != kh_end(g_hash); ++iter)
		if (kh_exist(g_hash, iter)) free(kh_val(g_hash, iter).a);
	kh_destroy(b128, g_hash);
	if (pac) {
		free(pac); bwt_destroy(bwt);
	}
}

int bwa_sai2sam_pe(int argc, char *argv[])
{
	int c;
	pe_opt_t *popt;
	char *prefix, *rg_line = 0;

	popt = bwa_init_pe_opt();
	while ((c = getopt(argc, argv, "a:o:sPn:N:c:f:Ar:")) >= 0) {
		switch (c) {
		case 'r':
			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
			break;
		case 'a': popt->max_isize = atoi(optarg); break;
		case 'o': popt->max_occ = atoi(optarg); break;
		case 's': popt->is_sw = 0; break;
		case 'P': popt->is_preload = 1; break;
		case 'n': popt->n_multi = atoi(optarg); break;
		case 'N': popt->N_multi = atoi(optarg); break;
		case 'c': popt->ap_prior = atof(optarg); break;
		case 'f': xreopen(optarg, "w", stdout); break;
		case 'A': popt->force_isize = 1; break;
		default: return 1;
		}
	}

	if (optind + 5 > argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   bwa sampe [options] <prefix> <in1.sai> <in2.sai> <in1.fq> <in2.fq>\n\n");
		fprintf(stderr, "Options: -a INT   maximum insert size [%d]\n", popt->max_isize);
		fprintf(stderr, "         -o INT   maximum occurrences for one end [%d]\n", popt->max_occ);
		fprintf(stderr, "         -n INT   maximum hits to output for paired reads [%d]\n", popt->n_multi);
		fprintf(stderr, "         -N INT   maximum hits to output for discordant pairs [%d]\n", popt->N_multi);
		fprintf(stderr, "         -c FLOAT prior of chimeric rate (lower bound) [%.1le]\n", popt->ap_prior);
        fprintf(stderr, "         -f FILE  sam file to output results to [stdout]\n");
		fprintf(stderr, "         -r STR   read group header line such as `@RG\\tID:foo\\tSM:bar' [null]\n");
		fprintf(stderr, "         -P       preload index into memory (for base-space reads only)\n");
		fprintf(stderr, "         -s       disable Smith-Waterman for the unmapped mate\n");
		fprintf(stderr, "         -A       disable insert size estimate (force -s)\n\n");
		fprintf(stderr, "Notes: 1. For SOLiD reads, <in1.fq> corresponds R3 reads and <in2.fq> to F3.\n");
		fprintf(stderr, "       2. For reads shorter than 30bp, applying a smaller -o is recommended to\n");
		fprintf(stderr, "          to get a sensible speed at the cost of pairing accuracy.\n");
		fprintf(stderr, "\n");
		return 1;
	}
	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
		return 0;
	}
	bwa_sai2sam_pe_core(prefix, argv + optind + 1, argv + optind+3, popt, rg_line);
	free(prefix); free(popt);
	return 0;
}
bwa-0.7.3a/bwase.c000644 000767 000024 00000044650 12120745361 013545 0ustar00lh3staff000000 000000 #include <unistd.h>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include "bwase.h"
#include "bwtaln.h"
#include "bntseq.h"
#include "utils.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"

int g_log_n[256];

void bwa_print_sam_PG();

void bwa_aln2seq_core(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s, int set_main, int n_multi)
{
	int i, cnt, best;
	if (n_aln == 0) {
		s->type = BWA_TYPE_NO_MATCH;
		s->c1 = s->c2 = 0;
		return;
	}

	if (set_main) {
		best = aln[0].score;
		for (i = cnt = 0; i < n_aln; ++i) {
			const bwt_aln1_t *p = aln + i;
			if (p->score > best) break;
			if (drand48() * (p->l - p->k + 1 + cnt) > (double)cnt) {
				s->n_mm = p->n_mm; s->n_gapo = p->n_gapo; s->n_gape = p->n_gape;
				s->score = p->score;
				s->sa = p->k + (bwtint_t)((p->l - p->k + 1) * drand48());
			}
			cnt += p->l - p->k + 1;
		}
		s->c1 = cnt;
		for (; i < n_aln; ++i) cnt += aln[i].l - aln[i].k + 1;
		s->c2 = cnt - s->c1;
		s->type = s->c1 > 1? BWA_TYPE_REPEAT : BWA_TYPE_UNIQUE;
	}

	if (n_multi) {
		int k, rest, n_occ, z = 0;
		for (k = n_occ = 0; k < n_aln; ++k) {
			const bwt_aln1_t *q = aln + k;
			n_occ += q->l - q->k + 1;
		}
		if (s->multi) free(s->multi);
		if (n_occ > n_multi + 1) { // if there are too many hits, generate none of them
			s->multi = 0; s->n_multi = 0;
			return;
		}
		/* The following code is more flexible than what is required
		 * here. In principle, due to the requirement above, we can
		 * simply output all hits, but the following samples "rest"
		 * number of random hits. */
		rest = n_occ > n_multi + 1? n_multi + 1 : n_occ; // find one additional for ->sa
		s->multi = calloc(rest, sizeof(bwt_multi1_t));
		for (k = 0; k < n_aln; ++k) {
			const bwt_aln1_t *q = aln + k;
			if (q->l - q->k + 1 <= rest) {
				bwtint_t l;
				for (l = q->k; l <= q->l; ++l) {
					s->multi[z].pos = l;
					s->multi[z].gap = q->n_gapo + q->n_gape;
					s->multi[z++].mm = q->n_mm;
				}
				rest -= q->l - q->k + 1;
			} else { // Random sampling (http://code.activestate.com/recipes/272884/). In fact, we never come here. 
				int j, i;
				for (j = rest, i = q->l - q->k + 1; j > 0; --j) {
					double p = 1.0, x = drand48();
					while (x < p) p -= p * j / (i--);
					s->multi[z].pos = q->l - i;
					s->multi[z].gap = q->n_gapo + q->n_gape;
					s->multi[z++].mm = q->n_mm;
				}
				rest = 0;
				break;
			}
		}
		s->n_multi = z;
	}
}

void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s)
{
	bwa_aln2seq_core(n_aln, aln, s, 1, 0);
}

int bwa_approx_mapQ(const bwa_seq_t *p, int mm)
{
	int n;
	if (p->c1 == 0) return 23;
	if (p->c1 > 1) return 0;
	if (p->n_mm == mm) return 25;
	if (p->c2 == 0) return 37;
	n = (p->c2 >= 255)? 255 : p->c2;
	return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
}

bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand)
{
	bwtint_t pos_f;
	int is_rev;
	pos_f = bns_depos(bns, bwt_sa(bwt, sapos), &is_rev); // pos_f
	*strand = !is_rev;
	/* NB: For gapped alignment, pacpos may not be correct, which will be fixed
	 * in bwa_refine_gapped_core(). This line also determines the way "x" is
	 * calculated in bwa_refine_gapped_core() when (ext < 0 && is_end == 0). */
	if (is_rev) pos_f = pos_f + 1 < len? 0 : pos_f - len + 1; // mapped to the forward strand
	return pos_f; // FIXME: it is possible that pos_f < bns->anns[ref_id].offset
}

/**
 * Derive the actual position in the read from the given suffix array
 * coordinates. Note that the position will be approximate based on
 * whether indels appear in the read and whether calculations are
 * performed from the start or end of the read.
 */
void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t *bwt, bwa_seq_t *seq, const int max_mm, const float fnr)
{
	int max_diff, strand;
	if (seq->type != BWA_TYPE_UNIQUE && seq->type != BWA_TYPE_REPEAT) return;
	max_diff = fnr > 0.0? bwa_cal_maxdiff(seq->len, BWA_AVG_ERR, fnr) : max_mm;
	seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
	seq->pos = bwa_sa2pos(bns, bwt, seq->sa, seq->len, &strand);
	seq->strand = strand;
	seq->seQ = seq->mapQ = bwa_approx_mapQ(seq, max_diff);
}

void bwa_cal_pac_pos(const bntseq_t *bns, const char *prefix, int n_seqs, bwa_seq_t *seqs, int max_mm, float fnr)
{
	int i, j, strand, n_multi;
	char str[1024];
	bwt_t *bwt;
	// load forward SA
	strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
	strcpy(str, prefix); strcat(str, ".sa"); bwt_restore_sa(str, bwt);
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p = &seqs[i];
		bwa_cal_pac_pos_core(bns, bwt, p, max_mm, fnr);
		for (j = n_multi = 0; j < p->n_multi; ++j) {
			bwt_multi1_t *q = p->multi + j;
			q->pos = bwa_sa2pos(bns, bwt, q->pos, p->len, &strand);
			q->strand = strand;
			if (q->pos != p->pos)
				p->multi[n_multi++] = *q;
		}
		p->n_multi = n_multi;
	}
	bwt_destroy(bwt);
}

#define SW_BW 50

bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int len, ubyte_t *seq, bwtint_t *_pos, int *n_cigar, int is_rev)
{
	bwa_cigar_t *cigar = 0;
	uint32_t *cigar32 = 0;
	ubyte_t *rseq;
	int tle, qle, gtle, gscore;
	int64_t k, rb, re, rlen;
	int8_t mat[25];

	bwa_fill_scmat(1, 3, mat);
	if (!is_rev) { // forward strand, the end position is correct
		re = *_pos + len;
		if (re > l_pac) re = l_pac;
		rb = re - (len + SW_BW);
		if (rb < 0) rb = 0;
		rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
		seq_reverse(len, seq, 0); // as we need to do left extension, we have to reverse both query and reference sequences
		seq_reverse(rlen, rseq, 0);
		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
		if (gscore > 0) tle = gtle, qle = len;
		rb = re - tle; rlen = tle;
		seq_reverse(len, seq, 0);
		seq_reverse(rlen, rseq, 0);
		ksw_global(qle, &seq[len-qle], rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32);
		if (qle < len) { // write soft clip
			cigar = realloc(cigar, (*n_cigar + 1) * 4);
			memmove(cigar + 1, cigar, *n_cigar * 4);
			cigar[0] = (len - qle)<<4 | FROM_S;
			++(*n_cigar);
		}
	} else { // reverse strand, the start position is correct
		rb = *_pos; re = rb + len + SW_BW;
		if (re > l_pac) re = l_pac;
		rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
		ksw_extend(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, -1, len<<1, &qle, &tle, &gtle, &gscore, 0);
		if (gscore > 0) tle = gtle, qle = len;
		re = rb + tle; rlen = tle;
		ksw_global(qle, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); // right extension
		if (qle < len) {
			cigar = realloc(cigar, (*n_cigar + 1) * 4);
			cigar[*n_cigar - 1] = (len - qle)<<4 | FROM_S;
			++(*n_cigar);
		}
	}
	*_pos = rb;

	cigar = (bwa_cigar_t*)cigar32;
	for (k = 0; k < *n_cigar; ++k)
		cigar[k] = __cigar_create((cigar32[k]&0xf), (cigar32[k]>>4));
	free(rseq);
	return cigar;
}

char *bwa_cal_md1(int n_cigar, bwa_cigar_t *cigar, int len, bwtint_t pos, ubyte_t *seq,
				  bwtint_t l_pac, ubyte_t *pacseq, kstring_t *str, int *_nm)
{
	bwtint_t x, y;
	int z, u, c, nm = 0;
	str->l = 0; // reset
	x = pos; y = 0;
	if (cigar) {
		int k, l;
		for (k = u = 0; k < n_cigar; ++k) {
			l = __cigar_len(cigar[k]);
			if (__cigar_op(cigar[k]) == FROM_M) {
				for (z = 0; z < l && x+z < l_pac; ++z) {
					c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
					if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
						ksprintf(str, "%d", u);
						kputc("ACGTN"[c], str);
						++nm;
						u = 0;
					} else ++u;
				}
				x += l; y += l;
			} else if (__cigar_op(cigar[k]) == FROM_I || __cigar_op(cigar[k]) == FROM_S) {
				y += l;
				if (__cigar_op(cigar[k]) == FROM_I) nm += l;
			} else if (__cigar_op(cigar[k]) == FROM_D) {
				ksprintf(str, "%d", u);
				kputc('^', str);
				for (z = 0; z < l && x+z < l_pac; ++z)
					kputc("ACGT"[pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3], str);
				u = 0;
				x += l; nm += l;
			}
		}
	} else { // no gaps
		for (z = u = 0; z < (bwtint_t)len && x+z < l_pac; ++z) {
			c = pacseq[(x+z)>>2] >> ((~(x+z)&3)<<1) & 3;
			if (c > 3 || seq[y+z] > 3 || c != seq[y+z]) {
				ksprintf(str, "%d", u);
				kputc("ACGTN"[c], str);
				++nm;
				u = 0;
			} else ++u;
		}
	}
	ksprintf(str, "%d", u);
	*_nm = nm;
	return strdup(str->s);
}

void bwa_correct_trimmed(bwa_seq_t *s)
{
	if (s->len == s->full_len) return;
	if (s->strand == 0) { // forward
		if (s->cigar && __cigar_op(s->cigar[s->n_cigar-1]) == FROM_S) { // the last is S
			s->cigar[s->n_cigar-1] += s->full_len - s->len;
		} else {
			if (s->cigar == 0) {
				s->n_cigar = 2;
				s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
				s->cigar[0] = __cigar_create(0, s->len);
			} else {
				++s->n_cigar;
				s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
			}
			s->cigar[s->n_cigar-1] = __cigar_create(3, (s->full_len - s->len));
		}
	} else { // reverse
		if (s->cigar && __cigar_op(s->cigar[0]) == FROM_S) { // the first is S
			s->cigar[0] += s->full_len - s->len;
		} else {
			if (s->cigar == 0) {
				s->n_cigar = 2;
				s->cigar = calloc(s->n_cigar, sizeof(bwa_cigar_t));
				s->cigar[1] = __cigar_create(0, s->len);
			} else {
				++s->n_cigar;
				s->cigar = realloc(s->cigar, s->n_cigar * sizeof(bwa_cigar_t));
				memmove(s->cigar + 1, s->cigar, (s->n_cigar-1) * sizeof(bwa_cigar_t));
			}
			s->cigar[0] = __cigar_create(3, (s->full_len - s->len));
		}
	}
	s->len = s->full_len;
}

void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq)
{
	ubyte_t *pacseq;
	int i, j;
	kstring_t *str;

	if (!_pacseq) {
		pacseq = (ubyte_t*)calloc(bns->l_pac/4+1, 1);
		rewind(bns->fp_pac);
		fread(pacseq, 1, bns->l_pac/4+1, bns->fp_pac);
	} else pacseq = _pacseq;
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *s = seqs + i;
		seq_reverse(s->len, s->seq, 0); // IMPORTANT: s->seq is reversed here!!!
		for (j = 0; j < s->n_multi; ++j) {
			bwt_multi1_t *q = s->multi + j;
			int n_cigar;
			if (q->gap == 0) continue;
			q->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, q->strand? s->rseq : s->seq, &q->pos, &n_cigar, q->strand);
			q->n_cigar = n_cigar;
		}
		if (s->type == BWA_TYPE_NO_MATCH || s->type == BWA_TYPE_MATESW || s->n_gapo == 0) continue;
		s->cigar = bwa_refine_gapped_core(bns->l_pac, pacseq, s->len, s->strand? s->rseq : s->seq, &s->pos, &s->n_cigar, s->strand);
	}
	// generate MD tag
	str = (kstring_t*)calloc(1, sizeof(kstring_t));
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *s = seqs + i;
		if (s->type != BWA_TYPE_NO_MATCH) {
			int nm;
			s->md = bwa_cal_md1(s->n_cigar, s->cigar, s->len, s->pos, s->strand? s->rseq : s->seq,
								bns->l_pac, pacseq, str, &nm);
			s->nm = nm;
		}
	}
	free(str->s); free(str);

	// correct for trimmed reads
	for (i = 0; i < n_seqs; ++i) bwa_correct_trimmed(seqs + i);

	if (!_pacseq) free(pacseq);
}

int64_t pos_end(const bwa_seq_t *p)
{
	if (p->cigar) {
		int j;
		int64_t x = p->pos;
		for (j = 0; j != p->n_cigar; ++j) {
			int op = __cigar_op(p->cigar[j]);
			if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
		}
		return x;
	} else return p->pos + p->len;
}

int64_t pos_end_multi(const bwt_multi1_t *p, int len) // analogy to pos_end()
{
	if (p->cigar) {
		int j;
		int64_t x = p->pos;
		for (j = 0; j != p->n_cigar; ++j) {
			int op = __cigar_op(p->cigar[j]);
			if (op == 0 || op == 2) x += __cigar_len(p->cigar[j]);
		}
		return x;
	} else return p->pos + len;
}

static int64_t pos_5(const bwa_seq_t *p)
{
	if (p->type != BWA_TYPE_NO_MATCH)
		return p->strand? pos_end(p) : p->pos;
	return -1;
}

void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
{
	int j;
	if (p->type != BWA_TYPE_NO_MATCH || (mate && mate->type != BWA_TYPE_NO_MATCH)) {
		int seqid, nn, am = 0, flag = p->extra_flag;
		char XT;

		if (p->type == BWA_TYPE_NO_MATCH) {
			p->pos = mate->pos;
			p->strand = mate->strand;
			flag |= SAM_FSU;
			j = 1;
		} else j = pos_end(p) - p->pos; // j is the length of the reference in the alignment

		// get seqid
		nn = bns_cnt_ambi(bns, p->pos, j, &seqid);
		if (p->type != BWA_TYPE_NO_MATCH && p->pos + j - bns->anns[seqid].offset > bns->anns[seqid].len)
			flag |= SAM_FSU; // flag UNMAP as this alignment bridges two adjacent reference sequences

		// update flag and print it
		if (p->strand) flag |= SAM_FSR;
		if (mate) {
			if (mate->type != BWA_TYPE_NO_MATCH) {
				if (mate->strand) flag |= SAM_FMR;
			} else flag |= SAM_FMU;
		}
		err_printf("%s\t%d\t%s\t", p->name, flag, bns->anns[seqid].name);
		err_printf("%d\t%d\t", (int)(p->pos - bns->anns[seqid].offset + 1), p->mapQ);

		// print CIGAR
		if (p->cigar) {
			for (j = 0; j != p->n_cigar; ++j)
				err_printf("%d%c", __cigar_len(p->cigar[j]), "MIDS"[__cigar_op(p->cigar[j])]);
		} else if (p->type == BWA_TYPE_NO_MATCH) err_printf("*");
		else err_printf("%dM", p->len);

		// print mate coordinate
		if (mate && mate->type != BWA_TYPE_NO_MATCH) {
			int m_seqid;
			long long isize;
			am = mate->seQ < p->seQ? mate->seQ : p->seQ; // smaller single-end mapping quality
			// redundant calculation here, but should not matter too much
			bns_cnt_ambi(bns, mate->pos, mate->len, &m_seqid);
			err_printf("\t%s\t", (seqid == m_seqid)? "=" : bns->anns[m_seqid].name);
			isize = (seqid == m_seqid)? pos_5(mate) - pos_5(p) : 0;
			if (p->type == BWA_TYPE_NO_MATCH) isize = 0;
			err_printf("%d\t%lld\t", (int)(mate->pos - bns->anns[m_seqid].offset + 1), isize);
		} else if (mate) err_printf("\t=\t%d\t0\t", (int)(p->pos - bns->anns[seqid].offset + 1));
		else err_printf("\t*\t0\t0\t");

		// print sequence and quality
		if (p->strand == 0)
			for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
		else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
		putchar('\t');
		if (p->qual) {
			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
			err_printf("%s", p->qual);
		} else err_printf("*");

		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
		if (p->type != BWA_TYPE_NO_MATCH) {
			int i;
			// calculate XT tag
			XT = "NURM"[p->type];
			if (nn > 10) XT = 'N';
			// print tags
			err_printf("\tXT:A:%c\t%s:i:%d", XT, (mode & BWA_MODE_COMPREAD)? "NM" : "CM", p->nm);
			if (nn) err_printf("\tXN:i:%d", nn);
			if (mate) err_printf("\tSM:i:%d\tAM:i:%d", p->seQ, am);
			if (p->type != BWA_TYPE_MATESW) { // X0 and X1 are not available for this type of alignment
				err_printf("\tX0:i:%d", p->c1);
				if (p->c1 <= max_top2) err_printf("\tX1:i:%d", p->c2);
			}
			err_printf("\tXM:i:%d\tXO:i:%d\tXG:i:%d", p->n_mm, p->n_gapo, p->n_gapo+p->n_gape);
			if (p->md) err_printf("\tMD:Z:%s", p->md);
			// print multiple hits
			if (p->n_multi) {
				err_printf("\tXA:Z:");
				for (i = 0; i < p->n_multi; ++i) {
					bwt_multi1_t *q = p->multi + i;
					int k;
					j = pos_end_multi(q, p->len) - q->pos;
					nn = bns_cnt_ambi(bns, q->pos, j, &seqid);
					err_printf("%s,%c%d,", bns->anns[seqid].name, q->strand? '-' : '+',
						   (int)(q->pos - bns->anns[seqid].offset + 1));
					if (q->cigar) {
						for (k = 0; k < q->n_cigar; ++k)
							err_printf("%d%c", __cigar_len(q->cigar[k]), "MIDS"[__cigar_op(q->cigar[k])]);
					} else err_printf("%dM", p->len);
					err_printf(",%d;", q->gap + q->mm);
				}
			}
		}
		putchar('\n');
	} else { // this read has no match
		ubyte_t *s = p->strand? p->rseq : p->seq;
		int flag = p->extra_flag | SAM_FSU;
		if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
		err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
		for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
		putchar('\t');
		if (p->qual) {
			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
			err_printf("%s", p->qual);
		} else err_printf("*");
		if (bwa_rg_id[0]) err_printf("\tRG:Z:%s", bwa_rg_id);
		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
		putchar('\n');
	}
}

void bwase_initialize() 
{
	int i;
	for (i = 1; i != 256; ++i) g_log_n[i] = (int)(4.343 * log(i) + 0.5);
}

void bwa_sai2sam_se_core(const char *prefix, const char *fn_sa, const char *fn_fa, int n_occ, const char *rg_line)
{
	extern bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa);
	int i, n_seqs, tot_seqs = 0, m_aln;
	bwt_aln1_t *aln = 0;
	bwa_seq_t *seqs;
	bwa_seqio_t *ks;
	clock_t t;
	bntseq_t *bns;
	FILE *fp_sa;
	gap_opt_t opt;

	// initialization
	bwase_initialize();
	bns = bns_restore(prefix);
	srand48(bns->seed);
	fp_sa = xopen(fn_sa, "r");

	m_aln = 0;
	fread(&opt, sizeof(gap_opt_t), 1, fp_sa);
	bwa_print_sam_hdr(bns, rg_line);
	//bwa_print_sam_PG();
	// set ks
	ks = bwa_open_reads(opt.mode, fn_fa);
	// core loop
	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt.mode, opt.trim_qual)) != 0) {
		tot_seqs += n_seqs;
		t = clock();

		// read alignment
		for (i = 0; i < n_seqs; ++i) {
			bwa_seq_t *p = seqs + i;
			int n_aln;
			fread(&n_aln, 4, 1, fp_sa);
			if (n_aln > m_aln) {
				m_aln = n_aln;
				aln = (bwt_aln1_t*)realloc(aln, sizeof(bwt_aln1_t) * m_aln);
			}
			fread(aln, sizeof(bwt_aln1_t), n_aln, fp_sa);
			bwa_aln2seq_core(n_aln, aln, p, 1, n_occ);
		}

		fprintf(stderr, "[bwa_aln_core] convert to sequence coordinate... ");
		bwa_cal_pac_pos(bns, prefix, n_seqs, seqs, opt.max_diff, opt.fnr); // forward bwt will be destroyed here
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		fprintf(stderr, "[bwa_aln_core] refine gapped alignments... ");
		bwa_refine_gapped(bns, n_seqs, seqs, 0);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		fprintf(stderr, "[bwa_aln_core] print alignments... ");
		for (i = 0; i < n_seqs; ++i)
			bwa_print_sam1(bns, seqs + i, 0, opt.mode, opt.max_top2);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		bwa_free_read_seq(n_seqs, seqs);
		fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
	}

	// destroy
	bwa_seq_close(ks);
	bns_destroy(bns);
	fclose(fp_sa);
	free(aln);
}

int bwa_sai2sam_se(int argc, char *argv[])
{
	int c, n_occ = 3;
	char *prefix, *rg_line = 0;
	while ((c = getopt(argc, argv, "hn:f:r:")) >= 0) {
		switch (c) {
		case 'h': break;
		case 'r':
			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1;
			break;
		case 'n': n_occ = atoi(optarg); break;
		case 'f': xreopen(optarg, "w", stdout); break;
		default: return 1;
		}
	}

	if (optind + 3 > argc) {
		fprintf(stderr, "Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>\n");
		return 1;
	}
	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
		return 0;
	}
	bwa_sai2sam_se_core(prefix, argv[optind+1], argv[optind+2], n_occ, rg_line);
	free(prefix);
	return 0;
}
bwa-0.7.3a/bwase.h000644 000767 000024 00000002011 12120745361 013533 0ustar00lh3staff000000 000000 #ifndef BWASE_H
#define BWASE_H

#include "bntseq.h"
#include "bwt.h"
#include "bwtaln.h"

#ifdef __cplusplus
extern "C" {
#endif

	// Initialize mapping tables in the bwa single-end mapper.
	void bwase_initialize();
	// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
	void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
	// Refine the approximate position of the sequence to an actual placement for the sequence.
	void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq);
	// Backfill certain alignment properties mainly centering around number of matches.
	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
	// Calculate the end position of a read given a certain sequence.
	int64_t pos_end(const bwa_seq_t *p);
	//
	bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);

#ifdef __cplusplus
}
#endif

#endif // BWASE_H
bwa-0.7.3a/bwaseqio.c000644 000767 000024 00000014673 12120745361 014260 0ustar00lh3staff000000 000000 #include <zlib.h>
#include <ctype.h>
#include "bwtaln.h"
#include "utils.h"
#include "bamlite.h"

#include "kseq.h"
KSEQ_DECLARE(gzFile)

extern unsigned char nst_nt4_table[256];
static char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };

struct __bwa_seqio_t {
	// for BAM input
	int is_bam, which; // 1st bit: read1, 2nd bit: read2, 3rd: SE
	bamFile fp;
	// for fastq input
	kseq_t *ks;
};

bwa_seqio_t *bwa_bam_open(const char *fn, int which)
{
	bwa_seqio_t *bs;
	bam_header_t *h;
	bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
	bs->is_bam = 1;
	bs->which = which;
	bs->fp = bam_open(fn, "r");
	h = bam_header_read(bs->fp);
	bam_header_destroy(h);
	return bs;
}

bwa_seqio_t *bwa_seq_open(const char *fn)
{
	gzFile fp;
	bwa_seqio_t *bs;
	bs = (bwa_seqio_t*)calloc(1, sizeof(bwa_seqio_t));
	fp = xzopen(fn, "r");
	bs->ks = kseq_init(fp);
	return bs;
}

void bwa_seq_close(bwa_seqio_t *bs)
{
	if (bs == 0) return;
	if (bs->is_bam) bam_close(bs->fp);
	else {
		gzclose(bs->ks->f->f);
		kseq_destroy(bs->ks);
	}
	free(bs);
}

void seq_reverse(int len, ubyte_t *seq, int is_comp)
{
	int i;
	if (is_comp) {
		for (i = 0; i < len>>1; ++i) {
			char tmp = seq[len-1-i];
			if (tmp < 4) tmp = 3 - tmp;
			seq[len-1-i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
			seq[i] = tmp;
		}
		if (len&1) seq[i] = (seq[i] >= 4)? seq[i] : 3 - seq[i];
	} else {
		for (i = 0; i < len>>1; ++i) {
			char tmp = seq[len-1-i];
			seq[len-1-i] = seq[i]; seq[i] = tmp;
		}
	}
}

int bwa_trim_read(int trim_qual, bwa_seq_t *p)
{
	int s = 0, l, max = 0, max_l = p->len;
	if (trim_qual < 1 || p->qual == 0) return 0;
	for (l = p->len - 1; l >= BWA_MIN_RDLEN; --l) {
		s += trim_qual - (p->qual[l] - 33);
		if (s < 0) break;
		if (s > max) max = s, max_l = l;
	}
	p->clip_len = p->len = max_l;
	return p->full_len - p->len;
}

static bwa_seq_t *bwa_read_bam(bwa_seqio_t *bs, int n_needed, int *n, int is_comp, int trim_qual)
{
	bwa_seq_t *seqs, *p;
	int n_seqs, l, i;
	long n_trimmed = 0, n_tot = 0;
	bam1_t *b;

	b = bam_init1();
	n_seqs = 0;
	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
	while (bam_read1(bs->fp, b) >= 0) {
		uint8_t *s, *q;
		int go = 0;
		if ((bs->which & 1) && (b->core.flag & BAM_FREAD1)) go = 1;
		if ((bs->which & 2) && (b->core.flag & BAM_FREAD2)) go = 1;
		if ((bs->which & 4) && !(b->core.flag& BAM_FREAD1) && !(b->core.flag& BAM_FREAD2))go = 1;
		if (go == 0) continue;
		l = b->core.l_qseq;
		p = &seqs[n_seqs++];
		p->tid = -1; // no assigned to a thread
		p->qual = 0;
		p->full_len = p->clip_len = p->len = l;
		n_tot += p->full_len;
		s = bam1_seq(b); q = bam1_qual(b);
		p->seq = (ubyte_t*)calloc(p->len + 1, 1);
		p->qual = (ubyte_t*)calloc(p->len + 1, 1);
		for (i = 0; i != p->full_len; ++i) {
			p->seq[i] = bam_nt16_nt4_table[(int)bam1_seqi(s, i)];
			p->qual[i] = q[i] + 33 < 126? q[i] + 33 : 126;
		}
		if (bam1_strand(b)) { // then reverse 
			seq_reverse(p->len, p->seq, 1);
			seq_reverse(p->len, p->qual, 0);
		}
		if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
		p->rseq = (ubyte_t*)calloc(p->full_len, 1);
		memcpy(p->rseq, p->seq, p->len);
		seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
		seq_reverse(p->len, p->rseq, is_comp);
		p->name = strdup((const char*)bam1_qname(b));
		if (n_seqs == n_needed) break;
	}
	*n = n_seqs;
	if (n_seqs && trim_qual >= 1)
		fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
	if (n_seqs == 0) {
		free(seqs);
		bam_destroy1(b);
		return 0;
	}
	bam_destroy1(b);
	return seqs;
}

#define BARCODE_LOW_QUAL 13

bwa_seq_t *bwa_read_seq(bwa_seqio_t *bs, int n_needed, int *n, int mode, int trim_qual)
{
	bwa_seq_t *seqs, *p;
	kseq_t *seq = bs->ks;
	int n_seqs, l, i, is_comp = mode&BWA_MODE_COMPREAD, is_64 = mode&BWA_MODE_IL13, l_bc = mode>>24;
	long n_trimmed = 0, n_tot = 0;

	if (l_bc > BWA_MAX_BCLEN) {
		fprintf(stderr, "[%s] the maximum barcode length is %d.\n", __func__, BWA_MAX_BCLEN);
		return 0;
	}
	if (bs->is_bam) return bwa_read_bam(bs, n_needed, n, is_comp, trim_qual); // l_bc has no effect for BAM input
	n_seqs = 0;
	seqs = (bwa_seq_t*)calloc(n_needed, sizeof(bwa_seq_t));
	while ((l = kseq_read(seq)) >= 0) {
		if ((mode & BWA_MODE_CFY) && (seq->comment.l != 0)) {
			// skip reads that are marked to be filtered by Casava
			char *s = index(seq->comment.s, ':');
			if (s && *(++s) == 'Y') {
				continue;
			}
		}
		if (is_64 && seq->qual.l)
			for (i = 0; i < seq->qual.l; ++i) seq->qual.s[i] -= 31;
		if (seq->seq.l <= l_bc) continue; // sequence length equals or smaller than the barcode length
		p = &seqs[n_seqs++];
		if (l_bc) { // then trim barcode
			for (i = 0; i < l_bc; ++i)
				p->bc[i] = (seq->qual.l && seq->qual.s[i]-33 < BARCODE_LOW_QUAL)? tolower(seq->seq.s[i]) : toupper(seq->seq.s[i]);
			p->bc[i] = 0;
			for (; i < seq->seq.l; ++i)
				seq->seq.s[i - l_bc] = seq->seq.s[i];
			seq->seq.l -= l_bc; seq->seq.s[seq->seq.l] = 0;
			if (seq->qual.l) {
				for (i = l_bc; i < seq->qual.l; ++i)
					seq->qual.s[i - l_bc] = seq->qual.s[i];
				seq->qual.l -= l_bc; seq->qual.s[seq->qual.l] = 0;
			}
			l = seq->seq.l;
		} else p->bc[0] = 0;
		p->tid = -1; // no assigned to a thread
		p->qual = 0;
		p->full_len = p->clip_len = p->len = l;
		n_tot += p->full_len;
		p->seq = (ubyte_t*)calloc(p->len, 1);
		for (i = 0; i != p->full_len; ++i)
			p->seq[i] = nst_nt4_table[(int)seq->seq.s[i]];
		if (seq->qual.l) { // copy quality
			p->qual = (ubyte_t*)strdup((char*)seq->qual.s);
			if (trim_qual >= 1) n_trimmed += bwa_trim_read(trim_qual, p);
		}
		p->rseq = (ubyte_t*)calloc(p->full_len, 1);
		memcpy(p->rseq, p->seq, p->len);
		seq_reverse(p->len, p->seq, 0); // *IMPORTANT*: will be reversed back in bwa_refine_gapped()
		seq_reverse(p->len, p->rseq, is_comp);
		p->name = strdup((const char*)seq->name.s);
		{ // trim /[12]$
			int t = strlen(p->name);
			if (t > 2 && p->name[t-2] == '/' && (p->name[t-1] == '1' || p->name[t-1] == '2')) p->name[t-2] = '\0';
		}
		if (n_seqs == n_needed) break;
	}
	*n = n_seqs;
	if (n_seqs && trim_qual >= 1)
		fprintf(stderr, "[bwa_read_seq] %.1f%% bases are trimmed.\n", 100.0f * n_trimmed/n_tot);
	if (n_seqs == 0) {
		free(seqs);
		return 0;
	}
	return seqs;
}

void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs)
{
	int i, j;
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p = seqs + i;
		for (j = 0; j < p->n_multi; ++j)
			if (p->multi[j].cigar) free(p->multi[j].cigar);
		free(p->name);
		free(p->seq); free(p->rseq); free(p->qual); free(p->aln); free(p->md); free(p->multi);
		free(p->cigar);
	}
	free(seqs);
}
bwa-0.7.3a/bwt.c000644 000767 000024 00000032714 12120745361 013236 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <assert.h>
#include <stdint.h>
#include "utils.h"
#include "bwt.h"
#include "kvec.h"

void bwt_gen_cnt_table(bwt_t *bwt)
{
	int i, j;
	for (i = 0; i != 256; ++i) {
		uint32_t x = 0;
		for (j = 0; j != 4; ++j)
			x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
		bwt->cnt_table[i] = x;
	}
}

static inline bwtint_t bwt_invPsi(const bwt_t *bwt, bwtint_t k) // compute inverse CSA
{
	bwtint_t x = k - (k > bwt->primary);
	x = bwt_B0(bwt, x);
	x = bwt->L2[x] + bwt_occ(bwt, k, x);
	return k == bwt->primary? 0 : x;
}

// bwt->bwt and bwt->occ must be precalculated
void bwt_cal_sa(bwt_t *bwt, int intv)
{
	bwtint_t isa, sa, i; // S(isa) = sa
	int intv_round = intv;

	kv_roundup32(intv_round);
	xassert(intv_round == intv, "SA sample interval is not a power of 2.");
	xassert(bwt->bwt, "bwt_t::bwt is not initialized.");

	if (bwt->sa) free(bwt->sa);
	bwt->sa_intv = intv;
	bwt->n_sa = (bwt->seq_len + intv) / intv;
	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
	if (bwt->sa == 0) {
		fprintf(stderr, "[%s] Fail to allocate %.3fMB memory. Abort!\n", __func__, bwt->n_sa * sizeof(bwtint_t) / 1024.0/1024.0);
		abort();
	}
	// calculate SA value
	isa = 0; sa = bwt->seq_len;
	for (i = 0; i < bwt->seq_len; ++i) {
		if (isa % intv == 0) bwt->sa[isa/intv] = sa;
		--sa;
		isa = bwt_invPsi(bwt, isa);
	}
	if (isa % intv == 0) bwt->sa[isa/intv] = sa;
	bwt->sa[0] = (bwtint_t)-1; // before this line, bwt->sa[0] = bwt->seq_len
}

bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
{
	bwtint_t sa = 0, mask = bwt->sa_intv - 1;
	while (k & mask) {
		++sa;
		k = bwt_invPsi(bwt, k);
	}
	/* without setting bwt->sa[0] = -1, the following line should be
	   changed to (sa + bwt->sa[k/bwt->sa_intv]) % (bwt->seq_len + 1) */
	return sa + bwt->sa[k/bwt->sa_intv];
}

static inline int __occ_aux(uint64_t y, int c)
{
	// reduce nucleotide counting to bits counting
	y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
	// count the number of 1s in y
	y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
	return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
}

bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
{
	bwtint_t n;
	uint32_t *p, *end;

	if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
	if (k == (bwtint_t)(-1)) return 0;
	k -= (k >= bwt->primary); // because $ is not in bwt

	// retrieve Occ at k/OCC_INTERVAL
	n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
	p += sizeof(bwtint_t); // jump to the start of the first BWT cell

	// calculate Occ up to the last k/32
	end = p + (((k>>5) - ((k&~OCC_INTV_MASK)>>5))<<1);
	for (; p < end; p += 2) n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);

	// calculate Occ
	n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
	if (c == 0) n -= ~k&31; // corrected for the masked bits

	return n;
}

// an analogy to bwt_occ() but more efficient, requiring k <= l
void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
{
	bwtint_t _k, _l;
	_k = (k >= bwt->primary)? k-1 : k;
	_l = (l >= bwt->primary)? l-1 : l;
	if (_l/OCC_INTERVAL != _k/OCC_INTERVAL || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
		*ok = bwt_occ(bwt, k, c);
		*ol = bwt_occ(bwt, l, c);
	} else {
		bwtint_t m, n, i, j;
		uint32_t *p;
		if (k >= bwt->primary) --k;
		if (l >= bwt->primary) --l;
		n = ((bwtint_t*)(p = bwt_occ_intv(bwt, k)))[c];
		p += sizeof(bwtint_t);
		// calculate *ok
		j = k >> 5 << 5;
		for (i = k/OCC_INTERVAL*OCC_INTERVAL; i < j; i += 32, p += 2)
			n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
		m = n;
		n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
		if (c == 0) n -= ~k&31; // corrected for the masked bits
		*ok = n;
		// calculate *ol
		j = l >> 5 << 5;
		for (; i < j; i += 32, p += 2)
			m += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
		m += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~l&31)<<1)) - 1), c);
		if (c == 0) m -= ~l&31; // corrected for the masked bits
		*ol = m;
	}
}

#define __occ_aux4(bwt, b)											\
	((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff]		\
	 + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])

void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
{
	bwtint_t x;
	uint32_t *p, tmp, *end;
	if (k == (bwtint_t)(-1)) {
		memset(cnt, 0, 4 * sizeof(bwtint_t));
		return;
	}
	k -= (k >= bwt->primary); // because $ is not in bwt
	p = bwt_occ_intv(bwt, k);
	memcpy(cnt, p, 4 * sizeof(bwtint_t));
	p += sizeof(bwtint_t); // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
	end = p + ((k>>4) - ((k&~OCC_INTV_MASK)>>4)); // this is the end point of the following loop
	for (x = 0; p < end; ++p) x += __occ_aux4(bwt, *p);
	tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
	x += __occ_aux4(bwt, tmp) - (~k&15);
	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
}

// an analogy to bwt_occ4() but more efficient, requiring k <= l
void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
{
	bwtint_t _k, _l;
	_k = k - (k >= bwt->primary);
	_l = l - (l >= bwt->primary);
	if (_l>>OCC_INTV_SHIFT != _k>>OCC_INTV_SHIFT || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
		bwt_occ4(bwt, k, cntk);
		bwt_occ4(bwt, l, cntl);
	} else {
		bwtint_t x, y;
		uint32_t *p, tmp, *endk, *endl;
		k -= (k >= bwt->primary); // because $ is not in bwt
		l -= (l >= bwt->primary);
		p = bwt_occ_intv(bwt, k);
		memcpy(cntk, p, 4 * sizeof(bwtint_t));
		p += sizeof(bwtint_t); // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
		// prepare cntk[]
		endk = p + ((k>>4) - ((k&~OCC_INTV_MASK)>>4));
		endl = p + ((l>>4) - ((l&~OCC_INTV_MASK)>>4));
		for (x = 0; p < endk; ++p) x += __occ_aux4(bwt, *p);
		y = x;
		tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
		x += __occ_aux4(bwt, tmp) - (~k&15);
		// calculate cntl[] and finalize cntk[]
		for (; p < endl; ++p) y += __occ_aux4(bwt, *p);
		tmp = *p & ~((1U<<((~l&15)<<1)) - 1);
		y += __occ_aux4(bwt, tmp) - (~l&15);
		memcpy(cntl, cntk, 4 * sizeof(bwtint_t));
		cntk[0] += x&0xff; cntk[1] += x>>8&0xff; cntk[2] += x>>16&0xff; cntk[3] += x>>24;
		cntl[0] += y&0xff; cntl[1] += y>>8&0xff; cntl[2] += y>>16&0xff; cntl[3] += y>>24;
	}
}

int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end)
{
	bwtint_t k, l, ok, ol;
	int i;
	k = 0; l = bwt->seq_len;
	for (i = len - 1; i >= 0; --i) {
		ubyte_t c = str[i];
		if (c > 3) return 0; // no match
		bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
		k = bwt->L2[c] + ok + 1;
		l = bwt->L2[c] + ol;
		if (k > l) break; // no match
	}
	if (k > l) return 0; // no match
	if (sa_begin) *sa_begin = k;
	if (sa_end)   *sa_end = l;
	return l - k + 1;
}

int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0)
{
	int i;
	bwtint_t k, l, ok, ol;
	k = *k0; l = *l0;
	for (i = len - 1; i >= 0; --i) {
		ubyte_t c = str[i];
		if (c > 3) return 0; // there is an N here. no match
		bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
		k = bwt->L2[c] + ok + 1;
		l = bwt->L2[c] + ol;
		if (k > l) return 0; // no match
	}
	*k0 = k; *l0 = l;
	return l - k + 1;
}

/*********************
 * Bidirectional BWT *
 *********************/

void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back)
{
	bwtint_t tk[4], tl[4];
	int i;
	bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
	for (i = 0; i != 4; ++i) {
		ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i];
		ok[i].x[2] = tl[i] - tk[i];
	}
	ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
	ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
	ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
	ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
}

static void bwt_reverse_intvs(bwtintv_v *p)
{
	if (p->n > 1) {
		int j;
		for (j = 0; j < p->n>>1; ++j) {
			bwtintv_t tmp = p->a[p->n - 1 - j];
			p->a[p->n - 1 - j] = p->a[j];
			p->a[j] = tmp;
		}
	}
}

int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2])
{
	int i, j, c, ret;
	bwtintv_t ik, ok[4];
	bwtintv_v a[2], *prev, *curr, *swap;

	mem->n = 0;
	if (q[x] > 3) return x + 1;
	if (min_intv < 1) min_intv = 1; // the interval size should be at least 1
	kv_init(a[0]); kv_init(a[1]);
	prev = tmpvec && tmpvec[0]? tmpvec[0] : &a[0]; // use the temporary vector if provided
	curr = tmpvec && tmpvec[1]? tmpvec[1] : &a[1];
	bwt_set_intv(bwt, q[x], ik); // the initial interval of a single base
	ik.info = x + 1;

	for (i = x + 1, curr->n = 0; i < len; ++i) { // forward search
		if (q[i] < 4) { // an A/C/G/T base
			c = 3 - q[i]; // complement of q[i]
			bwt_extend(bwt, &ik, ok, 0);
			if (ok[c].x[2] != ik.x[2]) { // change of the interval size
				kv_push(bwtintv_t, *curr, ik);
				if (ok[c].x[2] < min_intv) break; // the interval size is too small to be extended further
			}
			ik = ok[c]; ik.info = i + 1;
		} else { // an ambiguous base
			kv_push(bwtintv_t, *curr, ik);
			break; // always terminate extension at an ambiguous base; in this case, i<len always stands
		}
	}
	if (i == len) kv_push(bwtintv_t, *curr, ik); // push the last interval if we reach the end
	bwt_reverse_intvs(curr); // s.t. smaller intervals (i.e. longer matches) visited first
	ret = curr->a[0].info; // this will be the returned value
	swap = curr; curr = prev; prev = swap;

	for (i = x - 1; i >= -1; --i) { // backward search for MEMs
		c = i < 0? -1 : q[i] < 4? q[i] : -1; // c==-1 if i<0 or q[i] is an ambiguous base
		for (j = 0, curr->n = 0; j < prev->n; ++j) {
			bwtintv_t *p = &prev->a[j];
			bwt_extend(bwt, p, ok, 1);
			if (c < 0 || ok[c].x[2] < min_intv) { // keep the hit if reaching the beginning or an ambiguous base or the intv is small enough
				if (curr->n == 0) { // test curr->n>0 to make sure there are no longer matches
					if (mem->n == 0 || i + 1 < mem->a[mem->n-1].info>>32) { // skip contained matches
						ik = *p; ik.info |= (uint64_t)(i + 1)<<32;
						kv_push(bwtintv_t, *mem, ik);
					}
				} // otherwise the match is contained in another longer match
			} else if (curr->n == 0 || ok[c].x[2] != curr->a[curr->n-1].x[2]) {
				ok[c].info = p->info;
				kv_push(bwtintv_t, *curr, ok[c]);
			}
		}
		if (curr->n == 0) break;
		swap = curr; curr = prev; prev = swap;
	}
	bwt_reverse_intvs(mem); // s.t. sorted by the start coordinate

	if (tmpvec == 0 || tmpvec[0] == 0) free(a[0].a);
	if (tmpvec == 0 || tmpvec[1] == 0) free(a[1].a);
	return ret;
}

/*************************
 * Read/write BWT and SA *
 *************************/

void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
{
	FILE *fp;
	fp = xopen(fn, "wb");
	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
	fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
	fclose(fp);
}

void bwt_dump_sa(const char *fn, const bwt_t *bwt)
{
	FILE *fp;
	fp = xopen(fn, "wb");
	fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
	fwrite(bwt->L2+1, sizeof(bwtint_t), 4, fp);
	fwrite(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
	fwrite(&bwt->seq_len, sizeof(bwtint_t), 1, fp);
	fwrite(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
	fclose(fp);
}

void bwt_restore_sa(const char *fn, bwt_t *bwt)
{
	char skipped[256];
	FILE *fp;
	bwtint_t primary;

	fp = xopen(fn, "rb");
	fread(&primary, sizeof(bwtint_t), 1, fp);
	xassert(primary == bwt->primary, "SA-BWT inconsistency: primary is not the same.");
	fread(skipped, sizeof(bwtint_t), 4, fp); // skip
	fread(&bwt->sa_intv, sizeof(bwtint_t), 1, fp);
	fread(&primary, sizeof(bwtint_t), 1, fp);
	xassert(primary == bwt->seq_len, "SA-BWT inconsistency: seq_len is not the same.");

	bwt->n_sa = (bwt->seq_len + bwt->sa_intv) / bwt->sa_intv;
	bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
	bwt->sa[0] = -1;

	fread(bwt->sa + 1, sizeof(bwtint_t), bwt->n_sa - 1, fp);
	fclose(fp);
}

bwt_t *bwt_restore_bwt(const char *fn)
{
	bwt_t *bwt;
	FILE *fp;

	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
	fp = xopen(fn, "rb");
	fseek(fp, 0, SEEK_END);
	bwt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 5) >> 2;
	bwt->bwt = (uint32_t*)calloc(bwt->bwt_size, 4);
	fseek(fp, 0, SEEK_SET);
	fread(&bwt->primary, sizeof(bwtint_t), 1, fp);
	fread(bwt->L2+1, sizeof(bwtint_t), 4, fp);
	fread(bwt->bwt, 4, bwt->bwt_size, fp);
	bwt->seq_len = bwt->L2[4];
	fclose(fp);
	bwt_gen_cnt_table(bwt);

	return bwt;
}

void bwt_destroy(bwt_t *bwt)
{
	if (bwt == 0) return;
	free(bwt->sa); free(bwt->bwt);
	free(bwt);
}
bwa-0.7.3a/bwt.h000644 000767 000024 00000011100 12120745361 013225 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#ifndef BWA_BWT_H
#define BWA_BWT_H

#include <stdint.h>
#include <stddef.h>

// requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line because some part of the code assume OCC_INTERVAL=0x80
#define OCC_INTV_SHIFT 7
#define OCC_INTERVAL   (1LL<<OCC_INTV_SHIFT)
#define OCC_INTV_MASK  (OCC_INTERVAL - 1)

#ifndef BWA_UBYTE
#define BWA_UBYTE
typedef unsigned char ubyte_t;
#endif

typedef uint64_t bwtint_t;

typedef struct {
	bwtint_t primary; // S^{-1}(0), or the primary index of BWT
	bwtint_t L2[5]; // C(), cumulative count
	bwtint_t seq_len; // sequence length
	bwtint_t bwt_size; // size of bwt, about seq_len/4
	uint32_t *bwt; // BWT
	// occurance array, separated to two parts
	uint32_t cnt_table[256];
	// suffix array
	int sa_intv;
	bwtint_t n_sa;
	bwtint_t *sa;
} bwt_t;

typedef struct {
	bwtint_t x[3], info;
} bwtintv_t;

typedef struct { size_t n, m; bwtintv_t *a; } bwtintv_v;

/* For general OCC_INTERVAL, the following is correct:
#define bwt_bwt(b, k) ((b)->bwt[(k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4) + sizeof(bwtint_t)/4*4 + (k)%OCC_INTERVAL/16])
#define bwt_occ_intv(b, k) ((b)->bwt + (k)/OCC_INTERVAL * (OCC_INTERVAL/(sizeof(uint32_t)*8/2) + sizeof(bwtint_t)/4*4)
*/

// The following two lines are ONLY correct when OCC_INTERVAL==0x80
#define bwt_bwt(b, k) ((b)->bwt[((k)>>7<<4) + sizeof(bwtint_t) + (((k)&0x7f)>>4)])
#define bwt_occ_intv(b, k) ((b)->bwt + ((k)>>7<<4))

/* retrieve a character from the $-removed BWT string. Note that
 * bwt_t::bwt is not exactly the BWT string and therefore this macro is
 * called bwt_B0 instead of bwt_B */
#define bwt_B0(b, k) (bwt_bwt(b, k)>>((~(k)&0xf)<<1)&3)

#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]-(bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3-(c)]+1, (ik).info = 0)

#ifdef __cplusplus
extern "C" {
#endif

	void bwt_dump_bwt(const char *fn, const bwt_t *bwt);
	void bwt_dump_sa(const char *fn, const bwt_t *bwt);

	bwt_t *bwt_restore_bwt(const char *fn);
	void bwt_restore_sa(const char *fn, bwt_t *bwt);

	void bwt_destroy(bwt_t *bwt);

	void bwt_bwtgen(const char *fn_pac, const char *fn_bwt); // from BWT-SW
	void bwt_cal_sa(bwt_t *bwt, int intv);

	void bwt_bwtupdate_core(bwt_t *bwt);

	inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c);
	inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]);
	bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k);

	// more efficient version of bwt_occ/bwt_occ4 for retrieving two close Occ values
	void bwt_gen_cnt_table(bwt_t *bwt);
	inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol);
	inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]);

	int bwt_match_exact(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *sa_begin, bwtint_t *sa_end);
	int bwt_match_exact_alt(const bwt_t *bwt, int len, const ubyte_t *str, bwtint_t *k0, bwtint_t *l0);

	/**
	 * Extend bi-SA-interval _ik_
	 */
	void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back);

	/**
	 * Given a query _q_, collect potential SMEMs covering position _x_ and store them in _mem_.
	 * Return the end of the longest exact match starting from _x_.
	 */
	int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);

	// SMEM iterator interface

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwt_gen.c000644 000767 000024 00000145315 12120745361 014071 0ustar00lh3staff000000 000000 /*

   BWTConstruct.c		BWT-Index Construction

   This module constructs BWT and auxiliary data structures.

   Copyright (C) 2004, Wong Chi Kwong.

   This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
   as published by the Free Software Foundation; either version 2
   of the License, or (at your option) any later version.

   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdint.h>
#include "QSufSort.h"

typedef uint64_t bgint_t;
typedef int64_t sbgint_t;

#define ALPHABET_SIZE				4
#define BIT_PER_CHAR				2
#define CHAR_PER_WORD				16
#define CHAR_PER_BYTE				4

#define BITS_IN_WORD 32
#define BITS_IN_BYTE 8
#define BYTES_IN_WORD 4

#define ALL_ONE_MASK 0xFFFFFFFF
#define DNA_OCC_CNT_TABLE_SIZE_IN_WORD	65536

#define BITS_PER_OCC_VALUE			16
#define OCC_VALUE_PER_WORD			2
#define OCC_INTERVAL				256
#define OCC_INTERVAL_MAJOR			65536

#define TRUE    1
#define FALSE   0

#define BWTINC_INSERT_SORT_NUM_ITEM 7

#define MIN_AVAILABLE_WORD 0x10000

#define average(value1, value2)					( ((value1) & (value2)) + ((value1) ^ (value2)) / 2 )
#define min(value1, value2)						( ((value1) < (value2)) ? (value1) : (value2) )
#define max(value1, value2)						( ((value1) > (value2)) ? (value1) : (value2) )
#define med3(a, b, c)							( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
#define swap(a, b, t);							t = a; a = b; b = t;
#define truncateLeft(value, offset)				( (value) << (offset) >> (offset) )
#define truncateRight(value, offset)			( (value) >> (offset) << (offset) )
#define DNA_OCC_SUM_EXCEPTION(sum)			((sum & 0xfefefeff) == 0)

typedef struct BWT {
	bgint_t textLength;					// length of the text
	bgint_t inverseSa0;					// SA-1[0]
	bgint_t *cumulativeFreq;			// cumulative frequency
	unsigned int *bwtCode;				// BWT code
	unsigned int *occValue;				// Occurrence values stored explicitly
	bgint_t *occValueMajor;				// Occurrence values stored explicitly
	unsigned int *decodeTable;			// For decoding BWT by table lookup
	bgint_t bwtSizeInWord;				// Temporary variable to hold the memory allocated
	bgint_t occSizeInWord;				// Temporary variable to hold the memory allocated
	bgint_t occMajorSizeInWord;			// Temporary variable to hold the memory allocated
} BWT;

typedef struct BWTInc {
	BWT *bwt;
	unsigned int numberOfIterationDone;
	bgint_t *cumulativeCountInCurrentBuild;
	bgint_t availableWord;
	bgint_t buildSize;
	bgint_t initialMaxBuildSize;
	bgint_t incMaxBuildSize;
	unsigned int firstCharInLastIteration;
	unsigned int *workingMemory;
	unsigned int *packedText;
	unsigned char *textBuffer;
	unsigned int *packedShift;
} BWTInc;

static bgint_t TextLengthFromBytePacked(bgint_t bytePackedLength, unsigned int bitPerChar,
											 unsigned int lastByteLength)
{
	return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
}

static void initializeVAL(unsigned int *startAddr, const bgint_t length, const unsigned int initValue)
{
	bgint_t i;
	for (i=0; i<length; i++) startAddr[i] = initValue;
}

static void initializeVAL_bg(bgint_t *startAddr, const bgint_t length, const bgint_t initValue)
{
	bgint_t i;
	for (i=0; i<length; i++) startAddr[i] = initValue;
}

static void GenerateDNAOccCountTable(unsigned int *dnaDecodeTable)
{
	unsigned int i, j, c, t;

	for (i=0; i<DNA_OCC_CNT_TABLE_SIZE_IN_WORD; i++) {
		dnaDecodeTable[i] = 0;
		c = i;
		for (j=0; j<8; j++) {
			t = c & 0x00000003;
			dnaDecodeTable[i] += 1 << (t * 8);
			c >>= 2;
		}
	}

}
// for BWTIncCreate()
static bgint_t BWTOccValueMajorSizeInWord(const bgint_t numChar)
{
	bgint_t numOfOccValue;
	unsigned numOfOccIntervalPerMajor;
	numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1; // Value at both end for bi-directional encoding
	numOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
	return (numOfOccValue + numOfOccIntervalPerMajor - 1) / numOfOccIntervalPerMajor * ALPHABET_SIZE;
}
// for BWTIncCreate()
static bgint_t BWTOccValueMinorSizeInWord(const bgint_t numChar)
{
	bgint_t numOfOccValue;
	numOfOccValue = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;		// Value at both end for bi-directional encoding
	return (numOfOccValue + OCC_VALUE_PER_WORD - 1) / OCC_VALUE_PER_WORD * ALPHABET_SIZE;
}
// for BWTIncCreate()
static bgint_t BWTResidentSizeInWord(const bgint_t numChar) {

	bgint_t numCharRoundUpToOccInterval;

	// The $ in BWT at the position of inverseSa0 is not encoded
	numCharRoundUpToOccInterval = (numChar + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL;

	return (numCharRoundUpToOccInterval + CHAR_PER_WORD - 1) / CHAR_PER_WORD;

}

static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
{
	bgint_t maxBuildSize;

	if (bwtInc->bwt->textLength == 0) {
		// initial build
		// Minus 2 because n+1 entries of seq and rank needed for n char
		maxBuildSize = (bwtInc->availableWord - (2 + OCC_INTERVAL / CHAR_PER_WORD) * (sizeof(bgint_t) / 4))
							/ (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD / (sizeof(bgint_t) / 4);
		if (bwtInc->initialMaxBuildSize > 0) {
			bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize);
		} else {
			bwtInc->buildSize = maxBuildSize;
		}
	} else {
		// Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char
		// Minus numberOfIterationDone because bwt slightly shift to left in each iteration
		maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord
							 - (3 + bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR) * (sizeof(bgint_t) / 4)) 
							 / 3 / (sizeof(bgint_t) / 4);
		if (maxBuildSize < CHAR_PER_WORD) {
			fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
			exit(1);
		}
		if (bwtInc->incMaxBuildSize > 0) {
            bwtInc->buildSize = min(bwtInc->incMaxBuildSize, maxBuildSize);
		} else {
			bwtInc->buildSize = maxBuildSize;
		}
		if (bwtInc->buildSize < CHAR_PER_WORD)
			bwtInc->buildSize = CHAR_PER_WORD;
	}

	if (bwtInc->buildSize < CHAR_PER_WORD) {
		fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
		exit(1);
	}

	bwtInc->buildSize = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;

	bwtInc->packedText = bwtInc->workingMemory + 2 * (bwtInc->buildSize + 1) * (sizeof(bgint_t) / 4);
	bwtInc->textBuffer = (unsigned char*)(bwtInc->workingMemory + (bwtInc->buildSize + 1) * (sizeof(bgint_t) / 4));
}

// for ceilLog2()
unsigned int leadingZero(const unsigned int input)
{
	unsigned int l;
	const static unsigned int leadingZero8bit[256] = {8,7,6,6,5,5,5,5,4,4,4,4,4,4,4,4,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
											 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
											 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
											 1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
											 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};

	if (input & 0xFFFF0000) {
		if (input & 0xFF000000) {
			l = leadingZero8bit[input >> 24];
		} else {
			l = 8 + leadingZero8bit[input >> 16];
		}
	} else {
		if (input & 0x0000FF00) {
			l = 16 + leadingZero8bit[input >> 8];
		} else {
			l = 24 + leadingZero8bit[input];
		}
	}
	return l;

}
// for BitPerBytePackedChar()
static unsigned int ceilLog2(const unsigned int input)
{
	if (input <= 1) return 0;
	return BITS_IN_WORD - leadingZero(input - 1);

}
// for ConvertBytePackedToWordPacked()
static unsigned int BitPerBytePackedChar(const unsigned int alphabetSize)
{
	unsigned int bitPerChar;
	bitPerChar = ceilLog2(alphabetSize);
	// Return the largest number of bit that does not affect packing efficiency
	if (BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar) > bitPerChar)
		bitPerChar = BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar);
	return bitPerChar;
}
// for ConvertBytePackedToWordPacked()
static unsigned int BitPerWordPackedChar(const unsigned int alphabetSize)
{
	return ceilLog2(alphabetSize);
}

static void ConvertBytePackedToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int alphabetSize,
										  const bgint_t textLength)
{
	bgint_t i;
	unsigned int j, k, c;
	unsigned int bitPerBytePackedChar;
	unsigned int bitPerWordPackedChar;
	unsigned int charPerWord;
	unsigned int charPerByte;
	unsigned int bytePerIteration;
	bgint_t byteProcessed = 0;
	bgint_t wordProcessed = 0;
	unsigned int mask, shift;
	
	unsigned int buffer[BITS_IN_WORD];

	bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
	bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
	charPerByte = BITS_IN_BYTE / bitPerBytePackedChar;
	charPerWord = BITS_IN_WORD / bitPerWordPackedChar;

	bytePerIteration = charPerWord / charPerByte;
	mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
	shift = BITS_IN_WORD - BITS_IN_BYTE + bitPerBytePackedChar - bitPerWordPackedChar;

	while ((wordProcessed + 1) * charPerWord < textLength) {

		k = 0;
		for (i=0; i<bytePerIteration; i++) {
			c = (unsigned int)input[byteProcessed] << shift;
			for (j=0; j<charPerByte; j++) {
				buffer[k] = c & mask;
				c <<= bitPerBytePackedChar;
				k++;
			}
			byteProcessed++;
		}

		c = 0;
		for (i=0; i<charPerWord; i++) {
			c |= buffer[i] >> bitPerWordPackedChar * i;
		}
		output[wordProcessed] = c;
		wordProcessed++;

	}

	k = 0;
	for (i=0; i < (textLength - wordProcessed * charPerWord - 1) / charPerByte + 1; i++) {
		c = (unsigned int)input[byteProcessed] << shift;
		for (j=0; j<charPerByte; j++) {
			buffer[k] = c & mask;
			c <<= bitPerBytePackedChar;
			k++;
		}
		byteProcessed++;
	}

	c = 0;
	for (i=0; i<textLength - wordProcessed * charPerWord; i++) {
		c |= buffer[i] >> bitPerWordPackedChar * i;
	}
	output[wordProcessed] = c;
}

BWT *BWTCreate(const bgint_t textLength, unsigned int *decodeTable)
{
	BWT *bwt;

	bwt = (BWT*)calloc(1, sizeof(BWT));

	bwt->textLength = 0;

	bwt->cumulativeFreq = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
	initializeVAL_bg(bwt->cumulativeFreq, ALPHABET_SIZE + 1, 0);

	bwt->bwtSizeInWord = 0;

	// Generate decode tables
	if (decodeTable == NULL) {
		bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
		GenerateDNAOccCountTable(bwt->decodeTable);
	} else {
		bwt->decodeTable = decodeTable;
	}

	bwt->occMajorSizeInWord = BWTOccValueMajorSizeInWord(textLength);
	bwt->occValueMajor = (bgint_t*)calloc(bwt->occMajorSizeInWord, sizeof(bgint_t));

	bwt->occSizeInWord = 0;
	bwt->occValue = NULL;

	return bwt;
}

BWTInc *BWTIncCreate(const bgint_t textLength, unsigned int initialMaxBuildSize, unsigned int incMaxBuildSize)
{
	BWTInc *bwtInc;
	unsigned int i, n_iter;

	if (textLength < incMaxBuildSize) incMaxBuildSize = textLength;
	if (textLength < initialMaxBuildSize) initialMaxBuildSize = textLength;

	bwtInc = (BWTInc*)calloc(1, sizeof(BWTInc));
	bwtInc->numberOfIterationDone = 0;
	bwtInc->bwt = BWTCreate(textLength, NULL);
	bwtInc->initialMaxBuildSize = initialMaxBuildSize;
	bwtInc->incMaxBuildSize = incMaxBuildSize;
	bwtInc->cumulativeCountInCurrentBuild = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
	initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);

	// Build frequently accessed data
	bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int));
	for (i=0; i<CHAR_PER_WORD; i++)
		bwtInc->packedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR;

	n_iter = (textLength - initialMaxBuildSize) / incMaxBuildSize + 1;
	bwtInc->availableWord = BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength) // minimal memory requirement
		+ OCC_INTERVAL / BIT_PER_CHAR * n_iter * 2 * (sizeof(bgint_t) / 4) // buffer at the end of occ array 
		+ incMaxBuildSize/5 * 3 * (sizeof(bgint_t) / 4); // space for the 3 temporary arrays in each iteration
	if (bwtInc->availableWord < MIN_AVAILABLE_WORD) bwtInc->availableWord = MIN_AVAILABLE_WORD; // lh3: otherwise segfaul when availableWord is too small
	fprintf(stderr, "[%s] textLength=%ld, availableWord=%ld\n", __func__, (long)textLength, (long)bwtInc->availableWord);
	bwtInc->workingMemory = (unsigned*)calloc(bwtInc->availableWord, BYTES_IN_WORD);

	return bwtInc;
}
// for BWTIncConstruct()
static void BWTIncPutPackedTextToRank(const unsigned int *packedText, bgint_t* __restrict rank,
									  bgint_t* __restrict cumulativeCount, const bgint_t numChar)
{
	bgint_t i;
	unsigned int j;
	unsigned int c, t;
	unsigned int packedMask;
	bgint_t rankIndex;
	bgint_t lastWord;
	unsigned int numCharInLastWord;

	lastWord = (numChar - 1) / CHAR_PER_WORD;
	numCharInLastWord = numChar - lastWord * CHAR_PER_WORD;

	packedMask = ALL_ONE_MASK >> (BITS_IN_WORD - BIT_PER_CHAR);
	rankIndex = numChar - 1;

	t = packedText[lastWord] >> (BITS_IN_WORD - numCharInLastWord * BIT_PER_CHAR);
	for (i=0; i<numCharInLastWord; i++) {
		c = t & packedMask;
		cumulativeCount[c+1]++;
		rank[rankIndex] = c;
		rankIndex--;
		t >>= BIT_PER_CHAR;
	}

	for (i=lastWord; i--;) {	// loop from lastWord - 1 to 0
		t = packedText[i];
		for (j=0; j<CHAR_PER_WORD; j++) {
			c = t & packedMask;
			cumulativeCount[c+1]++;
			rank[rankIndex] = c;
			rankIndex--;
			t >>= BIT_PER_CHAR;
		}
	}

	// Convert occurrence to cumulativeCount
	cumulativeCount[2] += cumulativeCount[1];
	cumulativeCount[3] += cumulativeCount[2];
	cumulativeCount[4] += cumulativeCount[3];
}


static void ForwardDNAAllOccCountNoLimit(const unsigned int*  dna, const bgint_t index,
										 bgint_t* __restrict occCount, const unsigned int*  dnaDecodeTable)
{
	static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
											   0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
											   0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
											   0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };

	bgint_t iteration, i;
	unsigned int wordToCount, charToCount;
	unsigned int j, c, sum;

	occCount[0] = 0;
	occCount[1] = 0;
	occCount[2] = 0;
	occCount[3] = 0;

	iteration = index / 256;
	wordToCount = (index - iteration * 256) / 16;
	charToCount = index - iteration * 256 - wordToCount * 16;

	for (i=0; i<iteration; i++) {

		sum = 0;
		for (j=0; j<16; j++) {
			sum += dnaDecodeTable[*dna >> 16];
			sum += dnaDecodeTable[*dna & 0x0000FFFF];
			dna++;
		}
		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
			occCount[0] += sum & 0x000000FF;	sum >>= 8;
			occCount[1] += sum & 0x000000FF;	sum >>= 8;
			occCount[2] += sum & 0x000000FF;	sum >>= 8;
			occCount[3] += sum;
		} else {
			// only some or all of the 3 bits are on
			// in reality, only one of the four cases are possible
			if (sum == 0x00000100) {
				occCount[0] += 256;
			} else if (sum == 0x00010000) {
				occCount[1] += 256;
			} else if (sum == 0x01000000) {
				occCount[2] += 256;
			} else if (sum == 0x00000000) {
				occCount[3] += 256;
			} else {
				fprintf(stderr, "ForwardDNAAllOccCountNoLimit(): DNA occ sum exception!\n");
				exit(1);
			}
		}

	}

	sum = 0;
	for (j=0; j<wordToCount; j++) {
		sum += dnaDecodeTable[*dna >> 16];
		sum += dnaDecodeTable[*dna & 0x0000FFFF];
		dna++;
	}

	if (charToCount > 0) {
		c = *dna & truncateRightMask[charToCount];	// increase count of 'a' by 16 - c;
		sum += dnaDecodeTable[c >> 16];
		sum += dnaDecodeTable[c & 0xFFFF];
		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
	}

	occCount[0] += sum & 0x000000FF;	sum >>= 8;
	occCount[1] += sum & 0x000000FF;	sum >>= 8;
	occCount[2] += sum & 0x000000FF;	sum >>= 8;
	occCount[3] += sum;
}

static void BWTIncBuildPackedBwt(const bgint_t *relativeRank, unsigned int* __restrict bwt, const bgint_t numChar,
								 const bgint_t *cumulativeCount, const unsigned int *packedShift) {

	bgint_t i, r;
	unsigned int c;
	bgint_t previousRank, currentRank;
	bgint_t wordIndex, charIndex;
	bgint_t inverseSa0;

	inverseSa0 = previousRank = relativeRank[0];

	for (i=1; i<=numChar; i++) {
		currentRank = relativeRank[i];
		// previousRank > cumulativeCount[c] because $ is one of the char
		c = (previousRank > cumulativeCount[1]) + (previousRank > cumulativeCount[2]) 
											    + (previousRank > cumulativeCount[3]);
		// set bwt for currentRank
		if (c > 0) {
			// c <> 'a'
			r = currentRank;
			if (r > inverseSa0) {
				// - 1 because $ at inverseSa0 is not encoded			
				r--;
			}
			wordIndex = r / CHAR_PER_WORD;
			charIndex = r - wordIndex * CHAR_PER_WORD;
			bwt[wordIndex] |= c << packedShift[charIndex];
		}
		previousRank = currentRank;
	}
}

static inline bgint_t BWTOccValueExplicit(const BWT *bwt, const bgint_t occIndexExplicit,
											   const unsigned int character)
{
	bgint_t occIndexMajor;

	occIndexMajor = occIndexExplicit * OCC_INTERVAL / OCC_INTERVAL_MAJOR;

	if (occIndexExplicit % OCC_VALUE_PER_WORD == 0) {
		return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
			   (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] >> 16);

	} else {
		return bwt->occValueMajor[occIndexMajor * ALPHABET_SIZE + character] +
			   (bwt->occValue[occIndexExplicit / OCC_VALUE_PER_WORD * ALPHABET_SIZE + character] & 0x0000FFFF);
	}
}


static unsigned int ForwardDNAOccCount(const unsigned int*  dna, const unsigned int index, const unsigned int character,
									   const unsigned int*  dnaDecodeTable)
{
	static const unsigned int truncateRightMask[16] = { 0x00000000, 0xC0000000, 0xF0000000, 0xFC000000,
											   0xFF000000, 0xFFC00000, 0xFFF00000, 0xFFFC0000,
											   0xFFFF0000, 0xFFFFC000, 0xFFFFF000, 0xFFFFFC00,
											   0xFFFFFF00, 0xFFFFFFC0, 0xFFFFFFF0, 0xFFFFFFFC };

	unsigned int wordToCount, charToCount;
	unsigned int i, c;
	unsigned int sum = 0;

	wordToCount = index / 16;
	charToCount = index - wordToCount * 16;

	for (i=0; i<wordToCount; i++) {
		sum += dnaDecodeTable[dna[i] >> 16];
		sum += dnaDecodeTable[dna[i] & 0x0000FFFF];
	}

	if (charToCount > 0) {
		c = dna[i] & truncateRightMask[charToCount];	// increase count of 'a' by 16 - c;
		sum += dnaDecodeTable[c >> 16];
		sum += dnaDecodeTable[c & 0xFFFF];
		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
	}

	return (sum >> (character * 8)) & 0x000000FF;

}

static unsigned int BackwardDNAOccCount(const unsigned int*  dna, const unsigned int index, const unsigned int character,
										const unsigned int*  dnaDecodeTable)
{
	static const unsigned int truncateLeftMask[16] =  { 0x00000000, 0x00000003, 0x0000000F, 0x0000003F,
											   0x000000FF, 0x000003FF, 0x00000FFF, 0x00003FFF,
											   0x0000FFFF, 0x0003FFFF, 0x000FFFFF, 0x003FFFFF,
											   0x00FFFFFF, 0x03FFFFFF, 0x0FFFFFFF, 0x3FFFFFFF };

	unsigned int wordToCount, charToCount;
	unsigned int i, c;
	unsigned int sum = 0;

	wordToCount = index / 16;
	charToCount = index - wordToCount * 16;

	dna -= wordToCount + 1;

	if (charToCount > 0) {
		c = *dna & truncateLeftMask[charToCount];	// increase count of 'a' by 16 - c;
		sum += dnaDecodeTable[c >> 16];
		sum += dnaDecodeTable[c & 0xFFFF];
		sum += charToCount - 16;	// decrease count of 'a' by 16 - positionToProcess
	}
	
	for (i=0; i<wordToCount; i++) {
		dna++;
		sum += dnaDecodeTable[*dna >> 16];
		sum += dnaDecodeTable[*dna & 0x0000FFFF];
	}

	return (sum >> (character * 8)) & 0x000000FF;

}

bgint_t BWTOccValue(const BWT *bwt, bgint_t index, const unsigned int character)
{
	bgint_t occValue;
	bgint_t occExplicitIndex, occIndex;

	// $ is supposed to be positioned at inverseSa0 but it is not encoded
	// therefore index is subtracted by 1 for adjustment
	if (index > bwt->inverseSa0)
		index--;

	occExplicitIndex = (index + OCC_INTERVAL / 2 - 1) / OCC_INTERVAL;	// Bidirectional encoding
	occIndex = occExplicitIndex * OCC_INTERVAL;
	occValue = BWTOccValueExplicit(bwt, occExplicitIndex, character);

	if (occIndex == index)
		return occValue;

	if (occIndex < index) {
		return occValue + ForwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, index - occIndex, character, bwt->decodeTable);
	} else {
		return occValue - BackwardDNAOccCount(bwt->bwtCode + occIndex / CHAR_PER_WORD, occIndex - index, character, bwt->decodeTable);
	}
}

static bgint_t BWTIncGetAbsoluteRank(BWT *bwt, bgint_t* __restrict absoluteRank, bgint_t* __restrict seq,
										  const unsigned int *packedText, const bgint_t numChar,
										  const bgint_t* cumulativeCount, const unsigned int firstCharInLastIteration)
{
	bgint_t saIndex;
	bgint_t lastWord;
	unsigned int packedMask;
	bgint_t i;
	unsigned int c, t, j;
	bgint_t rankIndex;
	unsigned int shift;
	bgint_t seqIndexFromStart[ALPHABET_SIZE];
	bgint_t seqIndexFromEnd[ALPHABET_SIZE];

	for (i=0; i<ALPHABET_SIZE; i++) {
		seqIndexFromStart[i] = cumulativeCount[i];
		seqIndexFromEnd[i] = cumulativeCount[i+1] - 1;
	}

	shift = BITS_IN_WORD - BIT_PER_CHAR;
	packedMask = ALL_ONE_MASK >> shift;
	saIndex = bwt->inverseSa0;
	rankIndex = numChar - 1;

	lastWord = numChar / CHAR_PER_WORD;
	for (i=lastWord; i--;) {	// loop from lastWord - 1 to 0
		t = packedText[i];
		for (j=0; j<CHAR_PER_WORD; j++) {
			c = t & packedMask;
			saIndex = bwt->cumulativeFreq[c] + BWTOccValue(bwt, saIndex, c) + 1;
			// A counting sort using the first character of suffix is done here
			// If rank > inverseSa0 -> fill seq from end, otherwise fill seq from start -> to leave the right entry for inverseSa0
			if (saIndex > bwt->inverseSa0) {
				seq[seqIndexFromEnd[c]] = rankIndex;
				absoluteRank[seqIndexFromEnd[c]] = saIndex;
				seqIndexFromEnd[c]--;
			} else {
				seq[seqIndexFromStart[c]] = rankIndex;
				absoluteRank[seqIndexFromStart[c]] = saIndex;
				seqIndexFromStart[c]++;
			}
			rankIndex--;
			t >>= BIT_PER_CHAR;
		}
	}

	absoluteRank[seqIndexFromStart[firstCharInLastIteration]] = bwt->inverseSa0;	// representing the substring of all preceding characters
	seq[seqIndexFromStart[firstCharInLastIteration]] = numChar;

	return seqIndexFromStart[firstCharInLastIteration];
}

static void BWTIncSortKey(bgint_t* __restrict key, bgint_t* __restrict seq, const bgint_t numItem)
{
	#define EQUAL_KEY_THRESHOLD	4	// Partition for equal key if data array size / the number of data with equal value with pivot < EQUAL_KEY_THRESHOLD

	int64_t lowIndex, highIndex, midIndex;
	int64_t lowPartitionIndex, highPartitionIndex;
	int64_t lowStack[32], highStack[32];
	int stackDepth;
	int64_t i, j;
	bgint_t tempSeq, tempKey;
	int64_t numberOfEqualKey;

	if (numItem < 2) return;

	stackDepth = 0;

    lowIndex = 0;
    highIndex = numItem - 1;

	for (;;) {

		for (;;) {

			// Sort small array of data
			if (highIndex - lowIndex < BWTINC_INSERT_SORT_NUM_ITEM) {	 // Insertion sort on smallest arrays
				for (i=lowIndex+1; i<=highIndex; i++) {
					tempSeq = seq[i];
					tempKey = key[i];
					for (j = i; j > lowIndex && key[j-1] > tempKey; j--) {
						seq[j] = seq[j-1];
						key[j] = key[j-1];
					}
					if (j != i) {
						seq[j] = tempSeq;
						key[j] = tempKey;
					}
				}
				break;
			}

			// Choose pivot as median of the lowest, middle, and highest data; sort the three data

			midIndex = average(lowIndex, highIndex);
			if (key[lowIndex] > key[midIndex]) {
				tempSeq = seq[lowIndex];
				tempKey = key[lowIndex];
				seq[lowIndex] = seq[midIndex];
				key[lowIndex] = key[midIndex];
				seq[midIndex] = tempSeq;
				key[midIndex] = tempKey;
			}
			if (key[lowIndex] > key[highIndex]) {
				tempSeq = seq[lowIndex];
				tempKey = key[lowIndex];
				seq[lowIndex] = seq[highIndex];
				key[lowIndex] = key[highIndex];
				seq[highIndex] = tempSeq;
				key[highIndex] = tempKey;
			}
			if (key[midIndex] > key[highIndex]) {
				tempSeq = seq[midIndex];
				tempKey = key[midIndex];
				seq[midIndex] = seq[highIndex];
				key[midIndex] = key[highIndex];
				seq[highIndex] = tempSeq;
				key[highIndex] = tempKey;
			}

			// Partition data

			numberOfEqualKey = 0;

			lowPartitionIndex = lowIndex + 1;
			highPartitionIndex = highIndex - 1;

			for (;;) {
				while (lowPartitionIndex <= highPartitionIndex && key[lowPartitionIndex] <= key[midIndex]) {
					numberOfEqualKey += (key[lowPartitionIndex] == key[midIndex]);
					lowPartitionIndex++;
				}
				while (lowPartitionIndex < highPartitionIndex) {
					if (key[midIndex] >= key[highPartitionIndex]) {
						numberOfEqualKey += (key[midIndex] == key[highPartitionIndex]);
						break;
					}
					highPartitionIndex--;
				}
				if (lowPartitionIndex >= highPartitionIndex) {
					break;
				}
				tempSeq = seq[lowPartitionIndex];
				tempKey = key[lowPartitionIndex];
				seq[lowPartitionIndex] = seq[highPartitionIndex];
				key[lowPartitionIndex] = key[highPartitionIndex];
				seq[highPartitionIndex] = tempSeq;
				key[highPartitionIndex] = tempKey;
				if (highPartitionIndex == midIndex) {
					// partition key has been moved
					midIndex = lowPartitionIndex;
				}
				lowPartitionIndex++;
				highPartitionIndex--;
			}

			// Adjust the partition index
			highPartitionIndex = lowPartitionIndex;
			lowPartitionIndex--;

			// move the partition key to end of low partition
			tempSeq = seq[midIndex];
			tempKey = key[midIndex];
			seq[midIndex] = seq[lowPartitionIndex];
			key[midIndex] = key[lowPartitionIndex];
			seq[lowPartitionIndex] = tempSeq;
			key[lowPartitionIndex] = tempKey;

			if (highIndex - lowIndex + BWTINC_INSERT_SORT_NUM_ITEM <= EQUAL_KEY_THRESHOLD * numberOfEqualKey) {

				// Many keys = partition key; separate the equal key data from the lower partition
		
				midIndex = lowIndex;

				for (;;) {
					while (midIndex < lowPartitionIndex && key[midIndex] < key[lowPartitionIndex]) {
						midIndex++;
					}
					while (midIndex < lowPartitionIndex && key[lowPartitionIndex] == key[lowPartitionIndex - 1]) {
						lowPartitionIndex--;
					}
					if (midIndex >= lowPartitionIndex) {
						break;
					}
					tempSeq = seq[midIndex];
					tempKey = key[midIndex];
					seq[midIndex] = seq[lowPartitionIndex - 1];
					key[midIndex] = key[lowPartitionIndex - 1];
					seq[lowPartitionIndex - 1] = tempSeq;
					key[lowPartitionIndex - 1] = tempKey;
					midIndex++;
					lowPartitionIndex--;
				}

			}

			if (lowPartitionIndex - lowIndex > highIndex - highPartitionIndex) {
				// put the larger partition to stack
				lowStack[stackDepth] = lowIndex;
				highStack[stackDepth] = lowPartitionIndex - 1;
				stackDepth++;
				// sort the smaller partition first
				lowIndex = highPartitionIndex;
			} else {
				// put the larger partition to stack
				lowStack[stackDepth] = highPartitionIndex;
				highStack[stackDepth] = highIndex;
				stackDepth++;
				// sort the smaller partition first
				if (lowPartitionIndex > lowIndex) {
					highIndex = lowPartitionIndex - 1;
				} else {
					// all keys in the partition equals to the partition key
					break;
				}
			}
			continue;
		}

		// Pop a range from stack
		if (stackDepth > 0) {
			stackDepth--;
			lowIndex = lowStack[stackDepth];
			highIndex = highStack[stackDepth];
			continue;
		} else return;
	}
}


static void BWTIncBuildRelativeRank(bgint_t* __restrict sortedRank, bgint_t* __restrict seq,
									bgint_t* __restrict relativeRank, const bgint_t numItem,
									bgint_t oldInverseSa0, const bgint_t *cumulativeCount)
{
	bgint_t i, c;
	bgint_t s, r;
	bgint_t lastRank, lastIndex;
	bgint_t oldInverseSa0RelativeRank = 0;
	bgint_t freq;

	lastIndex = numItem;
	lastRank = sortedRank[numItem];
	if (lastRank > oldInverseSa0) {
		sortedRank[numItem]--;	// to prepare for merging; $ is not encoded in bwt
	}
	s = seq[numItem];
	relativeRank[s] = numItem;
	if (lastRank == oldInverseSa0) {
		oldInverseSa0RelativeRank = numItem;
		oldInverseSa0++;	// so that this segment of code is not run again
		lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
	}

	c = ALPHABET_SIZE - 1;
	freq = cumulativeCount[c];

	for (i=numItem; i--;) {	// from numItem - 1 to 0
		r = sortedRank[i];
		if (r > oldInverseSa0)
			sortedRank[i]--;	// to prepare for merging; $ is not encoded in bwt
		s = seq[i];
		if (i < freq) {
			if (lastIndex >= freq)
				lastRank++;	// to trigger the group across alphabet boundary to be split
			c--;
			freq = cumulativeCount[c];
		}
		if (r == lastRank) {
			relativeRank[s] = lastIndex;
		} else {
			if (i == lastIndex - 1) {
				if (lastIndex < numItem && (sbgint_t)seq[lastIndex + 1] < 0) {
					seq[lastIndex] = seq[lastIndex + 1] - 1;
				} else {
					seq[lastIndex] = (bgint_t)-1;
				}
			}
			lastIndex = i;
			lastRank = r;
			relativeRank[s] = i;
			if (r == oldInverseSa0) {
				oldInverseSa0RelativeRank = i;
				oldInverseSa0++;	// so that this segment of code is not run again
				lastRank++;			// so that oldInverseSa0 become a sorted group with 1 item
			}
		}
	}

}

static void BWTIncBuildBwt(unsigned int* insertBwt, const bgint_t *relativeRank, const bgint_t numChar,
						   const bgint_t *cumulativeCount)
{
	unsigned int c;
	bgint_t i;
	bgint_t previousRank, currentRank;

	previousRank = relativeRank[0];

	for (i=1; i<=numChar; i++) {
		currentRank = relativeRank[i];
		c = (previousRank >= cumulativeCount[1]) + (previousRank >= cumulativeCount[2])
											  	 + (previousRank >= cumulativeCount[3]);
		insertBwt[currentRank] = c;
		previousRank = currentRank;
	}
}

static void BWTIncMergeBwt(const bgint_t *sortedRank, const unsigned int* oldBwt, const unsigned int *insertBwt,
						   unsigned int* __restrict mergedBwt, const bgint_t numOldBwt, const bgint_t numInsertBwt)
{
	unsigned int bitsInWordMinusBitPerChar;
	bgint_t leftShift, rightShift;
	bgint_t o;
	bgint_t oIndex, iIndex, mIndex;
	bgint_t mWord, mChar, oWord, oChar;
	bgint_t numInsert;

	bitsInWordMinusBitPerChar = BITS_IN_WORD - BIT_PER_CHAR;

	oIndex = 0;
	iIndex = 0;
	mIndex = 0;

	mWord = 0;
	mChar = 0;

	mergedBwt[0] = 0;	// this can be cleared as merged Bwt slightly shift to the left in each iteration

	while (oIndex < numOldBwt) {

		// copy from insertBwt
		while (iIndex <= numInsertBwt && sortedRank[iIndex] <= oIndex) {
			if (sortedRank[iIndex] != 0) {	// special value to indicate that this is for new inverseSa0
				mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
				mIndex++;
				mChar++;
				if (mChar == CHAR_PER_WORD) {
					mChar = 0;
					mWord++;
					mergedBwt[mWord] = 0;	// no need to worry about crossing mergedBwt boundary
				}
			}
			iIndex++;
		}

		// Copy from oldBwt to mergedBwt
		if (iIndex <= numInsertBwt) {
			o = sortedRank[iIndex];
		} else {
			o = numOldBwt;
		}
		numInsert = o - oIndex;

		oWord = oIndex / CHAR_PER_WORD;
		oChar = oIndex - oWord * CHAR_PER_WORD;
		if (oChar > mChar) {
			leftShift = (oChar - mChar) * BIT_PER_CHAR;
			rightShift = (CHAR_PER_WORD + mChar - oChar) * BIT_PER_CHAR;
			mergedBwt[mWord] = mergedBwt[mWord]
								| (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR))
								| (oldBwt[oWord+1] >> rightShift);
			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
			while (o > oIndex) {
				oWord++;
				mWord++;
				mergedBwt[mWord] = (oldBwt[oWord] << leftShift) | (oldBwt[oWord+1] >> rightShift);
				oIndex += CHAR_PER_WORD;
			}
		} else if (oChar < mChar) {
			rightShift = (mChar - oChar) * BIT_PER_CHAR;
			leftShift = (CHAR_PER_WORD + oChar - mChar) * BIT_PER_CHAR;
			mergedBwt[mWord] = mergedBwt[mWord] 
								| (oldBwt[oWord] << (oChar * BIT_PER_CHAR) >> (mChar * BIT_PER_CHAR));
			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
			while (o > oIndex) {
				oWord++;
				mWord++;
				mergedBwt[mWord] = (oldBwt[oWord-1] << leftShift) | (oldBwt[oWord] >> rightShift);
				oIndex += CHAR_PER_WORD;
			}
		} else { // oChar == mChar
			mergedBwt[mWord] = mergedBwt[mWord] | truncateLeft(oldBwt[oWord], mChar * BIT_PER_CHAR);
			oIndex += min(numInsert, CHAR_PER_WORD - mChar);
			while (o > oIndex) {
				oWord++;
				mWord++;
				mergedBwt[mWord] = oldBwt[oWord];
				oIndex += CHAR_PER_WORD;
			}
		}
		oIndex = o;
		mIndex += numInsert;

		// Clear the trailing garbage in mergedBwt
		mWord = mIndex / CHAR_PER_WORD;
		mChar = mIndex - mWord * CHAR_PER_WORD;
		if (mChar == 0) {
			mergedBwt[mWord] = 0;
		} else {
			mergedBwt[mWord] = truncateRight(mergedBwt[mWord], (BITS_IN_WORD - mChar * BIT_PER_CHAR));
		}

	}

	// copy from insertBwt
	while (iIndex <= numInsertBwt) {
		if (sortedRank[iIndex] != 0) {
			mergedBwt[mWord] |= insertBwt[iIndex] << (BITS_IN_WORD - (mChar + 1) * BIT_PER_CHAR);
			mIndex++;
			mChar++;
			if (mChar == CHAR_PER_WORD) {
				mChar = 0;
				mWord++;
				mergedBwt[mWord] = 0;	// no need to worry about crossing mergedBwt boundary
			}
		}
		iIndex++;
	}
}

void BWTClearTrailingBwtCode(BWT *bwt)
{
	bgint_t bwtResidentSizeInWord;
	bgint_t wordIndex, offset;
	bgint_t i;

	bwtResidentSizeInWord = BWTResidentSizeInWord(bwt->textLength);

	wordIndex = bwt->textLength / CHAR_PER_WORD;
	offset = (bwt->textLength - wordIndex * CHAR_PER_WORD) * BIT_PER_CHAR;
	if (offset > 0) {
		bwt->bwtCode[wordIndex] = truncateRight(bwt->bwtCode[wordIndex], BITS_IN_WORD - offset);
	} else {
		if (wordIndex < bwtResidentSizeInWord) {
			bwt->bwtCode[wordIndex] = 0;
		}
	}

	for (i=wordIndex+1; i<bwtResidentSizeInWord; i++) {
		bwt->bwtCode[i] = 0;
	}
}


void BWTGenerateOccValueFromBwt(const unsigned int*  bwt, unsigned int* __restrict occValue,
								bgint_t* __restrict occValueMajor,
								const bgint_t textLength, const unsigned int*  decodeTable)
{
	bgint_t numberOfOccValueMajor, numberOfOccValue;
	unsigned int wordBetweenOccValue;
	bgint_t numberOfOccIntervalPerMajor;
	unsigned int c;
	bgint_t i, j;
	bgint_t occMajorIndex;
	bgint_t occIndex, bwtIndex;
	bgint_t sum; // perhaps unsigned is big enough
	bgint_t tempOccValue0[ALPHABET_SIZE], tempOccValue1[ALPHABET_SIZE];

	wordBetweenOccValue = OCC_INTERVAL / CHAR_PER_WORD;

	// Calculate occValue
	numberOfOccValue = (textLength + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;				// Value at both end for bi-directional encoding
	numberOfOccIntervalPerMajor = OCC_INTERVAL_MAJOR / OCC_INTERVAL;
	numberOfOccValueMajor = (numberOfOccValue + numberOfOccIntervalPerMajor - 1) / numberOfOccIntervalPerMajor;

	tempOccValue0[0] = 0;
	tempOccValue0[1] = 0;
	tempOccValue0[2] = 0;
	tempOccValue0[3] = 0;
	occValueMajor[0] = 0;
	occValueMajor[1] = 0;
	occValueMajor[2] = 0;
	occValueMajor[3] = 0;

	occIndex = 0;
	bwtIndex = 0;
	for (occMajorIndex=1; occMajorIndex<numberOfOccValueMajor; occMajorIndex++) {

		for (i=0; i<numberOfOccIntervalPerMajor/2; i++) {

			sum = 0;
			tempOccValue1[0] = tempOccValue0[0];
			tempOccValue1[1] = tempOccValue0[1];
			tempOccValue1[2] = tempOccValue0[2];
			tempOccValue1[3] = tempOccValue0[3];

			for (j=0; j<wordBetweenOccValue; j++) {
				c = bwt[bwtIndex];
				sum += decodeTable[c >> 16];
				sum += decodeTable[c & 0x0000FFFF];
				bwtIndex++;
			}
			if (!DNA_OCC_SUM_EXCEPTION(sum)) {
				tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue1[3] += sum;
			} else {
				if (sum == 0x00000100) {
					tempOccValue1[0] += 256;
				} else if (sum == 0x00010000) {
					tempOccValue1[1] += 256;
				} else if (sum == 0x01000000) {
					tempOccValue1[2] += 256;
				} else {
					tempOccValue1[3] += 256;
				}
			}
			occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
			occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
			occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
			occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
			tempOccValue0[0] = tempOccValue1[0];
			tempOccValue0[1] = tempOccValue1[1];
			tempOccValue0[2] = tempOccValue1[2];
			tempOccValue0[3] = tempOccValue1[3];
			sum = 0;

			occIndex++;

			for (j=0; j<wordBetweenOccValue; j++) {
				c = bwt[bwtIndex];
				sum += decodeTable[c >> 16];
				sum += decodeTable[c & 0x0000FFFF];
				bwtIndex++;
			}
			if (!DNA_OCC_SUM_EXCEPTION(sum)) {
				tempOccValue0[0] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue0[1] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue0[2] += (sum & 0x000000FF);	sum >>= 8;
				tempOccValue0[3] += sum;
			} else {
				if (sum == 0x00000100) {
					tempOccValue0[0] += 256;
				} else if (sum == 0x00010000) {
					tempOccValue0[1] += 256;
				} else if (sum == 0x01000000) {
					tempOccValue0[2] += 256;
				} else {
					tempOccValue0[3] += 256;
				}
			}
		}

		occValueMajor[occMajorIndex * 4 + 0] = occValueMajor[(occMajorIndex - 1) * 4 + 0] + tempOccValue0[0];
		occValueMajor[occMajorIndex * 4 + 1] = occValueMajor[(occMajorIndex - 1) * 4 + 1] + tempOccValue0[1];
		occValueMajor[occMajorIndex * 4 + 2] = occValueMajor[(occMajorIndex - 1) * 4 + 2] + tempOccValue0[2];
		occValueMajor[occMajorIndex * 4 + 3] = occValueMajor[(occMajorIndex - 1) * 4 + 3] + tempOccValue0[3];
		tempOccValue0[0] = 0;
		tempOccValue0[1] = 0;
		tempOccValue0[2] = 0;
		tempOccValue0[3] = 0;

	}

	while (occIndex < (numberOfOccValue-1)/2) {
		sum = 0;
		tempOccValue1[0] = tempOccValue0[0];
		tempOccValue1[1] = tempOccValue0[1];
		tempOccValue1[2] = tempOccValue0[2];
		tempOccValue1[3] = tempOccValue0[3];
		for (j=0; j<wordBetweenOccValue; j++) {
			c = bwt[bwtIndex];
			sum += decodeTable[c >> 16];
			sum += decodeTable[c & 0x0000FFFF];
			bwtIndex++;
		}
		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
			tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[3] += sum;
		} else {
			if (sum == 0x00000100) {
				tempOccValue1[0] += 256;
			} else if (sum == 0x00010000) {
				tempOccValue1[1] += 256;
			} else if (sum == 0x01000000) {
				tempOccValue1[2] += 256;
			} else {
				tempOccValue1[3] += 256;
			}
		}
		occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
		occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
		occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
		occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];
		tempOccValue0[0] = tempOccValue1[0];
		tempOccValue0[1] = tempOccValue1[1];
		tempOccValue0[2] = tempOccValue1[2];
		tempOccValue0[3] = tempOccValue1[3];
		sum = 0;
		occIndex++;

		for (j=0; j<wordBetweenOccValue; j++) {
			c = bwt[bwtIndex];
			sum += decodeTable[c >> 16];
			sum += decodeTable[c & 0x0000FFFF];
			bwtIndex++;
		}
		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
			tempOccValue0[0] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue0[1] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue0[2] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue0[3] += sum;
		} else {
			if (sum == 0x00000100) {
				tempOccValue0[0] += 256;
			} else if (sum == 0x00010000) {
				tempOccValue0[1] += 256;
			} else if (sum == 0x01000000) {
				tempOccValue0[2] += 256;
			} else {
				tempOccValue0[3] += 256;
			}
		}
	}

	sum = 0;
	tempOccValue1[0] = tempOccValue0[0];
	tempOccValue1[1] = tempOccValue0[1];
	tempOccValue1[2] = tempOccValue0[2];
	tempOccValue1[3] = tempOccValue0[3];

	if (occIndex * 2 < numberOfOccValue - 1) {
		for (j=0; j<wordBetweenOccValue; j++) {
			c = bwt[bwtIndex];
			sum += decodeTable[c >> 16];
			sum += decodeTable[c & 0x0000FFFF];
			bwtIndex++;
		}
		if (!DNA_OCC_SUM_EXCEPTION(sum)) {
			tempOccValue1[0] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[1] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[2] += (sum & 0x000000FF);	sum >>= 8;
			tempOccValue1[3] += sum;
		} else {
			if (sum == 0x00000100) {
				tempOccValue1[0] += 256;
			} else if (sum == 0x00010000) {
				tempOccValue1[1] += 256;
			} else if (sum == 0x01000000) {
				tempOccValue1[2] += 256;
			} else {
				tempOccValue1[3] += 256;
			}
		}
	}

	occValue[occIndex * 4 + 0] = (tempOccValue0[0] << 16) | tempOccValue1[0];
	occValue[occIndex * 4 + 1] = (tempOccValue0[1] << 16) | tempOccValue1[1];
	occValue[occIndex * 4 + 2] = (tempOccValue0[2] << 16) | tempOccValue1[2];
	occValue[occIndex * 4 + 3] = (tempOccValue0[3] << 16) | tempOccValue1[3];

}

static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
{
	unsigned int i;
	bgint_t mergedBwtSizeInWord, mergedOccSizeInWord;
	unsigned int firstCharInThisIteration;

	bgint_t *relativeRank, *seq, *sortedRank;
	unsigned int *insertBwt, *mergedBwt;
	bgint_t newInverseSa0RelativeRank, oldInverseSa0RelativeRank, newInverseSa0;

	mergedBwtSizeInWord = BWTResidentSizeInWord(bwtInc->bwt->textLength + numChar);
	mergedOccSizeInWord = BWTOccValueMinorSizeInWord(bwtInc->bwt->textLength + numChar);

	initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);

	if (bwtInc->bwt->textLength == 0) {		// Initial build

		// Set address
		seq = (bgint_t*)bwtInc->workingMemory;
		relativeRank = seq + bwtInc->buildSize + 1;
		// mergedBwt and packedTex may share memory
		mergedBwt = insertBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord;	// build in place

		assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)bwtInc->packedText);
		assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)mergedBwt);

		// ->packedText is not used any more and may be overwritten by mergedBwt
		BWTIncPutPackedTextToRank(bwtInc->packedText, relativeRank, bwtInc->cumulativeCountInCurrentBuild, numChar);

		firstCharInThisIteration = relativeRank[0];
		relativeRank[numChar] = 0;

		// Sort suffix
		QSufSortSuffixSort((qsint_t*)relativeRank, (qsint_t*)seq, (qsint_t)numChar, (qsint_t)ALPHABET_SIZE - 1, 0, FALSE);
		newInverseSa0 = relativeRank[0];

		// Clear BWT area
		initializeVAL(insertBwt, mergedBwtSizeInWord, 0);

		// Build BWT
		BWTIncBuildPackedBwt(relativeRank, insertBwt, numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->packedShift);

		// so that the cumulativeCount is not deducted
		bwtInc->firstCharInLastIteration = ALPHABET_SIZE;

	} else {		// Incremental build
		// Set address
		sortedRank = (bgint_t*)bwtInc->workingMemory;
		seq = sortedRank + bwtInc->buildSize + 1;
		insertBwt = (unsigned*)seq; // insertBwt and seq share memory
		// relativeRank and ->packedText may share memory
		relativeRank = seq + bwtInc->buildSize + 1;

		assert((void*)relativeRank <= (void*)bwtInc->packedText);

		// Store the first character of this iteration
		firstCharInThisIteration = bwtInc->packedText[0] >> (BITS_IN_WORD - BIT_PER_CHAR);

		// Count occurrence of input text
		ForwardDNAAllOccCountNoLimit(bwtInc->packedText, numChar, bwtInc->cumulativeCountInCurrentBuild + 1, bwtInc->bwt->decodeTable);
		// Add the first character of the previous iteration to represent the inverseSa0 of the previous iteration
		bwtInc->cumulativeCountInCurrentBuild[bwtInc->firstCharInLastIteration + 1]++;
		bwtInc->cumulativeCountInCurrentBuild[2] += bwtInc->cumulativeCountInCurrentBuild[1];
		bwtInc->cumulativeCountInCurrentBuild[3] += bwtInc->cumulativeCountInCurrentBuild[2];
		bwtInc->cumulativeCountInCurrentBuild[4] += bwtInc->cumulativeCountInCurrentBuild[3];

		// Get rank of new suffix among processed suffix
		// The seq array is built into ALPHABET_SIZE + 2 groups; ALPHABET_SIZE groups + 1 group divided into 2 by inverseSa0 + inverseSa0 as 1 group
		// ->packedText is not used any more and will be overwritten by relativeRank
		oldInverseSa0RelativeRank = BWTIncGetAbsoluteRank(bwtInc->bwt, sortedRank, seq, bwtInc->packedText, 
														  numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->firstCharInLastIteration);

		// Sort rank by ALPHABET_SIZE + 2 groups (or ALPHABET_SIZE + 1 groups when inverseSa0 sit on the border of a group)
		for (i=0; i<ALPHABET_SIZE; i++) {
			if (bwtInc->cumulativeCountInCurrentBuild[i] > oldInverseSa0RelativeRank ||
				bwtInc->cumulativeCountInCurrentBuild[i+1] <= oldInverseSa0RelativeRank) {
				BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], bwtInc->cumulativeCountInCurrentBuild[i+1] - bwtInc->cumulativeCountInCurrentBuild[i]);
			} else {
				if (bwtInc->cumulativeCountInCurrentBuild[i] < oldInverseSa0RelativeRank) {
					BWTIncSortKey(sortedRank + bwtInc->cumulativeCountInCurrentBuild[i], seq + bwtInc->cumulativeCountInCurrentBuild[i], oldInverseSa0RelativeRank - bwtInc->cumulativeCountInCurrentBuild[i]);
				}
				if (bwtInc->cumulativeCountInCurrentBuild[i+1] > oldInverseSa0RelativeRank + 1) {
					BWTIncSortKey(sortedRank + oldInverseSa0RelativeRank + 1, seq + oldInverseSa0RelativeRank + 1, bwtInc->cumulativeCountInCurrentBuild[i+1] - oldInverseSa0RelativeRank - 1);
				}
			}
		}

		// build relative rank; sortedRank is updated for merging to cater for the fact that $ is not encoded in bwt
		// the cumulative freq information is used to make sure that inverseSa0 and suffix beginning with different characters are kept in different unsorted groups)
		BWTIncBuildRelativeRank(sortedRank, seq, relativeRank, numChar, bwtInc->bwt->inverseSa0, bwtInc->cumulativeCountInCurrentBuild);
		assert(relativeRank[numChar] == oldInverseSa0RelativeRank);

		// Sort suffix
		QSufSortSuffixSort((qsint_t*)relativeRank, (qsint_t*)seq, (qsint_t)numChar, (qsint_t)numChar, 1, TRUE);

		newInverseSa0RelativeRank = relativeRank[0];
		newInverseSa0 = sortedRank[newInverseSa0RelativeRank] + newInverseSa0RelativeRank;

		sortedRank[newInverseSa0RelativeRank] = 0;	// a special value so that this is skipped in the merged bwt

		// Build BWT; seq is overwritten by insertBwt
		BWTIncBuildBwt(insertBwt, relativeRank, numChar, bwtInc->cumulativeCountInCurrentBuild);

		// Merge BWT; relativeRank may be overwritten by mergedBwt
		mergedBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord 
				    - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR * (sizeof(bgint_t) / 4); // minus numberOfIteration * occInterval to create a buffer for merging
		assert(mergedBwt >= insertBwt + numChar);
		BWTIncMergeBwt(sortedRank, bwtInc->bwt->bwtCode, insertBwt, mergedBwt, bwtInc->bwt->textLength, numChar);
	}

	// Build auxiliary structure and update info and pointers in BWT
	bwtInc->bwt->textLength += numChar;
	bwtInc->bwt->bwtCode = mergedBwt;
	bwtInc->bwt->bwtSizeInWord = mergedBwtSizeInWord;
	bwtInc->bwt->occSizeInWord = mergedOccSizeInWord;
	assert(mergedBwt >= bwtInc->workingMemory + mergedOccSizeInWord);

	bwtInc->bwt->occValue = mergedBwt - mergedOccSizeInWord;

	BWTClearTrailingBwtCode(bwtInc->bwt);
	BWTGenerateOccValueFromBwt(bwtInc->bwt->bwtCode, bwtInc->bwt->occValue, bwtInc->bwt->occValueMajor,
							   bwtInc->bwt->textLength, bwtInc->bwt->decodeTable);

	bwtInc->bwt->inverseSa0 = newInverseSa0;
	
	bwtInc->bwt->cumulativeFreq[1] += bwtInc->cumulativeCountInCurrentBuild[1] - (bwtInc->firstCharInLastIteration <= 0);
	bwtInc->bwt->cumulativeFreq[2] += bwtInc->cumulativeCountInCurrentBuild[2] - (bwtInc->firstCharInLastIteration <= 1);
	bwtInc->bwt->cumulativeFreq[3] += bwtInc->cumulativeCountInCurrentBuild[3] - (bwtInc->firstCharInLastIteration <= 2);
	bwtInc->bwt->cumulativeFreq[4] += bwtInc->cumulativeCountInCurrentBuild[4] - (bwtInc->firstCharInLastIteration <= 3);

	bwtInc->firstCharInLastIteration = firstCharInThisIteration;

	// Set build size and text address for the next build
	BWTIncSetBuildSizeAndTextAddr(bwtInc);
	bwtInc->numberOfIterationDone++;

}

BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxBuildSize, bgint_t incMaxBuildSize)
{

	FILE *packedFile;
	bgint_t packedFileLen;
	bgint_t totalTextLength;
	bgint_t textToLoad, textSizeInByte;
	bgint_t processedTextLength;
	unsigned char lastByteLength;

	BWTInc *bwtInc;

	packedFile = (FILE*)fopen(inputFileName, "rb");

	if (packedFile == NULL) {
		fprintf(stderr, "BWTIncConstructFromPacked() : Cannot open inputFileName!\n");
		exit(1);
	}

	fseek(packedFile, -1, SEEK_END);
	packedFileLen = ftell(packedFile);
	fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
	totalTextLength = TextLengthFromBytePacked(packedFileLen, BIT_PER_CHAR, lastByteLength);

	bwtInc = BWTIncCreate(totalTextLength, initialMaxBuildSize, incMaxBuildSize);

	BWTIncSetBuildSizeAndTextAddr(bwtInc);

	if (bwtInc->buildSize > totalTextLength) {
		textToLoad = totalTextLength;
	} else {
		textToLoad = totalTextLength - ((totalTextLength - bwtInc->buildSize + CHAR_PER_WORD - 1) / CHAR_PER_WORD * CHAR_PER_WORD);
	}
	textSizeInByte = textToLoad / CHAR_PER_BYTE;	// excluded the odd byte

	fseek(packedFile, -2, SEEK_CUR);
	fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
	fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte + 1, packedFile);
	fseek(packedFile, -((long)textSizeInByte + 1), SEEK_CUR);

	ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
	BWTIncConstruct(bwtInc, textToLoad);

	processedTextLength = textToLoad;

	while (processedTextLength < totalTextLength) {
		textToLoad = bwtInc->buildSize / CHAR_PER_WORD * CHAR_PER_WORD;
		if (textToLoad > totalTextLength - processedTextLength) {
			textToLoad = totalTextLength - processedTextLength;
		}
		textSizeInByte = textToLoad / CHAR_PER_BYTE;
		fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
		fread(bwtInc->textBuffer, sizeof(unsigned char), textSizeInByte, packedFile);
		fseek(packedFile, -((long)textSizeInByte), SEEK_CUR);
		ConvertBytePackedToWordPacked(bwtInc->textBuffer, bwtInc->packedText, ALPHABET_SIZE, textToLoad);
		BWTIncConstruct(bwtInc, textToLoad);
		processedTextLength += textToLoad;
		if (bwtInc->numberOfIterationDone % 10 == 0) {
			fprintf(stderr, "[BWTIncConstructFromPacked] %lu iterations done. %lu characters processed.\n",
					(long)bwtInc->numberOfIterationDone, (long)processedTextLength);
		}
	}
	return bwtInc;
}

void BWTFree(BWT *bwt)
{
	if (bwt == 0) return;
	free(bwt->cumulativeFreq);
	free(bwt->bwtCode);
	free(bwt->occValue);
	free(bwt->occValueMajor);
	free(bwt->decodeTable);
	free(bwt);
}

void BWTIncFree(BWTInc *bwtInc)
{
	if (bwtInc == 0) return;
	free(bwtInc->bwt);
	free(bwtInc->workingMemory);
	free(bwtInc);
}

static bgint_t BWTFileSizeInWord(const bgint_t numChar)
{
	// The $ in BWT at the position of inverseSa0 is not encoded
	return (numChar + CHAR_PER_WORD - 1) / CHAR_PER_WORD;
}

void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *occValueFileName)
{
	FILE *bwtFile;
/*	FILE *occValueFile; */
	bgint_t bwtLength;

	bwtFile = (FILE*)fopen(bwtFileName, "wb");
	if (bwtFile == NULL) {
		fprintf(stderr, "BWTSaveBwtCodeAndOcc(): Cannot open BWT code file!\n");
		exit(1);
	}

	fwrite(&bwt->inverseSa0, sizeof(bgint_t), 1, bwtFile);
	fwrite(bwt->cumulativeFreq + 1, sizeof(bgint_t), ALPHABET_SIZE, bwtFile);
	bwtLength = BWTFileSizeInWord(bwt->textLength);
	fwrite(bwt->bwtCode, sizeof(unsigned int), bwtLength, bwtFile);
	fclose(bwtFile);
}

void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
{
	BWTInc *bwtInc;
	bwtInc = BWTIncConstructFromPacked(fn_pac, 10000000, 10000000);
	printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone);
	BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0);
	BWTIncFree(bwtInc);
}

int bwt_bwtgen_main(int argc, char *argv[])
{
	if (argc < 3) {
		fprintf(stderr, "Usage: bwtgen <in.pac> <out.bwt>\n");
		return 1;
	}
	bwt_bwtgen(argv[1], argv[2]);
	return 0;
}

#ifdef MAIN_BWT_GEN

int main(int argc, char *argv[])
{
	return bwt_bwtgen_main(argc, argv);
}

#endif
bwa-0.7.3a/bwt_lite.c000644 000767 000024 00000005103 12120745361 014243 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "bwt_lite.h"

int is_sa(const uint8_t *T, uint32_t *SA, int n);
int is_bwt(uint8_t *T, int n);

bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq)
{
	bwtl_t *b;
	int i;
	b = (bwtl_t*)calloc(1, sizeof(bwtl_t));
	b->seq_len = len;

	{ // calculate b->bwt
		uint8_t *s;
		b->sa = (uint32_t*)calloc(len + 1, 4);
		is_sa(seq, b->sa, len);
		s = (uint8_t*)calloc(len + 1, 1);
		for (i = 0; i <= len; ++i) {
			if (b->sa[i] == 0) b->primary = i;
			else s[i] = seq[b->sa[i] - 1];
		}
		for (i = b->primary; i < len; ++i) s[i] = s[i + 1];
		b->bwt_size = (len + 15) / 16;
		b->bwt = (uint32_t*)calloc(b->bwt_size, 4);
		for (i = 0; i < len; ++i)
			b->bwt[i>>4] |= s[i] << ((15 - (i&15)) << 1);
		free(s);
	}
	{ // calculate b->occ
		uint32_t c[4];
		b->n_occ = (len + 15) / 16 * 4;
		b->occ = (uint32_t*)calloc(b->n_occ, 4);
		memset(c, 0, 16);
		for (i = 0; i < len; ++i) {
			if (i % 16 == 0)
				memcpy(b->occ + (i/16) * 4, c, 16);
			++c[bwtl_B0(b, i)];
		}
		memcpy(b->L2+1, c, 16);
		for (i = 2; i < 5; ++i) b->L2[i] += b->L2[i-1];
	}
	{ // generate cnt_table
		for (i = 0; i != 256; ++i) {
			u_int32_t j, x = 0;
			for (j = 0; j != 4; ++j)
				x |= (((i&3) == j) + ((i>>2&3) == j) + ((i>>4&3) == j) + (i>>6 == j)) << (j<<3);
			b->cnt_table[i] = x;
		}
	}
	return b;
}
inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
{
	uint32_t n, b;
	if (k == bwt->seq_len) return bwt->L2[c+1] - bwt->L2[c];
	if (k == (uint32_t)(-1)) return 0;
	if (k >= bwt->primary) --k; // because $ is not in bwt
	n = bwt->occ[k/16<<2|c];
	b = bwt->bwt[k/16] & ~((1U<<((15-(k&15))<<1)) - 1);
	n += (bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
		  + bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24]) >> (c<<3) & 0xff;
	if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
	return n;
}
void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
{
	uint32_t x, b;
	if (k == (uint32_t)(-1)) {
		memset(cnt, 0, 16);
		return;
	}
	if (k >= bwt->primary) --k; // because $ is not in bwt
	memcpy(cnt, bwt->occ + (k>>4<<2), 16);
	b = bwt->bwt[k>>4] & ~((1U<<((~k&15)<<1)) - 1);
	x = bwt->cnt_table[b&0xff] + bwt->cnt_table[b>>8&0xff]
		+ bwt->cnt_table[b>>16&0xff] + bwt->cnt_table[b>>24];
	x -= 15 - (k&15);
	cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
}
void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
{
	bwtl_occ4(bwt, k, cntk);
	bwtl_occ4(bwt, l, cntl);
}
void bwtl_destroy(bwtl_t *bwt)
{
	if (bwt) {
		free(bwt->occ); free(bwt->bwt); free(bwt->sa);
		free(bwt);
	}
}
bwa-0.7.3a/bwt_lite.h000644 000767 000024 00000001242 12120745361 014250 0ustar00lh3staff000000 000000 #ifndef BWT_LITE_H_
#define BWT_LITE_H_

#include <stdint.h>

typedef struct {
	uint32_t seq_len, bwt_size, n_occ;
	uint32_t primary;
	uint32_t *bwt, *occ, *sa, L2[5];
	uint32_t cnt_table[256];
} bwtl_t;

#define bwtl_B0(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)

#ifdef __cplusplus
extern "C" {
#endif

	bwtl_t *bwtl_seq2bwtl(int len, const uint8_t *seq);
	inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c);
	inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]);
	inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]);
	void bwtl_destroy(bwtl_t *bwt);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwtaln.c000644 000767 000024 00000025070 12120745361 013726 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <unistd.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <stdint.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "bwtaln.h"
#include "bwtgap.h"
#include "utils.h"
#include "bwa.h"

#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif

gap_opt_t *gap_init_opt()
{
	gap_opt_t *o;
	o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
	/* IMPORTANT: s_mm*10 should be about the average base error
	   rate. Voilating this requirement will break pairing! */
	o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
	o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
	o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
	o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
	o->seed_len = 32; o->max_seed_diff = 2;
	o->fnr = 0.04;
	o->n_threads = 1;
	o->max_top2 = 30;
	o->trim_qual = 0;
	return o;
}

int bwa_cal_maxdiff(int l, double err, double thres)
{
	double elambda = exp(-l * err);
	double sum, y = 1.0;
	int k, x = 1;
	for (k = 1, sum = elambda; k < 1000; ++k) {
		y *= l * err;
		x *= k;
		sum += elambda * y / x;
		if (1.0 - sum < thres) return k;
	}
	return 2;
}

// width must be filled as zero
int bwt_cal_width(const bwt_t *bwt, int len, const ubyte_t *str, bwt_width_t *width)
{
	bwtint_t k, l, ok, ol;
	int i, bid;
	bid = 0;
	k = 0; l = bwt->seq_len;
	for (i = 0; i < len; ++i) {
		ubyte_t c = str[i];
		if (c < 4) {
			bwt_2occ(bwt, k - 1, l, c, &ok, &ol);
			k = bwt->L2[c] + ok + 1;
			l = bwt->L2[c] + ol;
		}
		if (k > l || c > 3) { // then restart
			k = 0;
			l = bwt->seq_len;
			++bid;
		}
		width[i].w = l - k + 1;
		width[i].bid = bid;
	}
	width[len].w = 0;
	width[len].bid = ++bid;
	return bid;
}

void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
{
	int i, j, max_l = 0, max_len;
	gap_stack_t *stack;
	bwt_width_t *w, *seed_w;
	gap_opt_t local_opt = *opt;

	// initiate priority stack
	for (i = max_len = 0; i != n_seqs; ++i)
		if (seqs[i].len > max_len) max_len = seqs[i].len;
	if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
	if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
	stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);

	seed_w = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
	w = 0;
	for (i = 0; i != n_seqs; ++i) {
		bwa_seq_t *p = seqs + i;
#ifdef HAVE_PTHREAD
		if (i % opt->n_threads != tid) continue;
#endif
		p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
		if (max_l < p->len) {
			max_l = p->len;
			w = (bwt_width_t*)realloc(w, (max_l + 1) * sizeof(bwt_width_t));
			memset(w, 0, (max_l + 1) * sizeof(bwt_width_t));
		}
		bwt_cal_width(bwt, p->len, p->seq, w);
		if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
		local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
		if (p->len > opt->seed_len)
			bwt_cal_width(bwt, opt->seed_len, p->seq + (p->len - opt->seed_len), seed_w);
		// core function
		for (j = 0; j < p->len; ++j) // we need to complement
			p->seq[j] = p->seq[j] > 3? 4 : 3 - p->seq[j];
		p->aln = bwt_match_gap(bwt, p->len, p->seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
		// clean up the unused data in the record
		free(p->name); free(p->seq); free(p->rseq); free(p->qual);
		p->name = 0; p->seq = p->rseq = p->qual = 0;
	}
	free(seed_w); free(w);
	gap_destroy_stack(stack);
}

#ifdef HAVE_PTHREAD
typedef struct {
	int tid;
	bwt_t *bwt;
	int n_seqs;
	bwa_seq_t *seqs;
	const gap_opt_t *opt;
} thread_aux_t;

static void *worker(void *data)
{
	thread_aux_t *d = (thread_aux_t*)data;
	bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
	return 0;
}
#endif

bwa_seqio_t *bwa_open_reads(int mode, const char *fn_fa)
{
	bwa_seqio_t *ks;
	if (mode & BWA_MODE_BAM) { // open BAM
		int which = 0;
		if (mode & BWA_MODE_BAM_SE) which |= 4;
		if (mode & BWA_MODE_BAM_READ1) which |= 1;
		if (mode & BWA_MODE_BAM_READ2) which |= 2;
		if (which == 0) which = 7; // then read all reads
		ks = bwa_bam_open(fn_fa, which);
	} else ks = bwa_seq_open(fn_fa);
	return ks;
}

void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
{
	int i, n_seqs, tot_seqs = 0;
	bwa_seq_t *seqs;
	bwa_seqio_t *ks;
	clock_t t;
	bwt_t *bwt;

	// initialization
	ks = bwa_open_reads(opt->mode, fn_fa);

	{ // load BWT
		char *str = (char*)calloc(strlen(prefix) + 10, 1);
		strcpy(str, prefix); strcat(str, ".bwt");  bwt = bwt_restore_bwt(str);
		free(str);
	}

	// core loop
	err_fwrite(opt, sizeof(gap_opt_t), 1, stdout);
	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode, opt->trim_qual)) != 0) {
		tot_seqs += n_seqs;
		t = clock();

		fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");

#ifdef HAVE_PTHREAD
		if (opt->n_threads <= 1) { // no multi-threading at all
			bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
		} else {
			pthread_t *tid;
			pthread_attr_t attr;
			thread_aux_t *data;
			int j;
			pthread_attr_init(&attr);
			pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
			data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
			tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
			for (j = 0; j < opt->n_threads; ++j) {
				data[j].tid = j; data[j].bwt = bwt;
				data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
				pthread_create(&tid[j], &attr, worker, data + j);
			}
			for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
			free(data); free(tid);
		}
#else
		bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
#endif

		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		t = clock();
		fprintf(stderr, "[bwa_aln_core] write to the disk... ");
		for (i = 0; i < n_seqs; ++i) {
			bwa_seq_t *p = seqs + i;
			err_fwrite(&p->n_aln, 4, 1, stdout);
			if (p->n_aln) err_fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
		}
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();

		bwa_free_read_seq(n_seqs, seqs);
		fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
	}

	// destroy
	bwt_destroy(bwt);
	bwa_seq_close(ks);
}

int bwa_aln(int argc, char *argv[])
{
	int c, opte = -1;
	gap_opt_t *opt;
	char *prefix;

	opt = gap_init_opt();
	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:LR:m:t:NM:O:E:q:f:b012IYB:")) >= 0) {
		switch (c) {
		case 'n':
			if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
			else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
			break;
		case 'o': opt->max_gapo = atoi(optarg); break;
		case 'e': opte = atoi(optarg); break;
		case 'M': opt->s_mm = atoi(optarg); break;
		case 'O': opt->s_gapo = atoi(optarg); break;
		case 'E': opt->s_gape = atoi(optarg); break;
		case 'd': opt->max_del_occ = atoi(optarg); break;
		case 'i': opt->indel_end_skip = atoi(optarg); break;
		case 'l': opt->seed_len = atoi(optarg); break;
		case 'k': opt->max_seed_diff = atoi(optarg); break;
		case 'm': opt->max_entries = atoi(optarg); break;
		case 't': opt->n_threads = atoi(optarg); break;
		case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
		case 'R': opt->max_top2 = atoi(optarg); break;
		case 'q': opt->trim_qual = atoi(optarg); break;
		case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
		case 'f': xreopen(optarg, "wb", stdout); break;
		case 'b': opt->mode |= BWA_MODE_BAM; break;
		case '0': opt->mode |= BWA_MODE_BAM_SE; break;
		case '1': opt->mode |= BWA_MODE_BAM_READ1; break;
		case '2': opt->mode |= BWA_MODE_BAM_READ2; break;
		case 'I': opt->mode |= BWA_MODE_IL13; break;
		case 'Y': opt->mode |= BWA_MODE_CFY; break;
		case 'B': opt->mode |= atoi(optarg) << 24; break;
		default: return 1;
		}
	}
	if (opte > 0) {
		opt->max_gape = opte;
		opt->mode &= ~BWA_MODE_GAPE;
	}

	if (optind + 2 > argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   bwa aln [options] <prefix> <in.fq>\n\n");
		fprintf(stderr, "Options: -n NUM    max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
				BWA_AVG_ERR, opt->fnr);
		fprintf(stderr, "         -o INT    maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
		fprintf(stderr, "         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
		fprintf(stderr, "         -i INT    do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
		fprintf(stderr, "         -d INT    maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
		fprintf(stderr, "         -l INT    seed length [%d]\n", opt->seed_len);
		fprintf(stderr, "         -k INT    maximum differences in the seed [%d]\n", opt->max_seed_diff);
		fprintf(stderr, "         -m INT    maximum entries in the queue [%d]\n", opt->max_entries);
		fprintf(stderr, "         -t INT    number of threads [%d]\n", opt->n_threads);
		fprintf(stderr, "         -M INT    mismatch penalty [%d]\n", opt->s_mm);
		fprintf(stderr, "         -O INT    gap open penalty [%d]\n", opt->s_gapo);
		fprintf(stderr, "         -E INT    gap extension penalty [%d]\n", opt->s_gape);
		fprintf(stderr, "         -R INT    stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
		fprintf(stderr, "         -q INT    quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
        fprintf(stderr, "         -f FILE   file to write output to instead of stdout\n");
		fprintf(stderr, "         -B INT    length of barcode\n");
		fprintf(stderr, "         -L        log-scaled gap penalty for long deletions\n");
		fprintf(stderr, "         -N        non-iterative mode: search for all n-difference hits (slooow)\n");
		fprintf(stderr, "         -I        the input is in the Illumina 1.3+ FASTQ-like format\n");
		fprintf(stderr, "         -b        the input read file is in the BAM format\n");
		fprintf(stderr, "         -0        use single-end reads only (effective with -b)\n");
		fprintf(stderr, "         -1        use the 1st read in a pair (effective with -b)\n");
		fprintf(stderr, "         -2        use the 2nd read in a pair (effective with -b)\n");
		fprintf(stderr, "         -Y        filter Casava-filtered sequences\n");
		fprintf(stderr, "\n");
		return 1;
	}
	if (opt->fnr > 0.0) {
		int i, k;
		for (i = 17, k = 0; i <= 250; ++i) {
			int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
			if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
			k = l;
		}
	}
	if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
		fprintf(stderr, "[%s] fail to locate the index\n", __func__);
		free(opt);
		return 0;
	}
	bwa_aln_core(prefix, argv[optind+1], opt);
	free(opt); free(prefix);
	return 0;
}
bwa-0.7.3a/bwtaln.h000644 000767 000024 00000007255 12120745361 013740 0ustar00lh3staff000000 000000 #ifndef BWTALN_H
#define BWTALN_H

#include <stdint.h>
#include "bwt.h"

#define BWA_TYPE_NO_MATCH 0
#define BWA_TYPE_UNIQUE 1
#define BWA_TYPE_REPEAT 2
#define BWA_TYPE_MATESW 3

#define SAM_FPD   1 // paired
#define SAM_FPP   2 // properly paired
#define SAM_FSU   4 // self-unmapped
#define SAM_FMU   8 // mate-unmapped
#define SAM_FSR  16 // self on the reverse strand
#define SAM_FMR  32 // mate on the reverse strand
#define SAM_FR1  64 // this is read one
#define SAM_FR2 128 // this is read two
#define SAM_FSC 256 // secondary alignment

#define BWA_AVG_ERR 0.02
#define BWA_MIN_RDLEN 35 // for read trimming

#define BWA_MAX_BCLEN 63 // maximum barcode length; 127 is the maximum

#ifndef bns_pac
#define bns_pac(pac, k) ((pac)[(k)>>2] >> ((~(k)&3)<<1) & 3)
#endif

#define FROM_M 0
#define FROM_I 1
#define FROM_D 2
#define FROM_S 3

typedef struct {
	bwtint_t w;
	int bid;
} bwt_width_t;

typedef struct {
	uint32_t n_mm:16, n_gapo:8, n_gape:8;
	int score;
	bwtint_t k, l;
} bwt_aln1_t;

typedef uint16_t bwa_cigar_t;
/* rgoya: If changing order of bytes, beware of operations like:
 *     s->cigar[0] += s->full_len - s->len;
 */
#define CIGAR_OP_SHIFT 14
#define CIGAR_LN_MASK 0x3fff

#define __cigar_op(__cigar) ((__cigar)>>CIGAR_OP_SHIFT)
#define __cigar_len(__cigar) ((__cigar)&CIGAR_LN_MASK)
#define __cigar_create(__op, __len) ((__op)<<CIGAR_OP_SHIFT | (__len))

typedef struct {
	uint32_t n_cigar:15, gap:8, mm:8, strand:1;
	bwtint_t pos;
	bwa_cigar_t *cigar;
} bwt_multi1_t;

typedef struct {
	char *name;
	ubyte_t *seq, *rseq, *qual;
	uint32_t len:20, strand:1, type:2, dummy:1, extra_flag:8;
	uint32_t n_mm:8, n_gapo:8, n_gape:8, mapQ:8;
	int score;
	int clip_len;
	// alignments in SA coordinates
	int n_aln;
	bwt_aln1_t *aln;
	// multiple hits
	int n_multi;
	bwt_multi1_t *multi;
	// alignment information
	bwtint_t sa, pos;
	uint64_t c1:28, c2:28, seQ:8; // number of top1 and top2 hits; single-end mapQ
	int n_cigar;
	bwa_cigar_t *cigar;
	// for multi-threading only
	int tid;
	// barcode
	char bc[BWA_MAX_BCLEN+1]; // null terminated; up to BWA_MAX_BCLEN bases
	// NM and MD tags
	uint32_t full_len:20, nm:12;
	char *md;
} bwa_seq_t;

#define BWA_MODE_GAPE       0x01
#define BWA_MODE_COMPREAD   0x02
#define BWA_MODE_LOGGAP     0x04
#define BWA_MODE_CFY        0x08
#define BWA_MODE_NONSTOP    0x10
#define BWA_MODE_BAM        0x20
#define BWA_MODE_BAM_SE     0x40
#define BWA_MODE_BAM_READ1  0x80
#define BWA_MODE_BAM_READ2  0x100
#define BWA_MODE_IL13       0x200

typedef struct {
	int s_mm, s_gapo, s_gape;
	int mode; // bit 24-31 are the barcode length
	int indel_end_skip, max_del_occ, max_entries;
	float fnr;
	int max_diff, max_gapo, max_gape;
	int max_seed_diff, seed_len;
	int n_threads;
	int max_top2;
	int trim_qual;
} gap_opt_t;

#define BWA_PET_STD   1

typedef struct {
	int max_isize, force_isize;
	int max_occ;
	int n_multi, N_multi;
	int type, is_sw, is_preload;
	double ap_prior;
} pe_opt_t;

struct __bwa_seqio_t;
typedef struct __bwa_seqio_t bwa_seqio_t;

#ifdef __cplusplus
extern "C" {
#endif

	gap_opt_t *gap_init_opt();
	void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);

	bwa_seqio_t *bwa_seq_open(const char *fn);
	bwa_seqio_t *bwa_bam_open(const char *fn, int which);
	void bwa_seq_close(bwa_seqio_t *bs);
	void seq_reverse(int len, ubyte_t *seq, int is_comp);
	bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
	void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);

	int bwa_cal_maxdiff(int l, double err, double thres);
	void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt, int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt);

	void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwtgap.c000644 000767 000024 00000020753 12120745361 013726 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "bwtgap.h"
#include "bwtaln.h"

#define STATE_M 0
#define STATE_I 1
#define STATE_D 2

#define aln_score(m,o,e,p) ((m)*(p)->s_mm + (o)*(p)->s_gapo + (e)*(p)->s_gape)

gap_stack_t *gap_init_stack2(int max_score)
{
	gap_stack_t *stack;
	stack = (gap_stack_t*)calloc(1, sizeof(gap_stack_t));
	stack->n_stacks = max_score;
	stack->stacks = (gap_stack1_t*)calloc(stack->n_stacks, sizeof(gap_stack1_t));
	return stack;
}

gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt)
{
	return gap_init_stack2(aln_score(max_mm+1, max_gapo+1, max_gape+1, opt));
}

void gap_destroy_stack(gap_stack_t *stack)
{
	int i;
	for (i = 0; i != stack->n_stacks; ++i) free(stack->stacks[i].stack);
	free(stack->stacks);
	free(stack);
}

static void gap_reset_stack(gap_stack_t *stack)
{
	int i;
	for (i = 0; i != stack->n_stacks; ++i)
		stack->stacks[i].n_entries = 0;
	stack->best = stack->n_stacks;
	stack->n_entries = 0;
}

static inline void gap_push(gap_stack_t *stack, int i, bwtint_t k, bwtint_t l, int n_mm, int n_gapo, int n_gape,
							int state, int is_diff, const gap_opt_t *opt)
{
	int score;
	gap_entry_t *p;
	gap_stack1_t *q;
	score = aln_score(n_mm, n_gapo, n_gape, opt);
	q = stack->stacks + score;
	if (q->n_entries == q->m_entries) {
		q->m_entries = q->m_entries? q->m_entries<<1 : 4;
		q->stack = (gap_entry_t*)realloc(q->stack, sizeof(gap_entry_t) * q->m_entries);
	}
	p = q->stack + q->n_entries;
	p->info = (u_int32_t)score<<21 | i; p->k = k; p->l = l;
	p->n_mm = n_mm; p->n_gapo = n_gapo; p->n_gape = n_gape; p->state = state;
	p->last_diff_pos = is_diff? i : 0;
	++(q->n_entries);
	++(stack->n_entries);
	if (stack->best > score) stack->best = score;
}

static inline void gap_pop(gap_stack_t *stack, gap_entry_t *e)
{
	gap_stack1_t *q;
	q = stack->stacks + stack->best;
	*e = q->stack[q->n_entries - 1];
	--(q->n_entries);
	--(stack->n_entries);
	if (q->n_entries == 0 && stack->n_entries) { // reset best
		int i;
		for (i = stack->best + 1; i < stack->n_stacks; ++i)
			if (stack->stacks[i].n_entries != 0) break;
		stack->best = i;
	} else if (stack->n_entries == 0) stack->best = stack->n_stacks;
}

static inline void gap_shadow(int x, int len, bwtint_t max, int last_diff_pos, bwt_width_t *w)
{
	int i, j;
	for (i = j = 0; i < last_diff_pos; ++i) {
		if (w[i].w > x) w[i].w -= x;
		else if (w[i].w == x) {
			w[i].bid = 1;
			w[i].w = max - (++j);
		} // else should not happen
	}
}

static inline int int_log2(uint32_t v)
{
	int c = 0;
	if (v & 0xffff0000u) { v >>= 16; c |= 16; }
	if (v & 0xff00) { v >>= 8; c |= 8; }
	if (v & 0xf0) { v >>= 4; c |= 4; }
	if (v & 0xc) { v >>= 2; c |= 2; }
	if (v & 0x2) c |= 1;
	return c;
}

bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *width,
						  bwt_width_t *seed_width, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack)
{
	int best_score = aln_score(opt->max_diff+1, opt->max_gapo+1, opt->max_gape+1, opt);
	int best_diff = opt->max_diff + 1, max_diff = opt->max_diff;
	int best_cnt = 0;
	int max_entries = 0, j, _j, n_aln, m_aln;
	bwt_aln1_t *aln;

	m_aln = 4; n_aln = 0;
	aln = (bwt_aln1_t*)calloc(m_aln, sizeof(bwt_aln1_t));

	// check whether there are too many N
	for (j = _j = 0; j < len; ++j)
		if (seq[j] > 3) ++_j;
	if (_j > max_diff) {
		*_n_aln = n_aln;
		return aln;
	}

	//for (j = 0; j != len; ++j) printf("#0 %d: [%d,%u]\t[%d,%u]\n", j, w[0][j].bid, w[0][j].w, w[1][j].bid, w[1][j].w);
	gap_reset_stack(stack); // reset stack
	gap_push(stack, len, 0, bwt->seq_len, 0, 0, 0, 0, 0, opt);

	while (stack->n_entries) {
		gap_entry_t e;
		int i, m, m_seed = 0, hit_found, allow_diff, allow_M, tmp;
		bwtint_t k, l, cnt_k[4], cnt_l[4], occ;

		if (max_entries < stack->n_entries) max_entries = stack->n_entries;
		if (stack->n_entries > opt->max_entries) break;
		gap_pop(stack, &e); // get the best entry
		k = e.k; l = e.l; // SA interval
		i = e.info&0xffff; // length
		if (!(opt->mode & BWA_MODE_NONSTOP) && e.info>>21 > best_score + opt->s_mm) break; // no need to proceed

		m = max_diff - (e.n_mm + e.n_gapo);
		if (opt->mode & BWA_MODE_GAPE) m -= e.n_gape;
		if (m < 0) continue;
		if (seed_width) { // apply seeding
			m_seed = opt->max_seed_diff - (e.n_mm + e.n_gapo);
			if (opt->mode & BWA_MODE_GAPE) m_seed -= e.n_gape;
		}
		//printf("#1\t[%d,%d,%d,%c]\t[%d,%d,%d]\t[%u,%u]\t[%u,%u]\t%d\n", stack->n_entries, a, i, "MID"[e.state], e.n_mm, e.n_gapo, e.n_gape, width[i-1].bid, width[i-1].w, k, l, e.last_diff_pos);
		if (i > 0 && m < width[i-1].bid) continue;

		// check whether a hit is found
		hit_found = 0;
		if (i == 0) hit_found = 1;
		else if (m == 0 && (e.state == STATE_M || (opt->mode&BWA_MODE_GAPE) || e.n_gape == opt->max_gape)) { // no diff allowed
			if (bwt_match_exact_alt(bwt, i, seq, &k, &l)) hit_found = 1;
			else continue; // no hit, skip
		}

		if (hit_found) { // action for found hits
			int score = aln_score(e.n_mm, e.n_gapo, e.n_gape, opt);
			int do_add = 1;
			//printf("#2 hits found: %d:(%u,%u)\n", e.n_mm+e.n_gapo, k, l);
			if (n_aln == 0) {
				best_score = score;
				best_diff = e.n_mm + e.n_gapo;
				if (opt->mode & BWA_MODE_GAPE) best_diff += e.n_gape;
				if (!(opt->mode & BWA_MODE_NONSTOP))
					max_diff = (best_diff + 1 > opt->max_diff)? opt->max_diff : best_diff + 1; // top2 behaviour
			}
			if (score == best_score) best_cnt += l - k + 1;
			else if (best_cnt > opt->max_top2) break; // top2b behaviour
			if (e.n_gapo) { // check whether the hit has been found. this may happen when a gap occurs in a tandem repeat
				for (j = 0; j != n_aln; ++j)
					if (aln[j].k == k && aln[j].l == l) break;
				if (j < n_aln) do_add = 0;
			}
			if (do_add) { // append
				bwt_aln1_t *p;
				gap_shadow(l - k + 1, len, bwt->seq_len, e.last_diff_pos, width);
				if (n_aln == m_aln) {
					m_aln <<= 1;
					aln = (bwt_aln1_t*)realloc(aln, m_aln * sizeof(bwt_aln1_t));
					memset(aln + m_aln/2, 0, m_aln/2*sizeof(bwt_aln1_t));
				}
				p = aln + n_aln;
				p->n_mm = e.n_mm; p->n_gapo = e.n_gapo; p->n_gape = e.n_gape;
				p->k = k; p->l = l;
				p->score = score;
				++n_aln;
			}
			continue;
		}

		--i;
		bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values
		occ = l - k + 1;
		// test whether diff is allowed
		allow_diff = allow_M = 1;
		if (i > 0) {
			int ii = i - (len - opt->seed_len);
			if (width[i-1].bid > m-1) allow_diff = 0;
			else if (width[i-1].bid == m-1 && width[i].bid == m-1 && width[i-1].w == width[i].w) allow_M = 0;
			if (seed_width && ii > 0) {
				if (seed_width[ii-1].bid > m_seed-1) allow_diff = 0;
				else if (seed_width[ii-1].bid == m_seed-1 && seed_width[ii].bid == m_seed-1
						 && seed_width[ii-1].w == seed_width[ii].w) allow_M = 0;
			}
		}
		// indels
		tmp = (opt->mode & BWA_MODE_LOGGAP)? int_log2(e.n_gape + e.n_gapo)/2+1 : e.n_gapo + e.n_gape;
		if (allow_diff && i >= opt->indel_end_skip + tmp && len - i >= opt->indel_end_skip + tmp) {
			if (e.state == STATE_M) { // gap open
				if (e.n_gapo < opt->max_gapo) { // gap open is allowed
					// insertion
					gap_push(stack, i, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_I, 1, opt);
					// deletion
					for (j = 0; j != 4; ++j) {
						k = bwt->L2[j] + cnt_k[j] + 1;
						l = bwt->L2[j] + cnt_l[j];
						if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo + 1, e.n_gape, STATE_D, 1, opt);
					}
				}
			} else if (e.state == STATE_I) { // extention of an insertion
				if (e.n_gape < opt->max_gape) // gap extention is allowed
					gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_I, 1, opt);
			} else if (e.state == STATE_D) { // extention of a deletion
				if (e.n_gape < opt->max_gape) { // gap extention is allowed
					if (e.n_gape + e.n_gapo < max_diff || occ < opt->max_del_occ) {
						for (j = 0; j != 4; ++j) {
							k = bwt->L2[j] + cnt_k[j] + 1;
							l = bwt->L2[j] + cnt_l[j];
							if (k <= l) gap_push(stack, i + 1, k, l, e.n_mm, e.n_gapo, e.n_gape + 1, STATE_D, 1, opt);
						}
					}
				}
			}
		}
		// mismatches
		if (allow_diff && allow_M) { // mismatch is allowed
			for (j = 1; j <= 4; ++j) {
				int c = (seq[i] + j) & 3;
				int is_mm = (j != 4 || seq[i] > 3);
				k = bwt->L2[c] + cnt_k[c] + 1;
				l = bwt->L2[c] + cnt_l[c];
				if (k <= l) gap_push(stack, i, k, l, e.n_mm + is_mm, e.n_gapo, e.n_gape, STATE_M, is_mm, opt);
			}
		} else if (seq[i] < 4) { // try exact match only
			int c = seq[i] & 3;
			k = bwt->L2[c] + cnt_k[c] + 1;
			l = bwt->L2[c] + cnt_l[c];
			if (k <= l) gap_push(stack, i, k, l, e.n_mm, e.n_gapo, e.n_gape, STATE_M, 0, opt);
		}
	}

	*_n_aln = n_aln;
	//fprintf(stderr, "max_entries = %d\n", max_entries);
	return aln;
}
bwa-0.7.3a/bwtgap.h000644 000767 000024 00000001710 12120745361 013723 0ustar00lh3staff000000 000000 #ifndef BWTGAP_H_
#define BWTGAP_H_

#include "bwt.h"
#include "bwtaln.h"

typedef struct { // recursion stack
	u_int32_t info; // score<<21 | i
	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
	int last_diff_pos;
} gap_entry_t;

typedef struct {
	int n_entries, m_entries;
	gap_entry_t *stack;
} gap_stack1_t;

typedef struct {
	int n_stacks, best, n_entries;
	gap_stack1_t *stacks;
} gap_stack_t;

#ifdef __cplusplus
extern "C" {
#endif

	gap_stack_t *gap_init_stack2(int max_score);
	gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
	void gap_destroy_stack(gap_stack_t *stack);
	bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w,
							  bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwtindex.c000644 000767 000024 00000020427 12120745361 014264 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <time.h>
#include <zlib.h>
#include "bntseq.h"
#include "bwt.h"
#include "utils.h"

#ifdef _DIVBWT
#include "divsufsort.h"
#endif

int is_bwt(ubyte_t *T, int n);

int64_t bwa_seq_len(const char *fn_pac)
{
	FILE *fp;
	int64_t pac_len;
	ubyte_t c;
	fp = xopen(fn_pac, "rb");
	fseek(fp, -1, SEEK_END);
	pac_len = ftell(fp);
	fread(&c, 1, 1, fp);
	fclose(fp);
	return (pac_len - 1) * 4 + (int)c;
}

bwt_t *bwt_pac2bwt(const char *fn_pac, int use_is)
{
	bwt_t *bwt;
	ubyte_t *buf, *buf2;
	int i, pac_size;
	FILE *fp;

	// initialization
	bwt = (bwt_t*)calloc(1, sizeof(bwt_t));
	bwt->seq_len = bwa_seq_len(fn_pac);
	bwt->bwt_size = (bwt->seq_len + 15) >> 4;
	fp = xopen(fn_pac, "rb");

	// prepare sequence
	pac_size = (bwt->seq_len>>2) + ((bwt->seq_len&3) == 0? 0 : 1);
	buf2 = (ubyte_t*)calloc(pac_size, 1);
	fread(buf2, 1, pac_size, fp);
	fclose(fp);
	memset(bwt->L2, 0, 5 * 4);
	buf = (ubyte_t*)calloc(bwt->seq_len + 1, 1);
	for (i = 0; i < bwt->seq_len; ++i) {
		buf[i] = buf2[i>>2] >> ((3 - (i&3)) << 1) & 3;
		++bwt->L2[1+buf[i]];
	}
	for (i = 2; i <= 4; ++i) bwt->L2[i] += bwt->L2[i-1];
	free(buf2);

	// Burrows-Wheeler Transform
	if (use_is) {
		bwt->primary = is_bwt(buf, bwt->seq_len);
	} else {
#ifdef _DIVBWT
		bwt->primary = divbwt(buf, buf, 0, bwt->seq_len);
#else
		err_fatal_simple("libdivsufsort is not compiled in.");
#endif
	}
	bwt->bwt = (u_int32_t*)calloc(bwt->bwt_size, 4);
	for (i = 0; i < bwt->seq_len; ++i)
		bwt->bwt[i>>4] |= buf[i] << ((15 - (i&15)) << 1);
	free(buf);
	return bwt;
}

int bwa_pac2bwt(int argc, char *argv[]) // the "pac2bwt" command; IMPORTANT: bwt generated at this step CANNOT be used with BWA. bwtupdate is required!
{
	bwt_t *bwt;
	int c, use_is = 1;
	while ((c = getopt(argc, argv, "d")) >= 0) {
		switch (c) {
		case 'd': use_is = 0; break;
		default: return 1;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: bwa pac2bwt [-d] <in.pac> <out.bwt>\n");
		return 1;
	}
	bwt = bwt_pac2bwt(argv[optind], use_is);
	bwt_dump_bwt(argv[optind+1], bwt);
	bwt_destroy(bwt);
	return 0;
}

#define bwt_B00(b, k) ((b)->bwt[(k)>>4]>>((~(k)&0xf)<<1)&3)

void bwt_bwtupdate_core(bwt_t *bwt)
{
	bwtint_t i, k, c[4], n_occ;
	uint32_t *buf;

	n_occ = (bwt->seq_len + OCC_INTERVAL - 1) / OCC_INTERVAL + 1;
	bwt->bwt_size += n_occ * sizeof(bwtint_t); // the new size
	buf = (uint32_t*)calloc(bwt->bwt_size, 4); // will be the new bwt
	c[0] = c[1] = c[2] = c[3] = 0;
	for (i = k = 0; i < bwt->seq_len; ++i) {
		if (i % OCC_INTERVAL == 0) {
			memcpy(buf + k, c, sizeof(bwtint_t) * 4);
			k += sizeof(bwtint_t); // in fact: sizeof(bwtint_t)=4*(sizeof(bwtint_t)/4)
		}
		if (i % 16 == 0) buf[k++] = bwt->bwt[i/16]; // 16 == sizeof(uint32_t)/2
		++c[bwt_B00(bwt, i)];
	}
	// the last element
	memcpy(buf + k, c, sizeof(bwtint_t) * 4);
	xassert(k + sizeof(bwtint_t) == bwt->bwt_size, "inconsistent bwt_size");
	// update bwt
	free(bwt->bwt); bwt->bwt = buf;
}

int bwa_bwtupdate(int argc, char *argv[]) // the "bwtupdate" command
{
	bwt_t *bwt;
	if (argc < 2) {
		fprintf(stderr, "Usage: bwa bwtupdate <the.bwt>\n");
		return 1;
	}
	bwt = bwt_restore_bwt(argv[1]);
	bwt_bwtupdate_core(bwt);
	bwt_dump_bwt(argv[1], bwt);
	bwt_destroy(bwt);
	return 0;
}

int bwa_bwt2sa(int argc, char *argv[]) // the "bwt2sa" command
{
	bwt_t *bwt;
	int c, sa_intv = 32;
	while ((c = getopt(argc, argv, "i:")) >= 0) {
		switch (c) {
		case 'i': sa_intv = atoi(optarg); break;
		default: return 1;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: bwa bwt2sa [-i %d] <in.bwt> <out.sa>\n", sa_intv);
		return 1;
	}
	bwt = bwt_restore_bwt(argv[optind]);
	bwt_cal_sa(bwt, sa_intv);
	bwt_dump_sa(argv[optind+1], bwt);
	bwt_destroy(bwt);
	return 0;
}

int bwa_index(int argc, char *argv[]) // the "index" command
{
	extern void bwa_pac_rev_core(const char *fn, const char *fn_rev);

	char *prefix = 0, *str, *str2, *str3;
	int c, algo_type = 0, is_64 = 0;
	clock_t t;
	int64_t l_pac;

	while ((c = getopt(argc, argv, "6a:p:")) >= 0) {
		switch (c) {
		case 'a': // if -a is not set, algo_type will be determined later
			if (strcmp(optarg, "div") == 0) algo_type = 1;
			else if (strcmp(optarg, "bwtsw") == 0) algo_type = 2;
			else if (strcmp(optarg, "is") == 0) algo_type = 3;
			else err_fatal(__func__, "unknown algorithm: '%s'.", optarg);
			break;
		case 'p': prefix = strdup(optarg); break;
		case '6': is_64 = 1; break;
		default: return 1;
		}
	}

	if (optind + 1 > argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   bwa index [-a bwtsw|is] [-c] <in.fasta>\n\n");
		fprintf(stderr, "Options: -a STR    BWT construction algorithm: bwtsw or is [auto]\n");
		fprintf(stderr, "         -p STR    prefix of the index [same as fasta name]\n");
		fprintf(stderr, "         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.* \n");
		fprintf(stderr, "\n");
		fprintf(stderr,	"Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
		fprintf(stderr, "         `-a div' do not work not for long genomes. Please choose `-a'\n");
		fprintf(stderr, "         according to the length of the genome.\n\n");
		return 1;
	}
	if (prefix == 0) {
		prefix = malloc(strlen(argv[optind]) + 4);
		strcpy(prefix, argv[optind]);
		if (is_64) strcat(prefix, ".64");
	}
	str  = (char*)calloc(strlen(prefix) + 10, 1);
	str2 = (char*)calloc(strlen(prefix) + 10, 1);
	str3 = (char*)calloc(strlen(prefix) + 10, 1);

	{ // nucleotide indexing
		gzFile fp = xzopen(argv[optind], "r");
		t = clock();
		fprintf(stderr, "[bwa_index] Pack FASTA... ");
		l_pac = bns_fasta2bntseq(fp, prefix, 0);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
		gzclose(fp);
	}
	if (algo_type == 0) algo_type = l_pac > 50000000? 2 : 3; // set the algorithm for generating BWT
	{
		strcpy(str, prefix); strcat(str, ".pac");
		strcpy(str2, prefix); strcat(str2, ".bwt");
		t = clock();
		fprintf(stderr, "[bwa_index] Construct BWT for the packed sequence...\n");
		if (algo_type == 2) bwt_bwtgen(str, str2);
		else if (algo_type == 1 || algo_type == 3) {
			bwt_t *bwt;
			bwt = bwt_pac2bwt(str, algo_type == 3);
			bwt_dump_bwt(str2, bwt);
			bwt_destroy(bwt);
		}
		fprintf(stderr, "[bwa_index] %.2f seconds elapse.\n", (float)(clock() - t) / CLOCKS_PER_SEC);
	}
	{
		bwt_t *bwt;
		strcpy(str, prefix); strcat(str, ".bwt");
		t = clock();
		fprintf(stderr, "[bwa_index] Update BWT... ");
		bwt = bwt_restore_bwt(str);
		bwt_bwtupdate_core(bwt);
		bwt_dump_bwt(str, bwt);
		bwt_destroy(bwt);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
	}
	{
		gzFile fp = xzopen(argv[optind], "r");
		t = clock();
		fprintf(stderr, "[bwa_index] Pack forward-only FASTA... ");
		l_pac = bns_fasta2bntseq(fp, prefix, 1);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
		gzclose(fp);
	}
	{
		bwt_t *bwt;
		strcpy(str, prefix); strcat(str, ".bwt");
		strcpy(str3, prefix); strcat(str3, ".sa");
		t = clock();
		fprintf(stderr, "[bwa_index] Construct SA from BWT and Occ... ");
		bwt = bwt_restore_bwt(str);
		bwt_cal_sa(bwt, 32);
		bwt_dump_sa(str3, bwt);
		bwt_destroy(bwt);
		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
	}
	free(str3); free(str2); free(str); free(prefix);
	return 0;
}
bwa-0.7.3a/bwtsw2.h000644 000767 000024 00000002764 12120745361 013701 0ustar00lh3staff000000 000000 #ifndef LH3_BWTSW2_H
#define LH3_BWTSW2_H

#include <stdint.h>
#include "bntseq.h"
#include "bwt_lite.h"
#include "bwt.h"

#define BSW2_FLAG_MATESW  0x100
#define BSW2_FLAG_TANDEM  0x200
#define BSW2_FLAG_MOVED   0x400
#define BSW2_FLAG_RESCUED 0x800

typedef struct {
	int skip_sw:8, cpy_cmt:8, hard_clip:16;
	int a, b, q, r, t, qr, bw, max_ins, max_chain_gap;
	int z, is, t_seeds, multi_2nd;
	float mask_level, coef;
	int n_threads, chunk_size;
} bsw2opt_t;

typedef struct {
	bwtint_t k, l;
	uint32_t flag:18, n_seeds:13, is_rev:1;
	int len, G, G2;
	int beg, end;
} bsw2hit_t;

typedef struct {
	int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
	uint32_t *cigar;
} bsw2aux_t;

typedef struct {
	int n, max;
	bsw2hit_t *hits;
	bsw2aux_t *aux;
} bwtsw2_t;

typedef struct {
	void *stack;
	int max_l;
	uint8_t *aln_mem;
} bsw2global_t;

typedef struct {
	int l, tid;
	char *name, *seq, *qual, *sam, *comment;
} bsw2seq1_t;

#ifdef __cplusplus
extern "C" {
#endif

	bsw2opt_t *bsw2_init_opt();
	bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
	void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2);
	void bsw2_destroy(bwtsw2_t *b);

	bsw2global_t *bsw2_global_init();
	void bsw2_global_destroy(bsw2global_t *_pool);

	void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/bwtsw2_aux.c000644 000767 000024 00000060567 12120745361 014556 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <stdio.h>
#include <math.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifdef HAVE_PTHREAD
#include <pthread.h>
#endif
#include "bntseq.h"
#include "bwt_lite.h"
#include "utils.h"
#include "bwtsw2.h"
#include "kstring.h"
#include "bwa.h"
#include "ksw.h"

#include "kseq.h"
KSEQ_DECLARE(gzFile)

#include "ksort.h"
#define __left_lt(a, b) ((a).end > (b).end)
KSORT_INIT(hit, bsw2hit_t, __left_lt)

extern unsigned char nst_nt4_table[256];

unsigned char nt_comp_table[256] = {
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
	'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
	'n','t','v','g', 'h','n','n','c', 'd','n','n','m', 'n','k','n','n',
	'n','n','y','s', 'a','n','b','w', 'x','r','n','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
	'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
};

extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
extern int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level);

bsw2opt_t *bsw2_init_opt()
{
	bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
	o->a = 1; o->b = 3; o->q = 5; o->r = 2; o->t = 30;
	o->bw = 50;
	o->max_ins = 20000;
	o->z = 1; o->is = 3; o->t_seeds = 5; o->hard_clip = 0; o->skip_sw = 0;
	o->mask_level = 0.50f; o->coef = 5.5f;
	o->qr = o->q + o->r; o->n_threads = 1; o->chunk_size = 10000000;
	o->max_chain_gap = 10000;
	o->cpy_cmt = 0;
	return o;
}

void bsw2_destroy(bwtsw2_t *b)
{
	int i;
	if (b == 0) return;
	if (b->aux)
		for (i = 0; i < b->n; ++i) free(b->aux[i].cigar);
	free(b->aux); free(b->hits);
	free(b);
}

bwtsw2_t *bsw2_dup_no_cigar(const bwtsw2_t *b)
{
	bwtsw2_t *p;
	p = calloc(1, sizeof(bwtsw2_t));
	p->max = p->n = b->n;
	if (b->n) {
		kroundup32(p->max);
		p->hits = calloc(p->max, sizeof(bsw2hit_t));
		memcpy(p->hits, b->hits, p->n * sizeof(bsw2hit_t));
	}
	return p;
}

#define __gen_ap(par, opt) do {									\
		int i;													\
		for (i = 0; i < 25; ++i) (par).matrix[i] = -(opt)->b;	\
		for (i = 0; i < 4; ++i) (par).matrix[i*5+i] = (opt)->a; \
		(par).gap_open = (opt)->q; (par).gap_ext = (opt)->r;	\
		(par).gap_end = (opt)->r;								\
		(par).row = 5; (par).band_width = opt->bw;				\
	} while (0)

void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
{
	int i;
	bwtint_t k;
	uint8_t *target = 0, *query;
	int8_t mat[25];

	bwa_fill_scmat(opt->a, opt->b, mat);
	query = calloc(lq, 1);
	// sort according to the descending order of query end
	ks_introsort(hit, b->n, b->hits);
	target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
	// reverse _query
	for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i];
	// core loop
	for (i = 0; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
		int score, j, qle, tle;
		p->n_seeds = 1;
		if (p->l || p->k == 0) continue;
		for (j = score = 0; j < i; ++j) {
			bsw2hit_t *q = b->hits + j;
			if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) {
				if (q->n_seeds < (1<<13) - 2) ++q->n_seeds;
				++score;
			}
		}
		if (score) continue;
		if (lt > p->k) lt = p->k;
		for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered!
			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
		lt = j;
		score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, p->G, &qle, &tle, 0, 0, 0);
		if (score > p->G) { // extensible
			p->G = score;
			p->k -= tle;
			p->len += tle;
			p->beg -= qle;
		}
	}
	free(query); free(target);
}

void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem)
{
	int i;
	bwtint_t k;
	uint8_t *target;
	int8_t mat[25];

	bwa_fill_scmat(opt->a, opt->b, mat);
	target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1);
	for (i = 0; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq;
		int j, score, qle, tle;
		if (p->l) continue;
		for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k)
			target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3;
		lt = j;
		score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, -1, 1, &qle, &tle, 0, 0, 0) - 1;
//		if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G);
		if (score >= p->G) {
			p->G = score;
			p->len = tle;
			p->end = p->beg + qle;
		}
	}
	free(target);
}

/* generate CIGAR array(s) in b->cigar[] */
static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], int64_t l_pac, const uint8_t *pac, bwtsw2_t *b, const char *name)
{
	int i;
	int8_t mat[25];

	bwa_fill_scmat(opt->a, opt->b, mat);
	for (i = 0; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		bsw2aux_t *q = b->aux + i;
		uint8_t *query;
		int beg, end, score;
		if (p->l) continue;
		beg = (p->flag & 0x10)? lq - p->end : p->beg;
		end = (p->flag & 0x10)? lq - p->beg : p->end;
		query = seq[(p->flag & 0x10)? 1 : 0] + beg;
		q->cigar = bwa_gen_cigar(mat, opt->q, opt->r, opt->bw, l_pac, pac, end - beg, query, p->k, p->k + p->len, &score, &q->n_cigar, &q->nm);
#if 0
		if (name && score != p->G) { // debugging only
			int j, glen = 0;
			for (j = 0; j < q->n_cigar; ++j)
				if ((q->cigar[j]&0xf) == 1 || (q->cigar[j]&0xf) == 2)
					glen += q->cigar[j]>>4;
			fprintf(stderr, "[E::%s] %s - unequal score: %d != %d; (qlen, aqlen, arlen, glen, bw) = (%d, %d, %d, %d, %d)\n",
					__func__, name, score, p->G, lq, end - beg, p->len, glen, opt->bw);
		}
#endif
		if (q->cigar && (beg != 0 || end < lq)) { // write soft clipping
			q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
			if (beg != 0) {
				memmove(q->cigar + 1, q->cigar, q->n_cigar * 4);
				q->cigar[0] = beg<<4 | 4;
				++q->n_cigar;
			}
			if (end < lq) {
				q->cigar[q->n_cigar] = (lq - end)<<4 | 4;
				++q->n_cigar;
			}
		}
	}
}

/* this is for the debugging purpose only */
void bsw2_debug_hits(const bwtsw2_t *b)
{
	int i;
	printf("# raw hits: %d\n", b->n);
	for (i = 0; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		if (p->G > 0)
			printf("G=%d, G2=%d, len=%d, [%d,%d), k=%lu, l=%lu, #seeds=%d, is_rev=%d\n", p->G, p->G2, p->len, p->beg, p->end, (long)p->k, (long)p->l, p->n_seeds, p->is_rev);
	}
}

static void merge_hits(bwtsw2_t *b[2], int l, int is_reverse)
{
	int i;
	if (b[0]->n + b[1]->n > b[0]->max) {
		b[0]->max = b[0]->n + b[1]->n;
		b[0]->hits = realloc(b[0]->hits, b[0]->max * sizeof(bsw2hit_t));
	}
	for (i = 0; i < b[1]->n; ++i) {
		bsw2hit_t *p = b[0]->hits + b[0]->n + i;
		*p = b[1]->hits[i];
		if (is_reverse) {
			int x = p->beg;
			p->beg = l - p->end;
			p->end = l - x;
			p->flag |= 0x10;
		}
	}
	b[0]->n += b[1]->n;
	bsw2_destroy(b[1]);
	b[1] = 0;
}
/* seq[0] is the forward sequence and seq[1] is the reverse complement. */
static bwtsw2_t *bsw2_aln1_core(const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target,
								int l, uint8_t *seq[2], bsw2global_t *pool)
{
	extern void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2]);
	bwtsw2_t *b[2], **bb[2], **_b, *p;
	int k, j;
	bwtl_t *query;
	query = bwtl_seq2bwtl(l, seq[0]);
	_b = bsw2_core(bns, opt, query, target, pool);
	bwtl_destroy(query);
	for (k = 0; k < 2; ++k) {
		bb[k] = calloc(2, sizeof(void*));
		bb[k][0] = calloc(1, sizeof(bwtsw2_t));
		bb[k][1] = calloc(1, sizeof(bwtsw2_t));
	}
	for (k = 0; k < 2; ++k) { // separate _b into bb[2] based on the strand
		for (j = 0; j < _b[k]->n; ++j) {
			bsw2hit_t *q;
			p = bb[_b[k]->hits[j].is_rev][k];
			if (p->n == p->max) {
				p->max = p->max? p->max<<1 : 8;
				p->hits = realloc(p->hits, p->max * sizeof(bsw2hit_t));
			}
			q = &p->hits[p->n++];
			*q = _b[k]->hits[j];
			if (_b[k]->hits[j].is_rev) {
				int x = q->beg;
				q->beg = l - q->end;
				q->end = l - x;
			}
		}
	}
	b[0] = bb[0][1]; b[1] = bb[1][1]; // bb[*][1] are "narrow SA hits"
	bsw2_chain_filter(opt, l, b); // NB: only unique seeds are chained
	for (k = 0; k < 2; ++k) {
		bsw2_extend_left(opt, bb[k][1], seq[k], l, pac, bns->l_pac, pool->aln_mem);
		merge_hits(bb[k], l, 0); // bb[k][1] is merged to bb[k][0] here
		bsw2_resolve_duphits(0, 0, bb[k][0], 0);
		bsw2_extend_rght(opt, bb[k][0], seq[k], l, pac, bns->l_pac, pool->aln_mem);
		bsw2_resolve_duphits(0, 0, bb[k][0], 0);
		b[k] = bb[k][0];
		free(bb[k]);		
	}
	merge_hits(b, l, 1); // again, b[1] is merged to b[0]
	bsw2_resolve_query_overlaps(b[0], opt->mask_level);
	bsw2_destroy(_b[0]); bsw2_destroy(_b[1]); free(_b);
	return b[0];
}

/* set ->flag to records the origin of the hit (to forward bwt or reverse bwt) */
static void flag_fr(bwtsw2_t *b[2])
{
	int i, j;
	for (i = 0; i < b[0]->n; ++i) {
		bsw2hit_t *p = b[0]->hits + i;
		p->flag |= 0x10000;
	}
	for (i = 0; i < b[1]->n; ++i) {
		bsw2hit_t *p = b[1]->hits + i;
		p->flag |= 0x20000;
	}
	for (i = 0; i < b[0]->n; ++i) {
		bsw2hit_t *p = b[0]->hits + i;
		for (j = 0; j < b[1]->n; ++j) {
			bsw2hit_t *q = b[1]->hits + j;
			if (q->beg == p->beg && q->end == p->end && q->k == p->k && q->len == p->len && q->G == p->G) {
				q->flag |= 0x30000; p->flag |= 0x30000;
				break;
			}
		}
	}
}

typedef struct {
	int n, max;
	bsw2seq1_t *seq;
} bsw2seq_t;

static int fix_cigar(const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
{
	// FIXME: this routine does not work if the query bridge three reference sequences
	int32_t coor, refl, lq;
	int x, y, i, seqid;
	bns_cnt_ambi(bns, p->k, p->len, &seqid);
	coor = p->k - bns->anns[seqid].offset;
	refl = bns->anns[seqid].len;
	x = coor; y = 0;
	// test if the alignment goes beyond the boundary
	for (i = 0; i < n_cigar; ++i) {
		int op = cigar[i]&0xf, ln = cigar[i]>>4;
		if (op == 1 || op == 4 || op == 5) y += ln;
		else if (op == 2) x += ln;
		else x += ln, y += ln;
	}
	lq = y; // length of the query sequence
	if (x > refl) { // then fix it
		int j, nc, mq[2], nlen[2];
		uint32_t *cn;
		bwtint_t kk = 0;
		nc = mq[0] = mq[1] = nlen[0] = nlen[1] = 0;
		cn = calloc(n_cigar + 3, 4);
		x = coor; y = 0;
		for (i = j = 0; i < n_cigar; ++i) {
			int op = cigar[i]&0xf, ln = cigar[i]>>4;
			if (op == 4 || op == 5 || op == 1) { // ins or clipping
				y += ln;
				cn[j++] = cigar[i];
			} else if (op == 2) { // del
				if (x + ln >= refl && nc == 0) {
					cn[j++] = (uint32_t)(lq - y)<<4 | 4;
					nc = j;
					cn[j++] = (uint32_t)y<<4 | 4;
					kk = p->k + (x + ln - refl);
					nlen[0] = x - coor;
					nlen[1] = p->len - nlen[0] - ln;
				} else cn[j++] = cigar[i];
				x += ln;
			} else if (op == 0) { // match
				if (x + ln >= refl && nc == 0) {
					// FIXME: not consider a special case where a split right between M and I
					cn[j++] = (uint32_t)(refl - x)<<4 | 0; // write M
					cn[j++] = (uint32_t)(lq - y - (refl - x))<<4 | 4; // write S
					nc = j;
					mq[0] += refl - x;
					cn[j++] = (uint32_t)(y + (refl - x))<<4 | 4;
					if (x + ln - refl) cn[j++] = (uint32_t)(x + ln - refl)<<4 | 0;
					mq[1] += x + ln - refl;
					kk = bns->anns[seqid].offset + refl;
					nlen[0] = refl - coor;
					nlen[1] = p->len - nlen[0];
				} else {
					cn[j++] = cigar[i];
					mq[nc?1:0] += ln;
				}
				x += ln; y += ln;
			}
		}
		if (mq[0] > mq[1]) { // then take the first alignment
			n_cigar = nc;
			memcpy(cigar, cn, 4 * nc);
			p->len = nlen[0];
		} else {
			p->k = kk; p->len = nlen[1];
			n_cigar = j - nc;
			memcpy(cigar, cn + nc, 4 * (j - nc));
		}
		free(cn);
	}
	return n_cigar;
}

static void write_aux(const bsw2opt_t *opt, const bntseq_t *bns, int qlen, uint8_t *seq[2], const uint8_t *pac, bwtsw2_t *b, const char *name)
{
	int i;
	// allocate for b->aux
	if (b->n<<1 < b->max) {
		b->max = b->n;
		kroundup32(b->max);
		b->hits = realloc(b->hits, b->max * sizeof(bsw2hit_t));
	}
	b->aux = calloc(b->n, sizeof(bsw2aux_t));
	// generate CIGAR
	gen_cigar(opt, qlen, seq, bns->l_pac, pac, b, name);
	// fix CIGAR, generate mapQ, and write chromosomal position
	for (i = 0; i < b->n; ++i) {
		bsw2hit_t *p = &b->hits[i];
		bsw2aux_t *q = &b->aux[i];
		q->flag = p->flag & 0xfe;
		q->isize = 0;
		if (p->l == 0) { // unique hit
			float c = 1.0;
			int subo;
			// fix out-of-boundary CIGAR
			q->n_cigar = fix_cigar(bns, p, q->n_cigar, q->cigar);
			// compute mapQ
			subo = p->G2 > opt->t? p->G2 : opt->t;
			if (p->flag>>16 == 1 || p->flag>>16 == 2) c *= .5;
			if (p->n_seeds < 2) c *= .2;
			q->qual = (int)(c * (p->G - subo) * (250.0 / p->G + 0.03 / opt->a) + .499);
			if (q->qual > 250) q->qual = 250;
			if (q->qual < 0) q->qual = 0;
			if (p->flag&1) q->qual = 0; // this is a random hit
			q->pqual = q->qual; // set the paired qual as qual
			// get the chromosomal position
			q->nn = bns_cnt_ambi(bns, p->k, p->len, &q->chr);
			q->pos = p->k - bns->anns[q->chr].offset;
		} else q->qual = 0, q->n_cigar = 0, q->chr = q->pos = -1, q->nn = 0;
	}
}

static void update_mate_aux(bwtsw2_t *b, const bwtsw2_t *m)
{
	int i;
	if (m == 0) return;
	// update flag, mchr and mpos
	for (i = 0; i < b->n; ++i) {
		bsw2aux_t *q = &b->aux[i];
		q->flag |= 1; // paired
		if (m->n == 0) q->flag |= 8; // mate unmapped
		if (m->n == 1) {
			q->mchr = m->aux[0].chr;
			q->mpos = m->aux[0].pos;
			if (m->aux[0].flag&0x10) q->flag |= 0x20; // mate reverse strand
			if (q->chr == q->mchr) { // set insert size
				if (q->mpos + m->hits[0].len > q->pos)
					q->isize = q->mpos + m->hits[0].len - q->pos;
				else q->isize = q->mpos - q->pos - b->hits[0].len;
			} else q->isize = 0;
		} else q->mchr = q->mpos = -1;
	}
	// update mapping quality
	if (b->n == 1 && m->n == 1) {
		bsw2hit_t *p = &b->hits[0];
		if (p->flag & BSW2_FLAG_MATESW) { // this alignment is found by Smith-Waterman
			if (!(p->flag & BSW2_FLAG_TANDEM) && b->aux[0].pqual < 20)
				b->aux[0].pqual = 20;
			if (b->aux[0].pqual >= m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
		} else if ((p->flag & 2) && !(m->hits[0].flag & BSW2_FLAG_MATESW)) { // properly paired
			if (!(p->flag & BSW2_FLAG_TANDEM)) { // pqual is bounded by [b->aux[0].qual,m->aux[0].qual]
				b->aux[0].pqual += 20;
				if (b->aux[0].pqual > m->aux[0].qual) b->aux[0].pqual = m->aux[0].qual;
				if (b->aux[0].pqual < b->aux[0].qual) b->aux[0].pqual = b->aux[0].qual;
			}
		}
	}
}

/* generate SAM lines for a sequence in ks with alignment stored in
 * b. ks->name and ks->seq will be freed and set to NULL in the end. */
static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks, bwtsw2_t *b, int is_pe, bwtsw2_t *bmate)
{
	int i, k;
	kstring_t str;
	memset(&str, 0, sizeof(kstring_t));
	if (b == 0 || b->n == 0) { // no hits
		ksprintf(&str, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t", ks->name);
		for (i = 0; i < ks->l; ++i) kputc(ks->seq[i], &str);
		if (ks->qual) {
			kputc('\t', &str);
			for (i = 0; i < ks->l; ++i) kputc(ks->qual[i], &str);
		} else kputs("\t*", &str);
		kputc('\n', &str);
	}
	for (i = 0; b && i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		bsw2aux_t *q = b->aux + i;
		int j, beg, end, type = 0;
		// print mandatory fields before SEQ
		if (q->cigar == 0) q->flag |= 0x4;
		ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
		ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
		if (p->l == 0 && q->cigar) { // not a repetitive hit
			ksprintf(&str, "\t%d\t", q->pqual);
			for (k = 0; k < q->n_cigar; ++k)
				ksprintf(&str, "%d%c", q->cigar[k]>>4, (opt->hard_clip? "MIDNHHP" : "MIDNSHP")[q->cigar[k]&0xf]);
		} else ksprintf(&str, "\t0\t*");
		if (!is_pe) kputs("\t*\t0\t0\t", &str);
		else ksprintf(&str, "\t%s\t%d\t%d\t", q->mchr==q->chr? "=" : (q->mchr<0? "*" : bns->anns[q->mchr].name), q->mpos+1, q->isize);
		// get the sequence begin and end
		beg = 0; end = ks->l;
		if (opt->hard_clip && q->cigar) {
			if ((q->cigar[0]&0xf) == 4) beg += q->cigar[0]>>4;
			if ((q->cigar[q->n_cigar-1]&0xf) == 4) end -= q->cigar[q->n_cigar-1]>>4;
		}
		for (j = beg; j < end; ++j) {
			if (p->flag&0x10) kputc(nt_comp_table[(int)ks->seq[ks->l - 1 - j]], &str);
			else kputc(ks->seq[j], &str);
		}
		// print base quality if present
		if (ks->qual) {
			kputc('\t', &str);
			for (j = beg; j < end; ++j) {
				if (p->flag&0x10) kputc(ks->qual[ks->l - 1 - j], &str);
				else kputc(ks->qual[j], &str);
			}
		} else kputs("\t*", &str);
		// print optional tags
		ksprintf(&str, "\tAS:i:%d\tXS:i:%d\tXF:i:%d\tXE:i:%d\tNM:i:%d", p->G, p->G2, p->flag>>16, p->n_seeds, q->nm);
		if (q->nn) ksprintf(&str, "\tXN:i:%d", q->nn);
		if (p->l) ksprintf(&str, "\tXI:i:%d", p->l - p->k + 1);
		if (p->flag&BSW2_FLAG_MATESW) type |= 1;
		if (p->flag&BSW2_FLAG_TANDEM) type |= 2;
		if (type) ksprintf(&str, "\tXT:i:%d", type);
		if (opt->cpy_cmt && ks->comment) {
			int l = strlen(ks->comment);
			if (l >= 6 && ks->comment[2] == ':' && ks->comment[4] == ':') {
				kputc('\t', &str); kputs(ks->comment, &str);
			}
		}
		kputc('\n', &str);
	}
	ks->sam = str.s;
	free(ks->seq); ks->seq = 0;
	free(ks->qual); ks->qual = 0;
	free(ks->name); ks->name = 0;
}

static void update_opt(bsw2opt_t *dst, const bsw2opt_t *src, int qlen)
{
	double ll = log(qlen);
	int i, k;
	*dst = *src;
	if (dst->t < ll * dst->coef) dst->t = (int)(ll * dst->coef + .499);
	// set band width: the query length sets a boundary on the maximum band width
	k = (qlen * dst->a - 2 * dst->q) / (2 * dst->r + dst->a);
	i = (qlen * dst->a - dst->a - dst->t) / dst->r;
	if (k > i) k = i;
	if (k < 1) k = 1; // I do not know if k==0 causes troubles
	dst->bw = src->bw < k? src->bw : k;
}

/* Core routine to align reads in _seq. It is separated from
 * process_seqs() to realize multi-threading */ 
static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
{
	int x;
	bsw2opt_t opt;
	bsw2global_t *pool = bsw2_global_init();
	bwtsw2_t **buf;
	buf = calloc(_seq->n, sizeof(void*));
	for (x = 0; x < _seq->n; ++x) {
		bsw2seq1_t *p = _seq->seq + x;
		uint8_t *seq[2], *rseq[2];
		int i, l, k;
		bwtsw2_t *b[2];
		l = p->l;
		update_opt(&opt, _opt, p->l);
		if (pool->max_l < l) { // then enlarge working space for aln_extend_core()
			int tmp = ((l + 1) / 2 * opt.a + opt.r) / opt.r + l;
			pool->max_l = l;
			pool->aln_mem = realloc(pool->aln_mem, (tmp + 2) * 24);
		}
		// set seq[2] and rseq[2]
		seq[0] = calloc(l * 4, 1);
		seq[1] = seq[0] + l;
		rseq[0] = seq[1] + l; rseq[1] = rseq[0] + l;
		// convert sequences to 2-bit representation
		for (i = k = 0; i < l; ++i) {
			int c = nst_nt4_table[(int)p->seq[i]];
			if (c >= 4) { c = (int)(drand48() * 4); ++k; } // FIXME: ambiguous bases are not properly handled
			seq[0][i] = c;
			seq[1][l-1-i] = 3 - c;
			rseq[0][l-1-i] = 3 - c;
			rseq[1][i] = c;
		}
		if (l - k < opt.t) { // too few unambiguous bases
			buf[x] = calloc(1, sizeof(bwtsw2_t));
			free(seq[0]); continue;
		}
		// alignment
		b[0] = bsw2_aln1_core(&opt, bns, pac, target, l, seq, pool);
		for (k = 0; k < b[0]->n; ++k)
			if (b[0]->hits[k].n_seeds < opt.t_seeds) break;
		if (k < b[0]->n) {
			b[1] = bsw2_aln1_core(&opt, bns, pac, target, l, rseq, pool);
			for (i = 0; i < b[1]->n; ++i) {
				bsw2hit_t *p = &b[1]->hits[i];
				int x = p->beg;
				p->flag ^= 0x10, p->is_rev ^= 1; // flip the strand
				p->beg = l - p->end;
				p->end = l - x;
			}
			flag_fr(b);
			merge_hits(b, l, 0);
			bsw2_resolve_duphits(0, 0, b[0], 0);
			bsw2_resolve_query_overlaps(b[0], opt.mask_level);
		} else b[1] = 0;
		// generate CIGAR and print SAM
		buf[x] = bsw2_dup_no_cigar(b[0]);
		// free
		free(seq[0]);
		bsw2_destroy(b[0]);
	}
	if (is_pe) bsw2_pair(&opt, bns->l_pac, pac, _seq->n, _seq->seq, buf);
	for (x = 0; x < _seq->n; ++x) {
		bsw2seq1_t *p = _seq->seq + x;
		uint8_t *seq[2];
		int i;
		seq[0] = malloc(p->l * 2); seq[1] = seq[0] + p->l;
		for (i = 0; i < p->l; ++i) {
			int c = nst_nt4_table[(int)p->seq[i]];
			if (c >= 4) c = (int)(drand48() * 4);
			seq[0][i] = c;
			seq[1][p->l-1-i] = 3 - c;
		}
		update_opt(&opt, _opt, p->l);
		write_aux(&opt, bns, p->l, seq, pac, buf[x], _seq->seq[x].name);
		free(seq[0]);
	}
	for (x = 0; x < _seq->n; ++x) {
		if (is_pe) update_mate_aux(buf[x], buf[x^1]);
		print_hits(bns, &opt, &_seq->seq[x], buf[x], is_pe, buf[x^1]);
	}
	for (x = 0; x < _seq->n; ++x) bsw2_destroy(buf[x]);
	free(buf);
	bsw2_global_destroy(pool);
}

#ifdef HAVE_PTHREAD
typedef struct {
	int tid, is_pe;
	bsw2seq_t *_seq;
	const bsw2opt_t *_opt;
	const bntseq_t *bns;
	uint8_t *pac;
	const bwt_t *target;
} thread_aux_t;

/* another interface to bsw2_aln_core() to facilitate pthread_create() */
static void *worker(void *data)
{
	thread_aux_t *p = (thread_aux_t*)data;
	bsw2_aln_core(p->_seq, p->_opt, p->bns, p->pac, p->target, p->is_pe);
	return 0;
}
#endif

/* process sequences stored in _seq, generate SAM lines for these
 * sequences and reset _seq afterwards. */
static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *bns, uint8_t *pac, const bwt_t *target, int is_pe)
{
	int i;
	is_pe = is_pe? 1 : 0;

#ifdef HAVE_PTHREAD
	if (opt->n_threads <= 1) {
		bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
	} else {
		pthread_t *tid;
		pthread_attr_t attr;
		thread_aux_t *data;
		int j;
		pthread_attr_init(&attr);
		pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
		data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
		for (j = 0; j < opt->n_threads; ++j) {
			thread_aux_t *p = data + j;
			p->tid = j; p->_opt = opt; p->bns = bns; p->is_pe = is_pe;
			p->pac = pac; p->target = target;
			p->_seq = calloc(1, sizeof(bsw2seq_t));
			p->_seq->max = (_seq->n + opt->n_threads - 1) / opt->n_threads + 1;
			p->_seq->n = 0;
			p->_seq->seq = calloc(p->_seq->max, sizeof(bsw2seq1_t));
		}
		for (i = 0; i < _seq->n; ++i) { // assign sequences to each thread
			bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
			p->seq[p->n++] = _seq->seq[i];
		}
		for (j = 0; j < opt->n_threads; ++j) pthread_create(&tid[j], &attr, worker, &data[j]);
		for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
		for (j = 0; j < opt->n_threads; ++j) data[j]._seq->n = 0;
		for (i = 0; i < _seq->n; ++i) { // copy the result from each thread back
			bsw2seq_t *p = data[(i>>is_pe)%opt->n_threads]._seq;
			_seq->seq[i] = p->seq[p->n++];
		}
		for (j = 0; j < opt->n_threads; ++j) {
			thread_aux_t *p = data + j;
			free(p->_seq->seq);
			free(p->_seq);
		}
		free(data); free(tid);
	}
#else
	bsw2_aln_core(_seq, opt, bns, pac, target, is_pe);
#endif

	// print and reset
	for (i = 0; i < _seq->n; ++i) {
		bsw2seq1_t *p = _seq->seq + i;
		if (p->sam) printf("%s", p->sam);
		free(p->name); free(p->seq); free(p->qual); free(p->sam);
		p->tid = -1; p->l = 0;
		p->name = p->seq = p->qual = p->sam = 0;
	}
	fflush(stdout);
	_seq->n = 0;
}

void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2)
{
	gzFile fp, fp2;
	kseq_t *ks, *ks2;
	int l, is_pe = 0, i, n;
	uint8_t *pac;
	bsw2seq_t *_seq;
	bseq1_t *bseq;

	pac = calloc(bns->l_pac/4+1, 1);
	if (pac == 0) {
		fprintf(stderr, "[bsw2_aln] insufficient memory!\n");
		return;
	}
	for (l = 0; l < bns->n_seqs; ++l)
		printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[l].name, bns->anns[l].len);
	fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
	fp = xzopen(fn, "r");
	ks = kseq_init(fp);
	_seq = calloc(1, sizeof(bsw2seq_t));
	if (fn2) {
		fp2 = xzopen(fn2, "r");
		ks2 = kseq_init(fp2);
		is_pe = 1;
	} else fp2 = 0, ks2 = 0, is_pe = 0;
	while ((bseq = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
		int size = 0;
		if (n > _seq->max) {
			_seq->max = n;
			kroundup32(_seq->max);
			_seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
		}
		_seq->n = n;
		for (i = 0; i < n; ++i) {
			bseq1_t *b = &bseq[i];
			bsw2seq1_t *p = &_seq->seq[i];
			p->tid = -1; p->l = b->l_seq;
			p->name = b->name; p->seq = b->seq; p->qual = b->qual; p->comment = b->comment; p->sam = 0;
			size += p->l;
		}
		fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp) ...\n", n, size);
		free(bseq);
		process_seqs(_seq, opt, bns, pac, target, is_pe);
	}
	// free
	free(pac);
	free(_seq->seq); free(_seq);
	kseq_destroy(ks);
	gzclose(fp);
	if (fn2) {
		kseq_destroy(ks2);
		gzclose(fp2);
	}
}
bwa-0.7.3a/bwtsw2_chain.c000644 000767 000024 00000005671 12120745361 015036 0ustar00lh3staff000000 000000 #include <stdio.h>
#include "bwtsw2.h"

typedef struct {
	uint32_t tbeg, tend;
	int qbeg, qend;
	uint32_t flag:1, idx:31;
	int chain; // also reuse as a counter
} hsaip_t;

#define _hsaip_lt(a, b) ((a).qbeg < (b).qbeg)

#include "ksort.h"
KSORT_INIT(hsaip, hsaip_t, _hsaip_lt)

static int chaining(const bsw2opt_t *opt, int shift, int n, hsaip_t *z, hsaip_t *chain)
{
	int j, k, m = 0;
	ks_introsort(hsaip, n, z);
	for (j = 0; j < n; ++j) {
		hsaip_t *p = z + j;
		for (k = m - 1; k >= 0; --k) {
			hsaip_t *q = chain + k;
			int x = p->qbeg - q->qbeg; // always positive
			int y = p->tbeg - q->tbeg;
			if (y > 0 && x < opt->max_chain_gap && y < opt->max_chain_gap && x - y <= opt->bw && y - x <= opt->bw) { // chained
				if (p->qend > q->qend) q->qend = p->qend;
				if (p->tend > q->tend) q->tend = p->tend;
				++q->chain;
				p->chain = shift + k;
				break;
			} else if (q->chain > opt->t_seeds * 2) k = 0; // if the chain is strong enough, do not check the previous chains
		}
		if (k < 0) { // not added to any previous chains
			chain[m] = *p;
			chain[m].chain = 1;
			chain[m].idx = p->chain = shift + m;
			++m;
		}
	}
	return m;
}

void bsw2_chain_filter(const bsw2opt_t *opt, int len, bwtsw2_t *b[2])
{
	hsaip_t *z[2], *chain[2];
	int i, j, k, n[2], m[2], thres = opt->t_seeds * 2;
	char *flag;
	// initialization
	n[0] = b[0]->n; n[1] = b[1]->n;
	z[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
	z[1] = z[0] + n[0];
	chain[0] = calloc(n[0] + n[1], sizeof(hsaip_t));
	for (k = j = 0; k < 2; ++k) {
		for (i = 0; i < b[k]->n; ++i) {
			bsw2hit_t *p = b[k]->hits + i;
			hsaip_t *q = z[k] + i;
			q->flag = k; q->idx = i;
			q->tbeg = p->k; q->tend = p->k + p->len;
			q->chain = -1;
			q->qbeg = p->beg; q->qend = p->end;
		}
	}
	// chaining
	m[0] = chaining(opt, 0,    n[0], z[0], chain[0]);
	chain[1] = chain[0] + m[0];
	m[1] = chaining(opt, m[0], n[1], z[1], chain[1]);	
	// change query coordinate on the reverse strand
	for (k = 0; k < m[1]; ++k) {
		hsaip_t *p = chain[1] + k;
		int tmp = p->qbeg;
		p->qbeg = len - p->qend; p->qend = len - tmp;
	}
	//for (k = 0; k < m[0]; ++k) printf("%d, [%d,%d), [%d,%d)\n", chain[0][k].chain, chain[0][k].tbeg, chain[0][k].tend, chain[0][k].qbeg, chain[0][k].qend);
	// filtering
	flag = calloc(m[0] + m[1], 1);
	ks_introsort(hsaip, m[0] + m[1], chain[0]);
	for (k = 1; k < m[0] + m[1]; ++k) {
		hsaip_t *p = chain[0] + k;
		for (j = 0; j < k; ++j) {
			hsaip_t *q = chain[0] + j;
			if (flag[q->idx]) continue;
			if (q->qend >= p->qend && q->chain > p->chain * thres && p->chain < thres) {
				flag[p->idx] = 1;
				break;
			}
		}
	}
	for (k = 0; k < n[0] + n[1]; ++k) {
		hsaip_t *p = z[0] + k;
		if (flag[p->chain])
			b[p->flag]->hits[p->idx].G = 0;
	}
	free(flag);
	// squeeze out filtered elements in b[2]
	for (k = 0; k < 2; ++k) {
		for (j = i = 0; j < n[k]; ++j) {
			bsw2hit_t *p = b[k]->hits + j;
			if (p->G) {
				if (i != j) b[k]->hits[i++] = *p;
				else ++i;
			}
		}
		b[k]->n = i;
	}
	// free
	free(z[0]); free(chain[0]);
}
bwa-0.7.3a/bwtsw2_core.c000644 000767 000024 00000044715 12120745361 014706 0ustar00lh3staff000000 000000 #include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <sys/resource.h>
#include <assert.h>
#include "bwt_lite.h"
#include "bwtsw2.h"
#include "bwt.h"
#include "kvec.h"

typedef struct {
	bwtint_t k, l;
} qintv_t;

#define qintv_eq(a, b) ((a).k == (b).k && (a).l == (b).l)
#define qintv_hash(a) ((a).k>>7^(a).l<<17)

#include "khash.h"
KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq)
KHASH_MAP_INIT_INT64(64, uint64_t)

#define MINUS_INF -0x3fffffff
#define MASK_LEVEL 0.90f

struct __mempool_t;
static void mp_destroy(struct __mempool_t*);
typedef struct {
	bwtint_t qk, ql;
	int I, D, G;
	uint32_t pj:2, qlen:30;
	int tlen;
	int ppos, upos;
	int cpos[4];
} bsw2cell_t;

#include "ksort.h"
KSORT_INIT_GENERIC(int)
#define __hitG_lt(a, b) (((a).G + ((int)(a).n_seeds<<2)) > (b).G + ((int)(b).n_seeds<<2))
KSORT_INIT(hitG, bsw2hit_t, __hitG_lt)

static const bsw2cell_t g_default_cell = { 0, 0, MINUS_INF, MINUS_INF, MINUS_INF, 0, 0, 0, -1, -1, {-1, -1, -1, -1} };

typedef struct {
	int n, max;
	uint32_t tk, tl; // this is fine
	bsw2cell_t *array;
} bsw2entry_t, *bsw2entry_p;

/* --- BEGIN: Stack operations --- */
typedef struct {
	int n_pending;
	kvec_t(bsw2entry_p) stack0, pending;
	struct __mempool_t *pool;
} bsw2stack_t;

#define stack_isempty(s) (kv_size(s->stack0) == 0 && s->n_pending == 0)
static void stack_destroy(bsw2stack_t *s) { mp_destroy(s->pool); kv_destroy(s->stack0); kv_destroy(s->pending); free(s); }
inline static void stack_push0(bsw2stack_t *s, bsw2entry_p e) { kv_push(bsw2entry_p, s->stack0, e); }
inline static bsw2entry_p stack_pop(bsw2stack_t *s)
{
	assert(!(kv_size(s->stack0) == 0 && s->n_pending != 0));
	return kv_pop(s->stack0);
}
/* --- END: Stack operations --- */

/* --- BEGIN: memory pool --- */
typedef struct __mempool_t {
	int cnt; // if cnt!=0, then there must be memory leak
	kvec_t(bsw2entry_p) pool;
} mempool_t;
inline static bsw2entry_p mp_alloc(mempool_t *mp)
{
	++mp->cnt;
	if (kv_size(mp->pool) == 0) return (bsw2entry_t*)calloc(1, sizeof(bsw2entry_t));
	else return kv_pop(mp->pool);
}
inline static void mp_free(mempool_t *mp, bsw2entry_p e)
{
	--mp->cnt; e->n = 0;
	kv_push(bsw2entry_p, mp->pool, e);
}
static void mp_destroy(struct __mempool_t *mp)
{
	int i;
	for (i = 0; i != kv_size(mp->pool); ++i) {
		free(kv_A(mp->pool, i)->array);
		free(kv_A(mp->pool, i));
	}
	kv_destroy(mp->pool);
	free(mp);
}
/* --- END: memory pool --- */

/* --- BEGIN: utilities --- */
static khash_t(64) *bsw2_connectivity(const bwtl_t *b)
{
	khash_t(64) *h;
	uint32_t k, l, cntk[4], cntl[4]; // this is fine
	uint64_t x;
	khiter_t iter;
	int j, ret;
	kvec_t(uint64_t) stack;

	kv_init(stack);
	h = kh_init(64);
	kh_resize(64, h, b->seq_len * 4);
	x = b->seq_len;
	kv_push(uint64_t, stack, x);
	while (kv_size(stack)) {
		x = kv_pop(stack);
		k = x>>32; l = (uint32_t)x;
		bwtl_2occ4(b, k-1, l, cntk, cntl);
		for (j = 0; j != 4; ++j) {
			k = b->L2[j] + cntk[j] + 1;
			l = b->L2[j] + cntl[j];
			if (k > l) continue;
			x = (uint64_t)k << 32 | l;
			iter = kh_put(64, h, x, &ret);
			if (ret) { // if not present
				kh_value(h, iter) = 1;
				kv_push(uint64_t, stack, x);
			} else ++kh_value(h, iter);
		}
	}
	kv_destroy(stack);
	//fprintf(stderr, "[bsw2_connectivity] %u nodes in the DAG\n", kh_size(h));
	return h;
}
// pick up top T matches at a node
static void cut_tail(bsw2entry_t *u, int T, bsw2entry_t *aux)
{
	int i, *a, n, x;
	if (u->n <= T) return;
	if (aux->max < u->n) {
		aux->max = u->n;
		aux->array = (bsw2cell_t*)realloc(aux->array, aux->max * sizeof(bsw2cell_t));
	}
	a = (int*)aux->array;
	for (i = n = 0; i != u->n; ++i)
		if (u->array[i].ql && u->array[i].G > 0)
			a[n++] = -u->array[i].G;
	if (n <= T) return;
	x = -ks_ksmall(int, n, a, T);
	n = 0;
	for (i = 0; i < u->n; ++i) {
		bsw2cell_t *p = u->array + i;
		if (p->G == x) ++n;
		if (p->G < x || (p->G == x && n >= T)) {
			p->qk = p->ql = 0; p->G = 0;
			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -1;
		}
	}
}
// remove duplicated cells
static inline void remove_duplicate(bsw2entry_t *u, khash_t(qintv) *hash)
{
	int i, ret, j;
	khiter_t k;
	qintv_t key;
	kh_clear(qintv, hash);
	for (i = 0; i != u->n; ++i) {
		bsw2cell_t *p = u->array + i;
		if (p->ql == 0) continue;
		key.k = p->qk; key.l = p->ql;
		k = kh_put(qintv, hash, key, &ret);
		j = -1;
		if (ret == 0) {
			if ((uint32_t)kh_value(hash, k) >= p->G) j = i;
			else {
				j = kh_value(hash, k)>>32;
				kh_value(hash, k) = (uint64_t)i<<32 | p->G;
			}
		} else kh_value(hash, k) = (uint64_t)i<<32 | p->G;
		if (j >= 0) {
			p = u->array + j;
			p->qk = p->ql = 0; p->G = 0;
			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
		}
	}
}
// merge two entries
static void merge_entry(const bsw2opt_t * __restrict opt, bsw2entry_t *u, bsw2entry_t *v, bwtsw2_t *b)
{
	int i;
	if (u->n + v->n >= u->max) {
		u->max = u->n + v->n;
		u->array = (bsw2cell_t*)realloc(u->array, u->max * sizeof(bsw2cell_t));
	}
	for (i = 0; i != v->n; ++i) {
		bsw2cell_t *p = v->array + i;
		if (p->ppos >= 0) p->ppos += u->n;
		if (p->cpos[0] >= 0) p->cpos[0] += u->n;
		if (p->cpos[1] >= 0) p->cpos[1] += u->n;
		if (p->cpos[2] >= 0) p->cpos[2] += u->n;
		if (p->cpos[3] >= 0) p->cpos[3] += u->n;
	}
	memcpy(u->array + u->n, v->array, v->n * sizeof(bsw2cell_t));
	u->n += v->n;
}

static inline bsw2cell_t *push_array_p(bsw2entry_t *e)
{
	if (e->n == e->max) {
		e->max = e->max? e->max<<1 : 256;
		e->array = (bsw2cell_t*)realloc(e->array, sizeof(bsw2cell_t) * e->max);
	}
	return e->array + e->n;
}

static inline double time_elapse(const struct rusage *curr, const struct rusage *last)
{
	long t1 = (curr->ru_utime.tv_sec - last->ru_utime.tv_sec) + (curr->ru_stime.tv_sec - last->ru_stime.tv_sec);
	long t2 = (curr->ru_utime.tv_usec - last->ru_utime.tv_usec) + (curr->ru_stime.tv_usec - last->ru_stime.tv_usec);
	return (double)t1 + t2 * 1e-6;
}
/* --- END: utilities --- */

/* --- BEGIN: processing partial hits --- */
static void save_hits(const bwtl_t *bwt, int thres, bsw2hit_t *hits, bsw2entry_t *u)
{
	int i;
	uint32_t k; // this is fine
	for (i = 0; i < u->n; ++i) {
		bsw2cell_t *p = u->array + i;
		if (p->G < thres) continue;
		for (k = u->tk; k <= u->tl; ++k) {
			int beg, end;
			bsw2hit_t *q = 0;
			beg = bwt->sa[k]; end = beg + p->tlen;
			if (p->G > hits[beg*2].G) {
				hits[beg*2+1] = hits[beg*2];
				q = hits + beg * 2;
			} else if (p->G > hits[beg*2+1].G) q = hits + beg * 2 + 1;
			if (q) {
				q->k = p->qk; q->l = p->ql; q->len = p->qlen; q->G = p->G;
				q->beg = beg; q->end = end; q->G2 = q->k == q->l? 0 : q->G;
				q->flag = q->n_seeds = 0;
			}
		}
	}
}
/* "narrow hits" are node-to-node hits that have a high score and
 * are not so repetitive (|SA interval|<=IS). */
static void save_narrow_hits(const bwtl_t *bwtl, bsw2entry_t *u, bwtsw2_t *b1, int t, int IS)
{
	int i;
	for (i = 0; i < u->n; ++i) {
		bsw2hit_t *q;
		bsw2cell_t *p = u->array + i;
		if (p->G >= t && p->ql - p->qk + 1 <= IS) { // good narrow hit
			if (b1->max == b1->n) {
				b1->max = b1->max? b1->max<<1 : 4;
				b1->hits = realloc(b1->hits, b1->max * sizeof(bsw2hit_t));
			}
			q = &b1->hits[b1->n++];
			q->k = p->qk; q->l = p->ql;
			q->len = p->qlen;
			q->G = p->G; q->G2 = 0;
			q->beg = bwtl->sa[u->tk]; q->end = q->beg + p->tlen;
			q->flag = 0;
			// delete p
			p->qk = p->ql = 0; p->G = 0;
			if (p->ppos >= 0) u->array[p->ppos].cpos[p->pj] = -3;
		}
	}
}
/* after this, "narrow SA hits" will be expanded and the coordinates
 * will be obtained and stored in b->hits[*].k. */
int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS)
{
	int i, j, n, is_rev;
	if (b->n == 0) return 0;
	if (bwt && bns) { // convert to chromosomal coordinates if requested
		int old_n = b->n;
		bsw2hit_t *old_hits = b->hits;
		for (i = n = 0; i < b->n; ++i) { // compute the memory to allocated
			bsw2hit_t *p = old_hits + i;
			if (p->l - p->k + 1 <= IS) n += p->l - p->k + 1;
			else if (p->G > 0) ++n;
		}
		b->n = b->max = n;
		b->hits = calloc(b->max, sizeof(bsw2hit_t));
		for (i = j = 0; i < old_n; ++i) {
			bsw2hit_t *p = old_hits + i;
			if (p->l - p->k + 1 <= IS) { // the hit is no so repetitive
				bwtint_t k;
				if (p->G == 0 && p->k == 0 && p->l == 0 && p->len == 0) continue;
				for (k = p->k; k <= p->l; ++k) {
					b->hits[j] = *p;
					b->hits[j].k = bns_depos(bns, bwt_sa(bwt, k), &is_rev);
					b->hits[j].l = 0;
					b->hits[j].is_rev = is_rev;
					if (is_rev) b->hits[j].k -= p->len - 1;
					++j;
				}
			} else if (p->G > 0) {
				b->hits[j] = *p;
				b->hits[j].k = bns_depos(bns, bwt_sa(bwt, p->k), &is_rev);
				b->hits[j].l = 0;
				b->hits[j].flag |= 1;
				b->hits[j].is_rev = is_rev;
				if (is_rev) b->hits[j].k -= p->len - 1;
				++j;
			}
		}
		free(old_hits);
	}
	for (i = j = 0; i < b->n; ++i) // squeeze out empty elements
		if (b->hits[i].G) b->hits[j++] = b->hits[i];
	b->n = j;
	ks_introsort(hitG, b->n, b->hits);
	for (i = 1; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		for (j = 0; j < i; ++j) {
			bsw2hit_t *q = b->hits + j;
			int compatible = 1;
			if (p->is_rev != q->is_rev) continue; // hits from opposite strands are not duplicates
			if (p->l == 0 && q->l == 0) {
				int qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg); // length of query overlap
				if (qol < 0) qol = 0;
				if ((float)qol / (p->end - p->beg) > MASK_LEVEL || (float)qol / (q->end - q->beg) > MASK_LEVEL) {
					int64_t tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
						- (int64_t)(p->k > q->k? p->k : q->k); // length of target overlap
					if ((double)tol / p->len > MASK_LEVEL || (double)tol / q->len > MASK_LEVEL)
						compatible = 0;
				}
			}
			if (!compatible) {
				p->G = 0;
				if (q->G2 < p->G2) q->G2 = p->G2;
				break;
			}
		}
	}
	n = i;
	for (i = j = 0; i < n; ++i) {
		if (b->hits[i].G == 0) continue;
		if (i != j) b->hits[j++] = b->hits[i];
		else ++j;
	}
	b->n = j;
	return b->n;
}

int bsw2_resolve_query_overlaps(bwtsw2_t *b, float mask_level)
{
	int i, j, n;
	if (b->n == 0) return 0;
	ks_introsort(hitG, b->n, b->hits);
	{ // choose a random one
		int G0 = b->hits[0].G;
		for (i = 1; i < b->n; ++i)
			if (b->hits[i].G != G0) break;
		j = (int)(i * drand48());
		if (j) {
			bsw2hit_t tmp;
			tmp = b->hits[0]; b->hits[0] = b->hits[j]; b->hits[j] = tmp;
		}
	}
	for (i = 1; i < b->n; ++i) {
		bsw2hit_t *p = b->hits + i;
		int all_compatible = 1;
		if (p->G == 0) break;
		for (j = 0; j < i; ++j) {
			bsw2hit_t *q = b->hits + j;
			int64_t tol = 0;
			int qol, compatible = 0;
			float fol;
			if (q->G == 0) continue;
			qol = (p->end < q->end? p->end : q->end) - (p->beg > q->beg? p->beg : q->beg);
			if (qol < 0) qol = 0;
			if (p->l == 0 && q->l == 0) {
				tol = (int64_t)(p->k + p->len < q->k + q->len? p->k + p->len : q->k + q->len)
					- (p->k > q->k? p->k : q->k);
				if (tol < 0) tol = 0;
			}
			fol = (float)qol / (p->end - p->beg < q->end - q->beg? p->end - p->beg : q->end - q->beg);
			if (fol < mask_level || (tol > 0 && qol < p->end - p->beg && qol < q->end - q->beg)) compatible = 1;
			if (!compatible) {
				if (q->G2 < p->G) q->G2 = p->G;
				all_compatible = 0;
			}
		}
		if (!all_compatible) p->G = 0;
	}
	n = i;
	for (i = j = 0; i < n; ++i) {
		if (b->hits[i].G == 0) continue;
		if (i != j) b->hits[j++] = b->hits[i];
		else ++j;
	}
	b->n = j;
	return j;
}
/* --- END: processing partial hits --- */

/* --- BEGIN: global mem pool --- */
bsw2global_t *bsw2_global_init()
{
	bsw2global_t *pool;
	bsw2stack_t *stack;
	pool = calloc(1, sizeof(bsw2global_t));
	stack = calloc(1, sizeof(bsw2stack_t));
	stack->pool = (mempool_t*)calloc(1, sizeof(mempool_t));
	pool->stack = (void*)stack;
	return pool;
}

void bsw2_global_destroy(bsw2global_t *pool)
{
	stack_destroy((bsw2stack_t*)pool->stack);
	free(pool->aln_mem);
	free(pool);
}
/* --- END: global mem pool --- */

static inline int fill_cell(const bsw2opt_t *o, int match_score, bsw2cell_t *c[4])
{
	int G = c[3]? c[3]->G + match_score : MINUS_INF;
	if (c[1]) {
		c[0]->I = c[1]->I > c[1]->G - o->q? c[1]->I - o->r : c[1]->G - o->qr;
		if (c[0]->I > G) G = c[0]->I;
	} else c[0]->I = MINUS_INF;
	if (c[2]) {
		c[0]->D = c[2]->D > c[2]->G - o->q? c[2]->D - o->r : c[2]->G - o->qr;
		if (c[0]->D > G) G = c[0]->D;
	} else c[0]->D = MINUS_INF;
	return(c[0]->G = G);
}

static void init_bwtsw2(const bwtl_t *target, const bwt_t *query, bsw2stack_t *s)
{
	bsw2entry_t *u;
	bsw2cell_t *x;

	u = mp_alloc(s->pool);
	u->tk = 0; u->tl = target->seq_len;
	x = push_array_p(u);
	*x = g_default_cell;
	x->G = 0; x->qk = 0; x->ql = query->seq_len;
	u->n++;
	stack_push0(s, u);
}
/* On return, ret[1] keeps not-so-repetitive hits (narrow SA hits); ret[0] keeps all hits (right?) */
bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool)
{
	bsw2stack_t *stack = (bsw2stack_t*)pool->stack;
	bwtsw2_t *b, *b1, **b_ret;
	int i, j, score_mat[16], *heap, heap_size, n_tot = 0;
	struct rusage curr, last;
	khash_t(qintv) *rhash;
	khash_t(64) *chash;

	// initialize connectivity hash (chash)
	chash = bsw2_connectivity(target);
	// calculate score matrix
	for (i = 0; i != 4; ++i)
		for (j = 0; j != 4; ++j)
			score_mat[i<<2|j] = (i == j)? opt->a : -opt->b;
	// initialize other variables
	rhash = kh_init(qintv);
	init_bwtsw2(target, query, stack);
	heap_size = opt->z;
	heap = calloc(heap_size, sizeof(int));
	// initialize the return struct
	b = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
	b->n = b->max = target->seq_len * 2;
	b->hits = calloc(b->max, sizeof(bsw2hit_t));
	b1 = (bwtsw2_t*)calloc(1, sizeof(bwtsw2_t));
	b_ret = calloc(2, sizeof(void*));
	b_ret[0] = b; b_ret[1] = b1;
	// initialize timer
	getrusage(0, &last);
	// the main loop: traversal of the DAG
	while (!stack_isempty(stack)) {
		int old_n, tj;
		bsw2entry_t *v;
		uint32_t tcntk[4], tcntl[4];
		bwtint_t k, l;

		v = stack_pop(stack); old_n = v->n;
		n_tot += v->n;

		for (i = 0; i < v->n; ++i) { // test max depth and band width
			bsw2cell_t *p = v->array + i;
			if (p->ql == 0) continue;
			if (p->tlen - (int)p->qlen > opt->bw || (int)p->qlen - p->tlen > opt->bw) {
				p->qk = p->ql = 0;
				if (p->ppos >= 0) v->array[p->ppos].cpos[p->pj] = -5;
			}
		}

		// get Occ for the DAG
		bwtl_2occ4(target, v->tk - 1, v->tl, tcntk, tcntl);
		for (tj = 0; tj != 4; ++tj) { // descend to the children
			bwtint_t qcntk[4], qcntl[4];
			int qj, *curr_score_mat = score_mat + tj * 4;
			khiter_t iter;
			bsw2entry_t *u;

			k = target->L2[tj] + tcntk[tj] + 1;
			l = target->L2[tj] + tcntl[tj];
			if (k > l) continue;
			// update counter
			iter = kh_get(64, chash, (uint64_t)k<<32 | l);
			--kh_value(chash, iter);
			// initialization
			u = mp_alloc(stack->pool);
			u->tk = k; u->tl = l;
			memset(heap, 0, sizeof(int) * opt->z);
			// loop through all the nodes in v
		    for (i = 0; i < v->n; ++i) {
				bsw2cell_t *p = v->array + i, *x, *c[4]; // c[0]=>current, c[1]=>I, c[2]=>D, c[3]=>G
				int is_added = 0;
				if (p->ql == 0) continue; // deleted node
				c[0] = x = push_array_p(u);
				x->G = MINUS_INF;
				p->upos = x->upos = -1;
				if (p->ppos >= 0) { // parent has been visited
					c[1] = (v->array[p->ppos].upos >= 0)? u->array + v->array[p->ppos].upos : 0;
					c[3] = v->array + p->ppos; c[2] = p;
					if (fill_cell(opt, curr_score_mat[p->pj], c) > 0) { // then update topology at p and x
						x->ppos = v->array[p->ppos].upos; // the parent pos in u
						p->upos = u->n++; // the current pos in u
						if (x->ppos >= 0) u->array[x->ppos].cpos[p->pj] = p->upos; // the child pos of its parent in u
						is_added = 1;
					}
				} else {
					x->D = p->D > p->G - opt->q? p->D - opt->r : p->G - opt->qr;
					if (x->D > 0) {
						x->G = x->D;
						x->I = MINUS_INF; x->ppos = -1;
						p->upos = u->n++;
						is_added = 1;
					}
				}
				if (is_added) { // x has been added to u->array. fill the remaining variables
					x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
					x->pj = p->pj; x->qk = p->qk; x->ql = p->ql; x->qlen = p->qlen; x->tlen = p->tlen + 1;
					if (x->G > -heap[0]) {
						heap[0] = -x->G;
						ks_heapadjust(int, 0, heap_size, heap);
					}
				}
				if ((x->G > opt->qr && x->G >= -heap[0]) || i < old_n) { // good node in u, or in v
					if (p->cpos[0] == -1 || p->cpos[1] == -1 || p->cpos[2] == -1 || p->cpos[3] == -1) {
						bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl);
						for (qj = 0; qj != 4; ++qj) { // descend to the prefix trie
							if (p->cpos[qj] != -1) continue; // this node will be visited later
							k = query->L2[qj] + qcntk[qj] + 1;
							l = query->L2[qj] + qcntl[qj];
							if (k > l) { p->cpos[qj] = -2; continue; }
							x = push_array_p(v);
							p = v->array + i; // p may not point to the correct position after realloc
							x->G = x->I = x->D = MINUS_INF;
							x->qk = k; x->ql = l; x->pj = qj; x->qlen = p->qlen + 1; x->ppos = i; x->tlen = p->tlen;
							x->cpos[0] = x->cpos[1] = x->cpos[2] = x->cpos[3] = -1;
							p->cpos[qj] = v->n++;
						} // ~for(qj)
					} // ~if(p->cpos[])
				} // ~if
			} // ~for(i)
			if (u->n) save_hits(target, opt->t, b->hits, u);
			{ // push u to the stack (or to the pending array)
				uint32_t cnt, pos;
				cnt = (uint32_t)kh_value(chash, iter);
				pos = kh_value(chash, iter)>>32;
				if (pos) { // something in the pending array, then merge
					bsw2entry_t *w = kv_A(stack->pending, pos-1);
					if (u->n) {
						if (w->n < u->n) { // swap
							w = u; u = kv_A(stack->pending, pos-1); kv_A(stack->pending, pos-1) = w;
						}
						merge_entry(opt, w, u, b);
					}
					if (cnt == 0) { // move from pending to stack0
						remove_duplicate(w, rhash);
						save_narrow_hits(target, w, b1, opt->t, opt->is);
						cut_tail(w, opt->z, u);
						stack_push0(stack, w);
						kv_A(stack->pending, pos-1) = 0;
						--stack->n_pending;
					}
					mp_free(stack->pool, u);
				} else if (cnt) { // the first time
					if (u->n) { // push to the pending queue
						++stack->n_pending;
						kv_push(bsw2entry_p, stack->pending, u);
						kh_value(chash, iter) = (uint64_t)kv_size(stack->pending)<<32 | cnt;
					} else mp_free(stack->pool, u);
				} else { // cnt == 0, then push to the stack
					bsw2entry_t *w = mp_alloc(stack->pool);
					save_narrow_hits(target, u, b1, opt->t, opt->is);
					cut_tail(u, opt->z, w);
					mp_free(stack->pool, w);
					stack_push0(stack, u);
				}
			}
		} // ~for(tj)
		mp_free(stack->pool, v);
	} // while(top)
	getrusage(0, &curr);
	for (i = 0; i < 2; ++i)
		for (j = 0; j < b_ret[i]->n; ++j)
			b_ret[i]->hits[j].n_seeds = 0;
	bsw2_resolve_duphits(bns, query, b, opt->is);
	bsw2_resolve_duphits(bns, query, b1, opt->is);
	//fprintf(stderr, "stats: %.3lf sec; %d elems\n", time_elapse(&curr, &last), n_tot);
	// free
	free(heap);
	kh_destroy(qintv, rhash);
	kh_destroy(64, chash);
	stack->pending.n = stack->stack0.n = 0;
	return b_ret;
}
bwa-0.7.3a/bwtsw2_main.c000644 000767 000024 00000007325 12120745361 014676 0ustar00lh3staff000000 000000 #include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <math.h>
#include "bwt.h"
#include "bwtsw2.h"
#include "utils.h"
#include "bwa.h"

int bwa_bwtsw2(int argc, char *argv[])
{
	bsw2opt_t *opt;
	bwaidx_t *idx;
	int c;

	opt = bsw2_init_opt();
	srand48(11);
	while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:MI:SG:C")) >= 0) {
		switch (c) {
		case 'q': opt->q = atoi(optarg); break;
		case 'r': opt->r = atoi(optarg); break;
		case 'a': opt->a = atoi(optarg); break;
		case 'b': opt->b = atoi(optarg); break;
		case 'w': opt->bw = atoi(optarg); break;
		case 'T': opt->t = atoi(optarg); break;
		case 't': opt->n_threads = atoi(optarg); break;
		case 'z': opt->z = atoi(optarg); break;
		case 's': opt->is = atoi(optarg); break;
		case 'm': opt->mask_level = atof(optarg); break;
		case 'c': opt->coef = atof(optarg); break;
		case 'N': opt->t_seeds = atoi(optarg); break;
		case 'M': opt->multi_2nd = 1; break;
		case 'H': opt->hard_clip = 1; break;
		case 'f': xreopen(optarg, "w", stdout); break;
		case 'I': opt->max_ins = atoi(optarg); break;
		case 'S': opt->skip_sw = 1; break;
		case 'C': opt->cpy_cmt = 1; break;
		case 'G': opt->max_chain_gap = atoi(optarg); break;
		}
	}
	opt->qr = opt->q + opt->r;

	if (optind + 2 > argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   bwa bwasw [options] <target.prefix> <query.fa> [query2.fa]\n\n");
		fprintf(stderr, "Options: -a INT   score for a match [%d]\n", opt->a);
		fprintf(stderr, "         -b INT   mismatch penalty [%d]\n", opt->b);
		fprintf(stderr, "         -q INT   gap open penalty [%d]\n", opt->q);
		fprintf(stderr, "         -r INT   gap extension penalty [%d]\n", opt->r);
		fprintf(stderr, "         -w INT   band width [%d]\n", opt->bw);
		fprintf(stderr, "         -m FLOAT mask level [%.2f]\n", opt->mask_level);
		fprintf(stderr, "\n");
		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
		fprintf(stderr, "         -f FILE  file to output results to instead of stdout\n");
		fprintf(stderr, "         -H       in SAM output, use hard clipping instead of soft clipping\n");
		fprintf(stderr, "         -C       copy FASTA/Q comment to SAM output\n");
		fprintf(stderr, "         -M       mark multi-part alignments as secondary\n");
		fprintf(stderr, "         -S       skip Smith-Waterman read pairing\n");
		fprintf(stderr, "         -I INT   ignore pairs with insert >=INT for inferring the size distr [%d]\n", opt->max_ins);
		fprintf(stderr, "\n");
		fprintf(stderr, "         -T INT   score threshold divided by a [%d]\n", opt->t);
		fprintf(stderr, "         -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
		fprintf(stderr, "         -z INT   Z-best [%d]\n", opt->z);
		fprintf(stderr, "         -s INT   maximum seeding interval size [%d]\n", opt->is);
		fprintf(stderr, "         -N INT   # seeds to trigger rev aln; 2*INT is also the chaining threshold [%d]\n", opt->t_seeds);
		fprintf(stderr, "         -G INT   maximum gap size during chaining [%d]\n", opt->max_chain_gap);
		fprintf(stderr, "\n");
		fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
		fprintf(stderr, "      BACs, the default setting usually works well. For the current PacBio\n");
		fprintf(stderr, "      reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");
		fprintf(stderr, "      increase '-z' for better sensitivity.\n");
		fprintf(stderr, "\n");

		return 1;
	}

	// adjust opt for opt->a
	opt->t *= opt->a;
	opt->coef *= opt->a;

	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 0;
	bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
	bwa_idx_destroy(idx);
	free(opt);
	
	return 0;
}
bwa-0.7.3a/bwtsw2_pair.c000644 000767 000024 00000023514 12120745361 014703 0ustar00lh3staff000000 000000 #include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "bwt.h"
#include "bntseq.h"
#include "bwtsw2.h"
#include "kstring.h"
#include "utils.h"
#include "ksw.h"

#define MIN_RATIO     0.8
#define OUTLIER_BOUND 2.0
#define MAX_STDDEV    4.0
#define EXT_STDDEV    4.0

typedef struct {
	int low, high, failed;
	double avg, std;
} bsw2pestat_t;

bsw2pestat_t bsw2_stat(int n, bwtsw2_t **buf, kstring_t *msg, int max_ins)
{
	int i, k, x, p25, p50, p75, tmp, max_len = 0;
	uint64_t *isize;
	bsw2pestat_t r;

	memset(&r, 0, sizeof(bsw2pestat_t));
	isize = calloc(n, 8);
	for (i = k = 0; i < n; i += 2) {
		bsw2hit_t *t[2];
		int l;
		if (buf[i] == 0 || buf[i]->n != 1 || buf[i+1]->n != 1) continue; // more than 1 hits
		t[0] = &buf[i]->hits[0]; t[1] = &buf[i+1]->hits[0];
		if (t[0]->G2 > 0.8 * t[0]->G) continue; // the best hit is not good enough
		if (t[1]->G2 > 0.8 * t[1]->G) continue; // the best hit is not good enough
		l = t[0]->k > t[1]->k? t[0]->k - t[1]->k + t[1]->len : t[1]->k - t[0]->k + t[0]->len;
		if (l >= max_ins) continue; // skip pairs with excessively large insert
		max_len = max_len > t[0]->end - t[0]->beg? max_len : t[0]->end - t[0]->beg;
		max_len = max_len > t[1]->end - t[1]->beg? max_len : t[1]->end - t[1]->beg;
		isize[k++] = l;
	}
	ks_introsort_64(k, isize);
	p25 = isize[(int)(.25 * k + .499)];
	p50 = isize[(int)(.50 * k + .499)];
	p75 = isize[(int)(.75 * k + .499)];
	ksprintf(msg, "[%s] infer the insert size distribution from %d high-quality pairs.\n", __func__, k);
	if (k < 8) {
		ksprintf(msg, "[%s] fail to infer the insert size distribution.\n", __func__);
		free(isize);
		r.failed = 1;
		return r;
	}
	tmp    = (int)(p25 - OUTLIER_BOUND * (p75 - p25) + .499);
	r.low  = tmp > max_len? tmp : max_len;
	if (r.low < 1) r.low = 1;
	r.high = (int)(p75 + OUTLIER_BOUND * (p75 - p25) + .499);
	ksprintf(msg, "[%s] (25, 50, 75) percentile: (%d, %d, %d)\n", __func__, p25, p50, p75);
	ksprintf(msg, "[%s] low and high boundaries for computing mean and std.dev: (%d, %d)\n", __func__, r.low, r.high);
	for (i = x = 0, r.avg = 0; i < k; ++i)
		if (isize[i] >= r.low && isize[i] <= r.high)
			r.avg += isize[i], ++x;
	r.avg /= x;
	for (i = 0, r.std = 0; i < k; ++i)
		if (isize[i] >= r.low && isize[i] <= r.high)
			r.std += (isize[i] - r.avg) * (isize[i] - r.avg);
	r.std = sqrt(r.std / x);
	ksprintf(msg, "[%s] mean and std.dev: (%.2f, %.2f)\n", __func__, r.avg, r.std);
	tmp  = (int)(p25 - 3. * (p75 - p25) + .499);
	r.low  = tmp > max_len? tmp : max_len;
	if (r.low < 1) r.low = 1;
	r.high = (int)(p75 + 3. * (p75 - p25) + .499);
	if (r.low > r.avg - MAX_STDDEV * r.std) r.low = (int)(r.avg - MAX_STDDEV * r.std + .499);
	r.low = tmp > max_len? tmp : max_len;
	if (r.high < r.avg - MAX_STDDEV * r.std) r.high = (int)(r.avg + MAX_STDDEV * r.std + .499);
	ksprintf(msg, "[%s] low and high boundaries for proper pairs: (%d, %d)\n", __func__, r.low, r.high);
	free(isize);
	return r;
}

typedef struct {
	int n_cigar, beg, end, len;
	int64_t pos;
	uint32_t *cigar;
} pairaux_t;

extern unsigned char nst_nt4_table[256];

void bsw2_pair1(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, const bsw2pestat_t *st, const bsw2hit_t *h, int l_mseq, const char *mseq, bsw2hit_t *a, int8_t g_mat[25])
{
	extern void seq_reverse(int len, ubyte_t *seq, int is_comp);
	int64_t k, beg, end;
	uint8_t *seq, *ref;
	int i;
	// compute the region start and end
	a->n_seeds = 1; a->flag |= BSW2_FLAG_MATESW; // before calling this routine, *a has been cleared with memset(0); the flag is set with 1<<6/7
	if (h->is_rev == 0) {
		beg = (int64_t)(h->k + st->avg - EXT_STDDEV * st->std - l_mseq + .499);
		if (beg < h->k) beg = h->k;
		end = (int64_t)(h->k + st->avg + EXT_STDDEV * st->std + .499);
		a->is_rev = 1; a->flag |= 16;
	} else {
		beg = (int64_t)(h->k + h->end - h->beg - st->avg - EXT_STDDEV * st->std + .499);
		end = (int64_t)(h->k + h->end - h->beg - st->avg + EXT_STDDEV * st->std + l_mseq + .499);
		if (end > h->k + (h->end - h->beg)) end = h->k + (h->end - h->beg);
		a->is_rev = 0;
	}
	if (beg < 1) beg = 1;
	if (end > l_pac) end = l_pac;
	if (end - beg < l_mseq) return;
	// generate the sequence
	seq = malloc(l_mseq + (end - beg));
	ref = seq + l_mseq;
	for (k = beg; k < end; ++k)
		ref[k - beg] = pac[k>>2] >> ((~k&3)<<1) & 0x3;
	if (h->is_rev == 0) {
		for (i = 0; i < l_mseq; ++i) { // on the reverse strand
			int c = nst_nt4_table[(int)mseq[i]];
			seq[l_mseq - 1 - i] = c > 3? 4 : 3 - c;
		}
	} else {
		for (i = 0; i < l_mseq; ++i) // on the forward strand
			seq[i] = nst_nt4_table[(int)mseq[i]];
	}
	{
		int flag = KSW_XSUBO | KSW_XSTART | (l_mseq * g_mat[0] < 250? KSW_XBYTE : 0) | opt->t;
		kswr_t aln;
		aln = ksw_align(l_mseq, seq, end - beg, ref, 5, g_mat, opt->q, opt->r, flag, 0);
		a->G = aln.score;
		a->G2 = aln.score2;
		if (a->G < opt->t) a->G = 0;
		if (a->G2 < opt->t) a->G2 = 0;
		if (a->G2) a->flag |= BSW2_FLAG_TANDEM;
		a->k = beg + aln.tb;
		a->len = aln.te - aln.tb + 1;
		a->beg = aln.qb;
		a->end = aln.qe + 1;
		/*
		printf("[Q] "); for (i = 0; i < l_mseq; ++i) putchar("ACGTN"[(int)seq[i]]); putchar('\n');
		printf("[R] "); for (i = 0; i < end - beg; ++i) putchar("ACGTN"[(int)ref[i]]); putchar('\n');
		printf("G=%d,G2=%d,beg=%d,end=%d,k=%lld,len=%d\n", a->G, a->G2, a->beg, a->end, a->k, a->len);
		*/
	}
	if (a->is_rev) i = a->beg, a->beg = l_mseq - a->end, a->end = l_mseq - i;
	free(seq);
}

void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hits)
{
	extern int bsw2_resolve_duphits(const bntseq_t *bns, const bwt_t *bwt, bwtsw2_t *b, int IS);
	bsw2pestat_t pes;
	int i, j, k, n_rescued = 0, n_moved = 0, n_fixed = 0;
	int8_t g_mat[25];
	kstring_t msg;
	memset(&msg, 0, sizeof(kstring_t));
	pes = bsw2_stat(n, hits, &msg, opt->max_ins);
	for (i = k = 0; i < 5; ++i) {
		for (j = 0; j < 4; ++j)
			g_mat[k++] = i == j? opt->a : -opt->b;
		g_mat[k++] = 0;
	}
	for (i = 0; i < n; i += 2) {
		bsw2hit_t a[2];
		memset(&a, 0, sizeof(bsw2hit_t) * 2);
		a[0].flag = 1<<6; a[1].flag = 1<<7;
		for (j = 0; j < 2; ++j) { // set the read1/2 flag
			if (hits[i+j] == 0) continue;
			for (k = 0; k < hits[i+j]->n; ++k) {
				bsw2hit_t *p = &hits[i+j]->hits[k];
				p->flag |= 1<<(6+j);
			}
		}
		if (pes.failed) continue;
		if (hits[i] == 0 || hits[i+1] == 0) continue; // one end has excessive N
		if (hits[i]->n != 1 && hits[i+1]->n != 1) continue; // no end has exactly one hit
		if (hits[i]->n > 1 || hits[i+1]->n > 1) continue; // one read has more than one hit
		if (!opt->skip_sw) {
			if (hits[i+0]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+0]->hits[0], seq[i+1].l, seq[i+1].seq, &a[1], g_mat);
			if (hits[i+1]->n == 1) bsw2_pair1(opt, l_pac, pac, &pes, &hits[i+1]->hits[0], seq[i+0].l, seq[i+0].seq, &a[0], g_mat);
		} // else a[0].G == a[1].G == a[0].G2 == a[1].G2 == 0
		// the following enumerate all possibilities. It is tedious but necessary...
		if (hits[i]->n + hits[i+1]->n == 1) { // one end mapped; the other not;
			bwtsw2_t *p[2];
			int which;
			if (hits[i]->n == 1) p[0] = hits[i], p[1] = hits[i+1], which = 1;
			else p[0] = hits[i+1], p[1] = hits[i], which = 0;
			if (a[which].G == 0) continue;
			a[which].flag |= BSW2_FLAG_RESCUED;
			if (p[1]->max == 0) {
				p[1]->max = 1;
				p[1]->hits = malloc(sizeof(bsw2hit_t));
			}
			p[1]->hits[0] = a[which];
			p[1]->n = 1;
			p[0]->hits[0].flag |= 2;
			p[1]->hits[0].flag |= 2;
			++n_rescued;
		} else { // then both ends mapped
			int is_fixed = 0;
			//fprintf(stderr, "%d; %lld,%lld; %d,%d\n", a[0].is_rev, hits[i]->hits[0].k, a[0].k, hits[i]->hits[0].end, a[0].end);
			for (j = 0; j < 2; ++j) { // fix wrong mappings and wrong suboptimal alignment score
				bsw2hit_t *p = &hits[i+j]->hits[0];
				if (p->G < a[j].G) { // the orginal mapping is suboptimal
					a[j].G2 = a[j].G2 > p->G? a[j].G2 : p->G; // FIXME: reset BSW2_FLAG_TANDEM?
					*p = a[j];
					++n_fixed;
					is_fixed = 1;
				} else if (p->k != a[j].k && p->G2 < a[j].G) {
					p->G2 = a[j].G;
				} else if (p->k == a[j].k && p->G2 < a[j].G2) {
					p->G2 = a[j].G2;
				}
			}
			if (hits[i]->hits[0].k == a[0].k && hits[i+1]->hits[0].k == a[1].k) { // properly paired and no ends need to be moved
				for (j = 0; j < 2; ++j)
					hits[i+j]->hits[0].flag |= 2 | (a[j].flag & BSW2_FLAG_TANDEM);
			} else if (hits[i]->hits[0].k == a[0].k || hits[i+1]->hits[0].k == a[1].k) { // a tandem match
				for (j = 0; j < 2; ++j) {
					hits[i+j]->hits[0].flag |= 2;
					if (hits[i+j]->hits[0].k != a[j].k)
						hits[i+j]->hits[0].flag |= BSW2_FLAG_TANDEM;
				}
			} else if (!is_fixed && (a[0].G || a[1].G)) { // it is possible to move one end
				if (a[0].G && a[1].G) { // now we have two "proper pairs"
					int G[2];
					double diff;
					G[0] = hits[i]->hits[0].G + a[1].G;
					G[1] = hits[i+1]->hits[0].G + a[0].G;
					diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.);
					if (diff > 0.05) a[G[0] > G[1]? 0 : 1].G = 0;
				}
				if (a[0].G == 0 || a[1].G == 0) { // one proper pair only
					bsw2hit_t *p[2]; // p[0] points the unchanged hit; p[1] to the hit to be moved
					int which, isize;
					double dev, diff;
					if (a[0].G) p[0] = &hits[i+1]->hits[0], p[1] = &hits[i]->hits[0], which = 0;
					else p[0] = &hits[i]->hits[0], p[1] = &hits[i+1]->hits[0], which = 1;
					isize = p[0]->is_rev? p[0]->k + p[0]->len - a[which].k : a[which].k + a[which].len - p[0]->k;
					dev = fabs(isize - pes.avg) / pes.std;
					diff = (double)(p[1]->G - a[which].G) / (opt->a + opt->b) / (p[1]->end - p[1]->beg) * 100.0;
					if (diff < dev * 2.) { // then move (heuristic)
						a[which].G2 = a[which].G;
						p[1][0] = a[which];
						p[1]->flag |= BSW2_FLAG_MOVED | 2;
						p[0]->flag |= 2;
						++n_moved;
					}
				}
			} else if (is_fixed) {
				hits[i+0]->hits[0].flag |= 2;
				hits[i+1]->hits[0].flag |= 2;
			}
		}
	}
	ksprintf(&msg, "[%s] #fixed=%d, #rescued=%d, #moved=%d\n", __func__, n_fixed, n_rescued, n_moved);
	fputs(msg.s, stderr);
	free(msg.s);
}
bwa-0.7.3a/ChangeLog000644 000767 000024 00000365331 12120745361 014054 0ustar00lh3staff000000 000000 ------------------------------------------------------------------------
r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.9rc1-2 (r1605)
 * fixed a typo/bug in bwasw

------------------------------------------------------------------------
r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

a typo in the manual

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r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/utils.c
   M /branches/prog/bwa/utils.h

 * bwa-0.5.9rc1-1 (r1586)
 * a few patches by John

------------------------------------------------------------------------
r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c

documentation on specifying @RG

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r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.5.9rc1 (r1561)

------------------------------------------------------------------------
r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/main.c

 * fixed a small memory leak caused by the BAM reader
 * fixed a memory violation, also in the BAM reader

------------------------------------------------------------------------
r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/Makefile

change Makefile gcc options

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r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.8-6 (r1557)
 * added a little more comments to BWA-SW
 * randomly choosing a mapping if there are more than one

------------------------------------------------------------------------
r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_aux.c

sometimes unmapped reads may not be printed...

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r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_aux.c

print unmapped reads

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r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.8-5 (r1555)
 * BAM input documentation

------------------------------------------------------------------------
r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.8-4 (r1544)
 * supporting adding RG tags and RG lines

------------------------------------------------------------------------
r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.8-3 (r1543)
 * fixed a memory leak

------------------------------------------------------------------------
r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.8-2 (r1542)
 * fixed a long existing bug in random placement of reads

------------------------------------------------------------------------
r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/bamlite.c
   A /branches/prog/bwa/bamlite.h
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

preliminary BAM input support

------------------------------------------------------------------------
r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1

change version number and ChangeLog

------------------------------------------------------------------------
r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c

 * fixed a bug in the scoring matrix
 * release bwa-0.5.8c (r1536)

------------------------------------------------------------------------
r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

version change

------------------------------------------------------------------------
r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c

 * bwa-0.5.8b (r1450)
 * fixed a bug in scoring matrix

------------------------------------------------------------------------
r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c

fixed a serious bug

------------------------------------------------------------------------
r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.5.8 (r1442)

------------------------------------------------------------------------
r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-r1440
 * sorry, forget to remove a debugging line

------------------------------------------------------------------------
r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-r1439
 * fixed a bug in bwasw caused by a recent modification
 * throwing insane insert size when estimating isize

------------------------------------------------------------------------
r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.7-7 (r1425)
 * fixed a minor bug in bwasw command-line parsing
 * When band-width is not large enough, bwasw may find two highly
   overlapping but not completely overlapping alignments. The old
   version will filter out one of them, which leads to false
   negatives. The current outputs both. This solution is obviously not
   ideal. The ideal one would be to increase the band-width and redo the
   alignment.


------------------------------------------------------------------------
r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.7-6 (r1399)
 * fixed a typo/bug (by Vaughn Iverson)

------------------------------------------------------------------------
r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

small correction

------------------------------------------------------------------------
r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.7-4 (r1328)
 * automatically adjust ap_prior based on alignment

------------------------------------------------------------------------
r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.5.7-3 (r1327)
 * evaluate hits obtained from SW alignment in a more proper way.

------------------------------------------------------------------------
r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwape.c

fixed a potential out-of-boundary error. Need more testing.

------------------------------------------------------------------------
r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwape.c

insert size is `weird' if the 3rd quatile larger than 100,000bp

------------------------------------------------------------------------
r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.7-2 (r1318)
 * in sampe, allow to disable insert size estimate

------------------------------------------------------------------------
r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/solid2fastq.pl

 * bwa-0.5.7-1 (r1317)
 * fixed a potential bug in solid2fastq.pl
 * fixed a bug in calculating mapping quality (by Rodrigo Goya)
 * fixed a very rare bug (if ever occur) about pairing

------------------------------------------------------------------------
r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.5.7

------------------------------------------------------------------------
r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.6-2 (r1309)
 * fixed an unfixed bug (by Carol Scott)
 * fixed some tiny formatting

------------------------------------------------------------------------
r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.6-1 (r1304)
 * optionally write output to a file (by Tim Fennel)

------------------------------------------------------------------------
r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

Release bwa-0.5.6

------------------------------------------------------------------------
r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-10 (r1302)
 * improve max insert size estimate (method suggested by Gerton Lunter)

------------------------------------------------------------------------
r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-9 (r1301)
 * improve mapping quality calculation for abnomalous pairs
 * fixed a bug in multiple hits
 * SOLiD multiple hits should work now

------------------------------------------------------------------------
r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-8 (r1300)
 * output kurtosis

------------------------------------------------------------------------
r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-7 (r1299)
 * calculate skewness in sampe
 * increase min_len in SW to 20
 * perform more SW to fix discordant pairs

------------------------------------------------------------------------
r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.5.5-6 (r1297)
 * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)

------------------------------------------------------------------------
r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines
Changed paths:
   M /branches/prog/bwa/solid2fastq.pl

the old fix seems not working!

------------------------------------------------------------------------
r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-5 (r1296)
 * fixed a minor issue that the lower bound of insert size is not correctly set.

------------------------------------------------------------------------
r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-4 (r1295)
 * fixed a memory leak
 * change the behaviour of -n (samse and sampe)
 * change the default of -n

------------------------------------------------------------------------
r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-3 (r1294)
 * improved multi-hit report

------------------------------------------------------------------------
r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/solid2fastq.pl

 * bwa-0.5.5-2 (r1293)
 * bugfix: truncated quality string
 * bugfix: quality -1 in solid->fastq conversion
 * bugfix: color reads on the reverse strand is not complemented

------------------------------------------------------------------------
r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwase.c
   A /branches/prog/bwa/bwase.h
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.5-1 (r1279)
 * incorporate changes from Matt Hanna for Java bindings.

------------------------------------------------------------------------
r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c
   A /branches/prog/bwa/qualfa2fq.pl

Release bwa-0.5.5 (r1273)

------------------------------------------------------------------------
r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.4-3 (r1272)
 * fixed another typo which may lead to incorrect single-end mapping quality

------------------------------------------------------------------------
r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.4-2 (r1271)
 * fixed a serious typo/bug which does not hurt if we allow one gap open
   and work with <200bp reads, but causes segfault for long reads.

------------------------------------------------------------------------
r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.4-1 (r1270)
 * fixed a bug in color alignment

------------------------------------------------------------------------
r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/main.c

Release bwa-0.5.4

------------------------------------------------------------------------
r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c

 * bwa-0.5.3-4 (r1244)
 * output the clipped length in XC:i: tag
 * skip mate alignment when stdaln is buggy
 * fixed a bug in NM:i: tag

------------------------------------------------------------------------
r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.3-3 (r1243)
 * sampe: fixed a bug when a read sequence is identical its reverse complement.

------------------------------------------------------------------------
r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.3-2 (r1242)
 * sampe: optionall preload the full index into memory
 * aln: change the default seed length to 32bp

------------------------------------------------------------------------
r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/khash.h

Improve portability of khash.h

------------------------------------------------------------------------
r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/main.c

fixed a typo

------------------------------------------------------------------------
r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.3-1 (r1226)
 * in dBWT-SW, optionall use hard clipping instead of soft clipping

------------------------------------------------------------------------
r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

Release bwa-0.5.3 (r1225)

------------------------------------------------------------------------
r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.5.2

------------------------------------------------------------------------
r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.1-5 (r1222)
 * fixed a typo. No real change

------------------------------------------------------------------------
r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.1-4 (r1221)
 * trim reads before alignment

------------------------------------------------------------------------
r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.5.1-3 (r1216)
 * fixed a bug about NM tags for gapped alignment
 * print SAM header

------------------------------------------------------------------------
r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.1-2 (r1215)
 * fixed a bug when read lengths vary (by John Marshall)

------------------------------------------------------------------------
r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.1-1 (r1213)
 * change default -T to 30

------------------------------------------------------------------------
r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.5.1

------------------------------------------------------------------------
r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog

 * ChangeLog

------------------------------------------------------------------------
r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.0-6 (r1206)
 * fixed two bugs caused by previous modification

------------------------------------------------------------------------
r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.0-4 (r1205)
 * reduce false coordinates and CIGAR when a query bridges two reference
   sequences, although some very rare cases may fail bwa.

------------------------------------------------------------------------
r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.0-3 (r1204)
 * choose one repetitive hit to extend

------------------------------------------------------------------------
r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.0-2 (r1203)
 * dBWT-SW: change a parameter in calculating mapping quality
 * fixed a bug in samse

------------------------------------------------------------------------
r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.5.0-1 (r1202)
 * change default band width to 50
 * improve mapping quality a bit

------------------------------------------------------------------------
r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.5.0 (r1200)

------------------------------------------------------------------------
r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1

Updated ChangeLog and the manual

------------------------------------------------------------------------
r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-36 (r1198)
 * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.

------------------------------------------------------------------------
r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_aux.c
   A /branches/prog/bwa/bwtsw2_chain.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-35 (r1197)
 * further heuristic acceleration for long queries

------------------------------------------------------------------------
r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-34 (r1196)
 * updated the manual page
 * output base quality if the input is fastq

------------------------------------------------------------------------
r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/simple_dp.c

 * bwa-0.4.9-33 (r1191)
 * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
 * in dbwtsw adjust -T and -c according to -a

------------------------------------------------------------------------
r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update manual

------------------------------------------------------------------------
r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtsw2_main.c

update documentation

------------------------------------------------------------------------
r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-32 (r1190)
 * only help messages are changed

------------------------------------------------------------------------
r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-31 (r1189)
 * in bwape/bwase, print CIGAR "*" if the read is unmapped
 * improved the calculation of mapping quality

------------------------------------------------------------------------
r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c

fflush()

------------------------------------------------------------------------
r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-30 (r1180)
 * fixed a memory problem
 * multi-threading sometimes does not work...

------------------------------------------------------------------------
r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-29 (r1179)
 * preliminary mutli-threading support in dbwtsw

------------------------------------------------------------------------
r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-28 (r1178)
 * fixed a bug in printing repetitive hits

------------------------------------------------------------------------
r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-27 (r1177)
 * bwtsw2: fixed a hidden memory leak

------------------------------------------------------------------------
r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-26
 * change the way mapping quality is calculated

------------------------------------------------------------------------
r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-25
 * code clean up
 * automatically adjust ->t and ->is_rev based on input

------------------------------------------------------------------------
r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-24
 * fixed a bug in printing the hits

------------------------------------------------------------------------
r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-23
 * allow to skip reverse alignment
 * increase opt->t to 37

------------------------------------------------------------------------
r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-22
 * report if the hit is found in both directions

------------------------------------------------------------------------
r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-21
 * dbwtsw: map to both forward and reverse BWT to reduce false alignment

------------------------------------------------------------------------
r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

save hits before cut_tail()

------------------------------------------------------------------------
r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.9-19
 * use a global memory pool to reduce the CPU time spent on malloc/free().

------------------------------------------------------------------------
r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-18
 * reduce unnecessary extension to the 5'-end
 * allow to use different interval size for the 2 rounds
 * change default parameters

------------------------------------------------------------------------
r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-17
 * dbwtsw: fixed THE memory leak.

------------------------------------------------------------------------
r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c

 * bwa-0.4.9-16
 * fixed a memory leak
 * a small memory leak still occurs to bwtsw2_core(). I will work on that later.
 * changed the default parameters

------------------------------------------------------------------------
r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c

 * bwa-0.4.9-15
 * generate CIGAR right before output. This saves unnecessary computation.
 * this version may be buggy as I have not tested it.

------------------------------------------------------------------------
r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.9-14

 * deplete unique hits in dbwtsw and postprocess them with standard sw

 * in principle, this stratgy should be faster and more accurate, but I
   have not tested this point. I may switch back to the old method if
   this does not work.

 * the code looks quite nasty now. it needs clean up...


------------------------------------------------------------------------
r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c

change a default parameter

------------------------------------------------------------------------
r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-13
 * dbwtsw: switch between small and large Z-best

------------------------------------------------------------------------
r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-12
 * changed the default -z to 100
 * heuristically speed up alignments for polyA reads

------------------------------------------------------------------------
r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-11

 * dbwtsw potentially generates less false alignments, although in
   practice, the modification brings no improvement.


------------------------------------------------------------------------
r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-10
 * disabled debugging code
 * add "BAM_FMU" if both ends are unmapped

------------------------------------------------------------------------
r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/main.c

nothing, really

------------------------------------------------------------------------
r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-9
 * bwtsw2: generate SAM output

------------------------------------------------------------------------
r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-8

 * fixed a weird deadloop which only happens to icc -O3. Thanks John
   Marshall for the fix.


------------------------------------------------------------------------
r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-7

 * fixed a typo in bwtsw2 alignment. Now score from the standard SW
   seems to agree with score from bwtsw2, except that in reporting
   alignments, bwtsw2 may report non-optimal segments. This is expected,
   though. I will improve in future.


------------------------------------------------------------------------
r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * aln_left_core() seems to work properly
 * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!

------------------------------------------------------------------------
r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/stdaln.c

removed debugging code...

------------------------------------------------------------------------
r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/stdaln.c

 * radical changes failed...
 * fixed a bug

------------------------------------------------------------------------
r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/stdaln.c

temporary changes. Will apply some radical changes to this file...

------------------------------------------------------------------------
r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/stdaln.c

fixed a long-existing bug in Smith-Waterman alignment

------------------------------------------------------------------------
r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.9-6
 * unexplained inconsistency still occurs, but the results largely look reasonable.

------------------------------------------------------------------------
r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/stdaln.c

half DP

------------------------------------------------------------------------
r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c

a bit code clean up

------------------------------------------------------------------------
r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-5
 * fixed a bug in determining sub-optimal hits
 * removed some debugging codes

------------------------------------------------------------------------
r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-4
 * better cmd interface
 * faster speed

------------------------------------------------------------------------
r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

bwtsw2 (dBWT-SW) is working apparently...


------------------------------------------------------------------------
r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.9-2
 * bwtsw2: change cut_tail() such that it is faster but more likely to
   miss true hits

------------------------------------------------------------------------
r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/bwt_lite.c
   A /branches/prog/bwa/bwt_lite.h
   A /branches/prog/bwa/bwtsw2.h
   A /branches/prog/bwa/bwtsw2_aux.c
   A /branches/prog/bwa/bwtsw2_core.c
   A /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * bwa-0.4.9-1
 * added back bwtsw2

------------------------------------------------------------------------
r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

Release bwa-0.4.9

------------------------------------------------------------------------
r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.4.8

------------------------------------------------------------------------
r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.7-2
 * change the default of "aln -R" to 30

------------------------------------------------------------------------
r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.7-1
 * search for suboptimal hits if the top hit is not so repetitive

------------------------------------------------------------------------
r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

Release bwa-0.4.7

------------------------------------------------------------------------
r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.6-9
 * fixed compiling errors on some Linux machines

------------------------------------------------------------------------
r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.6-8
 * avoid compilation error on some systems.

------------------------------------------------------------------------
r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.6-7
 * fixed an integer overflow caused by previous modifications
 * made insert size estimation more robust

------------------------------------------------------------------------
r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.6-5
 * fixed a integer overflow problem which may cause seg fault in very rare cases
 * made XN tags more accurate

------------------------------------------------------------------------
r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.6-4
 * heuristic rules to detect suboptimal alignment
 * stdsw: support double-strand and protein alignment

------------------------------------------------------------------------
r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.6-2
 * improve the functionality of stdsw
 * allow to add a threshold on SW alignment. Hope this does not incur new bugs...

------------------------------------------------------------------------
r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.6-1
 * output SM and AM tag

------------------------------------------------------------------------
r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.4.6

------------------------------------------------------------------------
r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   A /branches/prog/bwa/solid2fastq.pl

 * added notes to bwa
 * added a script to convert SOLiD reads
 * updated documentations

------------------------------------------------------------------------
r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/kstring.c
   M /branches/prog/bwa/main.c

fixed a bug in kstring

------------------------------------------------------------------------
r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtmisc.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.5-7
 * fixed a bug in pac2cspac

------------------------------------------------------------------------
r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile

disable debugging

------------------------------------------------------------------------
r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.5-6
 * fixed problems with coordinates for color gapped alignment

------------------------------------------------------------------------
r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.5-5
 * added support for gapped color alignment

------------------------------------------------------------------------
r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/cs2nt.c
   M /branches/prog/bwa/main.c

 * convert cs read to nt read (for ungapped alignment only)

------------------------------------------------------------------------
r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwase.c
   A /branches/prog/bwa/cs2nt.c

prepare to implement cs->nt conversion (have not yet...)

------------------------------------------------------------------------
r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/bwtmisc.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * bwa-0.4.5-3
 * generate color index from nucleotide fasta reference

------------------------------------------------------------------------
r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.5-2
 * improved mapping quality a bit if one end falls in a tandem repeat
   but the mate is unique.

------------------------------------------------------------------------
r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.5-1
 * make bwa work for SOLiD reads

------------------------------------------------------------------------
r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.4.5

------------------------------------------------------------------------
r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.4.4-6
 * fixed a bug in SW alignment when no residue matches

------------------------------------------------------------------------
r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.4-5
 * fixed that bounary bug

------------------------------------------------------------------------
r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwape.c

just change some logging information

------------------------------------------------------------------------
r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update manual

------------------------------------------------------------------------
r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.4-4
 * fixed a bug on boundary check in pair_sw

------------------------------------------------------------------------
r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.4-3
 * allow to change mismatch penalty

------------------------------------------------------------------------
r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.4-2
 * remove timer
 * allow to change default gapo and gape penalty at the command line

------------------------------------------------------------------------
r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update benchmark

------------------------------------------------------------------------
r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/kvec.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.4-1
 * automatically detect insert size
 * use insert size in pairing. This may potentially improve accuracy (untested!)

------------------------------------------------------------------------
r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.4.4

------------------------------------------------------------------------
r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.3-5
 * impose boundary check in refine_gapped

------------------------------------------------------------------------
r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.3-4
 * change MD tag to match the latest SAM specification

------------------------------------------------------------------------
r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

change MD tag to meet the latest SAM specification

------------------------------------------------------------------------
r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.3-2
 * fixed a bug on counting 'N'

------------------------------------------------------------------------
r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.3-1
 * fixed potential boundary problems
 * update benchmark result

------------------------------------------------------------------------
r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update some numbers

------------------------------------------------------------------------
r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update benchmark

------------------------------------------------------------------------
r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtindex.c

a warning message for index

------------------------------------------------------------------------
r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/main.c

forget to change release number

------------------------------------------------------------------------
r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS

Release bwa-0.4.3

------------------------------------------------------------------------
r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS

Release bwa-0.4.3

------------------------------------------------------------------------
r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-10
 * update documentation
 * fixed a bug on generating MD tags for SW alignment

------------------------------------------------------------------------
r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-9
 * fixed a bug in samse -n...

------------------------------------------------------------------------
r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-8
 * given -N, the previous version would stop if the top hit is a repeat. Now changed.

------------------------------------------------------------------------
r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-7
 * use a bit-wise flag to replace some member variables in the option struct
 * allow to switch off the iterative strategy

------------------------------------------------------------------------
r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-6
 * allow to dump multiple hits from samse, in another format, though

------------------------------------------------------------------------
r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/kseq.h
   A /branches/prog/bwa/kstring.c
   A /branches/prog/bwa/kstring.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/simple_dp.c

 * bwa-0.4.2-5
 * update kseq.h to the latest version
 * generate MD tag
 * print mate coordinate if only one end is unmapped

------------------------------------------------------------------------
r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-4
 * fixed a bug for SAM format

------------------------------------------------------------------------
r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-3
 * change default fnr to 0.04
 * print max_diff for valid fnr

------------------------------------------------------------------------
r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-2
 * automatically choose max_diff

------------------------------------------------------------------------
r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.4.2-1
 * take N as a mismatch

------------------------------------------------------------------------
r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/main.c

Release bwa-0.4.2

------------------------------------------------------------------------
r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

Release bwa-0.4.1

------------------------------------------------------------------------
r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.0-2
 * make mate_sw fully working

------------------------------------------------------------------------
r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.4.0-1
 * do SW alignment for unmapped mate. It is working.
 * I still need to do some extra work for SW alignment, but it is too late
   and I am getting tired... I will do tomorrow.

------------------------------------------------------------------------
r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.4.0

------------------------------------------------------------------------
r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-12
 * better lock

------------------------------------------------------------------------
r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-11
 * fixed a small memory leak in bwa_seq_close()
 * fixed "uninitialized memory" from bwt_aln1_t
 * multithreading for "aln" command

------------------------------------------------------------------------
r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   D /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwt_gen/bwt_gen.c
   A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748)
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   D /branches/prog/bwa/pac2bwt.c

 * bwa-0.3.0-10
 * a little bit code clean up

------------------------------------------------------------------------
r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-9
 * use 64-bit integer to speed up Occ calculate, although just a little bit

------------------------------------------------------------------------
r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-8
 * a little bit code cleanup

------------------------------------------------------------------------
r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-7
 * accelerate Occ calculation

------------------------------------------------------------------------
r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/pac2bwt.c

 * bwa-0.3.0-6
 * put occ table along with bwt to save another cache miss
 * this version is already faster than the previous and I can still improve it...

------------------------------------------------------------------------
r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-5
 * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be
   increased to keep the same memory. As a result, the speed is a little
   slower in fact.

------------------------------------------------------------------------
r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-4
 * added back optimization codes (it is a pain...)

------------------------------------------------------------------------
r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-3
 * faster bit operations

------------------------------------------------------------------------
r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-2
 * removed optimization codes again...
 * use a new method to count the bits

------------------------------------------------------------------------
r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.3.0-1
 * added back the optimization codes
 * added a new option to aln: max_entries, although this is disabled by default
 * updated benchmark

------------------------------------------------------------------------
r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

add URL

------------------------------------------------------------------------
r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.3.0

------------------------------------------------------------------------
r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines
Changed paths:
   A /branches/prog/bwa/COPYING
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/utils.c
   M /branches/prog/bwa/utils.h

added licensing information

------------------------------------------------------------------------
r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-31
 * better mapping quality
 * update benchmark

------------------------------------------------------------------------
r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1

update documentation

------------------------------------------------------------------------
r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update documentation

------------------------------------------------------------------------
r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-30
 * reduce memory a little bit
 * update documentation

------------------------------------------------------------------------
r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines
Changed paths:
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-29
 * sampe: removed -O option; changed default -o to 100000
 * sampe: fixed a bug in calculating paired mapping quality
 * aln: added an option to search for suboptimal hits even if the best is a repeat.
   This option will make sampe MUCH SLOWER.
 * sampe: set isize as zero if mapped to two different chr
 * update manual (unfinished)

------------------------------------------------------------------------
r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-28
 * fixed a bug in calculating paired mapping quality

------------------------------------------------------------------------
r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675)
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-27
 * accelerate sampe by storing visited large intervals

------------------------------------------------------------------------
r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-26
 * remove the optimation codes

------------------------------------------------------------------------
r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-25
 * accelerate OCC calculation by ~7%. However, it seems not worth doing
   this by complicate the codes. I will change back later.

------------------------------------------------------------------------
r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-24
 * change command "sai2sam_pe" to "sampe"
 * print usage for sampe command
 * in sampe: change default max_occ to 1000
 * fixed a few compiling warnings in bntseq.c

------------------------------------------------------------------------
r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-22
 * mating information can be printed to SAM

------------------------------------------------------------------------
r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-21
 * implement pairing (still UNFINISHED)
 * output all reads even if full of N

------------------------------------------------------------------------
r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/bwape.c
   M /branches/prog/bwa/bwase.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * bwa-0.2.0-20
 * remove "-t" from aln cmd
 * code clean up: move some functions in bwt2fmv.c to other source files
 * added sai2sam_pe cmd: *UNFINISHED*

------------------------------------------------------------------------
r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/bwase.c
   A /branches/prog/bwa/bwaseqio.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/kseq.h
   A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712)
   A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537)
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-19
 * considerable code cleanup; no actual changes

------------------------------------------------------------------------
r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-18
 * generate SAM output

------------------------------------------------------------------------
r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * bwa-0.2.0-17
 * remove bwtsw2 related codes
 * separate searching for SA interval from generating alignments

------------------------------------------------------------------------
r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt2fmv.c
   D /branches/prog/bwa/bwt_lite.c
   D /branches/prog/bwa/bwt_lite.h
   M /branches/prog/bwa/bwtgap.c
   D /branches/prog/bwa/bwtsw2.h
   D /branches/prog/bwa/bwtsw2_aux.c
   D /branches/prog/bwa/bwtsw2_core.c
   D /branches/prog/bwa/bwtsw2_main.c
   D /branches/prog/bwa/khash.h
   D /branches/prog/bwa/ksort.h
   D /branches/prog/bwa/kvec.h
   M /branches/prog/bwa/main.c

 * added interface to "aln -t"
 * remove bwtsw2 related codes

------------------------------------------------------------------------
r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-16
 * allow to set max mismatches based on read length, but I do not know
   whether this really works

------------------------------------------------------------------------
r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-15
 * fixed a bug in sequence parser.

------------------------------------------------------------------------
r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/utils.c

 * bwa-0.2.0-14
 * fixed a bug caused by the change of the FASTA/Q parser

------------------------------------------------------------------------
r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtsw2_core.c
   A /branches/prog/bwa/kseq.h
   D /branches/prog/bwa/seq.c
   D /branches/prog/bwa/seq.h
   M /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/utils.c
   M /branches/prog/bwa/utils.h

replace seq.* with kseq.h

------------------------------------------------------------------------
r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-13
 * make bwtsw2 output sub-optimal hits. not completed

------------------------------------------------------------------------
r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/kvec.h

little...

------------------------------------------------------------------------
r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/khash.h

improve interface of khash

------------------------------------------------------------------------
r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

improve minor things, which make bwtsw2 slower, but should miss less true hits

------------------------------------------------------------------------
r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

 * fixed a bug in calculating ->D
 * enforce band-width checking

------------------------------------------------------------------------
r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

delete a line of code that is never visited

------------------------------------------------------------------------
r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

a bit code clean up

------------------------------------------------------------------------
r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-12
 * max-depth can be set, although it does not help the speed at all

------------------------------------------------------------------------
r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

cut_tail after remove duplicate

------------------------------------------------------------------------
r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/khash.h
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-11
 * improved cut_tail()

------------------------------------------------------------------------
r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-10
 * fixed a bug in cut_tail()

------------------------------------------------------------------------
r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

a bit code clean up

------------------------------------------------------------------------
r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

improve speed (<1%)

------------------------------------------------------------------------
r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

 * fixed two potential bugs, although I have not seen their effects
 * improve speed a bit (<2%)

------------------------------------------------------------------------
r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c

nothing, really

------------------------------------------------------------------------
r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

disable X-drop, which has to be reimplemented in the current algorithm

------------------------------------------------------------------------
r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt_lite.c
   M /branches/prog/bwa/bwt_lite.h
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c

 * temporarily disable cut_tail()
 * calculate SA in bwt_lite.c
 * fixed a bug in reversing the sequence

------------------------------------------------------------------------
r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   A /branches/prog/bwa/ksort.h

n-best method

------------------------------------------------------------------------
r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_core.c

give correct result again

------------------------------------------------------------------------
r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

I think I know the reason. It needs more work...

------------------------------------------------------------------------
r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_core.c

fixed another bug, but still have

------------------------------------------------------------------------
r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

fixed another bug

------------------------------------------------------------------------
r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/khash.h

 * do not segfault, but the result is WRONG!
 * prepare to remove bsw2_connectivity_check()

------------------------------------------------------------------------
r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/kvec.h

more revisions

------------------------------------------------------------------------
r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

further simply codes with kvec.h

------------------------------------------------------------------------
r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

part of revisions... have not finished

------------------------------------------------------------------------
r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/khash.h
   A /branches/prog/bwa/kvec.h

prepare for abrupt change

------------------------------------------------------------------------
r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

fixed a bug; now "bwtsw2 -d" is useless

------------------------------------------------------------------------
r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

improve speed a little bit

------------------------------------------------------------------------
r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

remove debug codes

------------------------------------------------------------------------
r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

 * improve the speed a little bit (<5%)
 * prepare to remove BSW_DEBUG

------------------------------------------------------------------------
r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-9
 * support reverse strand
 * fixed a bug that causes missing hits

------------------------------------------------------------------------
r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-8
 * better progress report

------------------------------------------------------------------------
r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-7
 * avoid some missing hits
 * add maximum depth

------------------------------------------------------------------------
r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-6
 * bwtsw2 works although on the forward strand only for now
 * better progress information

------------------------------------------------------------------------
r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

 * implement memory pool
 * avoid some rehashing

------------------------------------------------------------------------
r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_main.c

 * fixed a memory leak
 * prepare to implement mempool

------------------------------------------------------------------------
r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/khash.h

 * add X-dropoff
 * remove duplicated results
 * switch to simple stack

------------------------------------------------------------------------
r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c

 * check whether t-node has been visited
 * prepare to remove two-level stack

------------------------------------------------------------------------
r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines
Changed paths:
   A /branches/prog/bwa/khash.h

khash library

------------------------------------------------------------------------
r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

add inline

------------------------------------------------------------------------
r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c

improve speed

------------------------------------------------------------------------
r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2_core.c

Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just
keep a copy in case I may need this in future.


------------------------------------------------------------------------
r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_core.c

 * no principal modification

------------------------------------------------------------------------
r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2_core.c

 * fixed a bug which may cause duplicated matching
 * accelerate the speed a bit, although using hash in avoiding duplications
   slows the speed down in the end

------------------------------------------------------------------------
r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtsw2.h
   M /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-5
 * indel seems to work on toy example
 * add band

------------------------------------------------------------------------
r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt_lite.c
   M /branches/prog/bwa/bwt_lite.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtsw2.h
   A /branches/prog/bwa/bwtsw2_aux.c
   M /branches/prog/bwa/bwtsw2_core.c
   M /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/is.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/simple_dp.c

 * bwa-0.2.0-4
 * updated bwtsw2, which seems to work properly on toy examples

------------------------------------------------------------------------
r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-3
 * tune for longer gaps, but it does not really work with kilo-bp gaps...

------------------------------------------------------------------------
r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-2
 * changed the way to extend long deletions. Now use max_del_occ.

------------------------------------------------------------------------
r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt_lite.c
   M /branches/prog/bwa/bwt_lite.h

updated from bwtsw2_lite

------------------------------------------------------------------------
r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.h
   A /branches/prog/bwa/bwt_lite.c
   A /branches/prog/bwa/bwt_lite.h
   A /branches/prog/bwa/bwtsw2.h
   A /branches/prog/bwa/bwtsw2_core.c
   A /branches/prog/bwa/bwtsw2_main.c
   M /branches/prog/bwa/main.c

 * bwa-0.2.0-1
 * add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
 * add core codes for bwtsw2: NOT TESTED!!!

------------------------------------------------------------------------
r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

Release bwa-0.2.0

------------------------------------------------------------------------
r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c

 * bwa-0.1.6-7
 * change default seed length to 31
 * add incomplete support to color sequences (not tested yet!)

------------------------------------------------------------------------
r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.6-6
 * change default seed length to 33bp

------------------------------------------------------------------------
r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.6-5
 * fixed a bug that may miss true alignments. this bugs exists in most
   early versions.
 * fixed a bug that yields wrong coordinates for reads mapped on the forward
   strands with gaps.

------------------------------------------------------------------------
r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines
Changed paths:
   D /branches/prog/bwa/Makefile.div

useless

------------------------------------------------------------------------
r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.6-4
 * fixed one bug
 * there is another one...

------------------------------------------------------------------------
r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.6-3
 * almost there, but not quite right

------------------------------------------------------------------------
r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * improve the seeding method
 * prepare to load two BWTs into memory. A BIG change!

------------------------------------------------------------------------
r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * added seeding
 * unfinished yet

------------------------------------------------------------------------
r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.1.6

------------------------------------------------------------------------
r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/simple_dp.c

sw: output alignment score

------------------------------------------------------------------------
r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   A /branches/prog/bwa/simple_dp.c
   M /branches/prog/bwa/stdaln.c
   M /branches/prog/bwa/stdaln.h

 * bwa-0.1.5-3
 * added a simple interface to SW/NW alignment
 * stdaln-0.9.8 (see header for more details)

------------------------------------------------------------------------
r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   A /branches/prog/bwa/stdaln.c
   A /branches/prog/bwa/stdaln.h

 * bwa-0.1.5-2
 * give accurate gap positions

------------------------------------------------------------------------
r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h

unfinished, but I am tired...

------------------------------------------------------------------------
r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.5-1
 * fixed a potential bug which may produce an alignment in N regions,
   although extremely rare.

------------------------------------------------------------------------
r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.1.5

------------------------------------------------------------------------
r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update documentation

------------------------------------------------------------------------
r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * 

------------------------------------------------------------------------
r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.4-4
 * add timer for debugging

------------------------------------------------------------------------
r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.4-3
 * fixed a bug in the previous code
 * this version gives identical result to bwa-0.1.4, just 10% faster

------------------------------------------------------------------------
r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * bwa-0.1.4-2
 * further improve the speed
 * The result is slightly different from bwa-0.1.4 now. I need to check...

------------------------------------------------------------------------
r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt.c

comments only

------------------------------------------------------------------------
r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

further improve the speed in Occ functions

------------------------------------------------------------------------
r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/main.c

Release bwa-0.1.4

------------------------------------------------------------------------
r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1

update documentation and ChangeLog

------------------------------------------------------------------------
r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.3-2
 * fixed the bug in the last modification
 * now the alignment should be more clearly defined

------------------------------------------------------------------------
r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.3-1
 * this is a buggy verion!
 * i will fix the bug tomorrow. It is late...

------------------------------------------------------------------------
r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.1.3

------------------------------------------------------------------------
r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.2-3
 * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
 * aln: more command-line options

------------------------------------------------------------------------
r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.2-2
 * further improve the speed
 * this version gives exactly the same result as bwa-0.1.2

------------------------------------------------------------------------
r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.2-1
 * speed up by about 5%

------------------------------------------------------------------------
r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.1.2

------------------------------------------------------------------------
r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   D /branches/prog/bwa/bwt1away.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   D /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-9
 * some code cleanup
 * remove 1away and top2

------------------------------------------------------------------------
r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/is.c

Yuta Mori's implementation of IS algorithm.

------------------------------------------------------------------------
r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-8
 * improve gapped alignment
 * this version will miss more gapped alignments, but the speed is much faster
 * prepare to remove top2 and 1away algorithms
 * prepare to add SAIS algorithm for bwt construction

------------------------------------------------------------------------
r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-7
 * change END_SKIP from 3 to 5, but still gaps may be wrongly added
 * change default '-g' from 5 to 3

------------------------------------------------------------------------
r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-6
 * fix a bug in nested stack

------------------------------------------------------------------------
r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   A /branches/prog/bwa/bwtgap.h
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-5
 * replace heap with nested stacks
 * there are still obvious bugs...

------------------------------------------------------------------------
r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * bwa-0.1.1-4
 * add interface to affine gap alignment
 * there are obvious bugs and I will fix them later

------------------------------------------------------------------------
r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-3
 * affine gap seems to work, at least partially

------------------------------------------------------------------------
r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   A /branches/prog/bwa/bwtgap.c
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-2
 * initial gapped alignment. not work at the moment

------------------------------------------------------------------------
r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.1-1
 * ungap: remove a useless varible in top2_entry_t

------------------------------------------------------------------------
r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/ChangeLog
   A /branches/prog/bwa/NEWS
   M /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/main.c

Release bwa-0.1.1

------------------------------------------------------------------------
r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwa.1

update documentation

------------------------------------------------------------------------
r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines
Changed paths:
   A /branches/prog/bwa/ChangeLog
   A /branches/prog/bwa/bwa.1
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-11
 * improve approximating mapping qualities
 * add documentation
 * add ChangeLog

------------------------------------------------------------------------
r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-10
 * output a random position for repetitive reads

------------------------------------------------------------------------
r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/pac2bwt.c

 * bwa-0.1.0-9
 * fix memory leaks
 * fix a potential bug in coverting to the real coordinate

------------------------------------------------------------------------
r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile.div
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-8
 * fix a bug about strand
 * update Makefile.div
 * change top2b as the default method

------------------------------------------------------------------------
r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt1away.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-7
 * use bwt_2occ() and bwt_2occ4() in other functions

------------------------------------------------------------------------
r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-6
 * fix a bug for missing hits

------------------------------------------------------------------------
r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-5
 * accelerate comparisons in heap, a bit

------------------------------------------------------------------------
r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-4
 * avoid marginal repeated calculation in occ

------------------------------------------------------------------------
r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-3
 * fix a bug caused by previours change
 * fix a bug in heap
 * order the heap by more criteria

------------------------------------------------------------------------
r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c

 * bwa-0.1.0-2
 * also sort sa range in heapsort, in attempt to improve cache performance.
   Unfortunately, it does not work well at all.

------------------------------------------------------------------------
r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/Makefile.div
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/main.c

 * 0.1.0-1
 * fix a bug in calculating the real coordinate

------------------------------------------------------------------------
r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile

nothing, really

------------------------------------------------------------------------
r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/Makefile.div
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/pac2bwt.c

use IS algorithm by default

------------------------------------------------------------------------
r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/is.c
   M /branches/prog/bwa/pac2bwt.c

 * a bit code clean up in is.c
 * add IS algorithm for constructing BWT, albeit slower

------------------------------------------------------------------------
r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines
Changed paths:
   A /branches/prog/bwa/is.c

IS linear-time algorithm for constructing SA/BWT

------------------------------------------------------------------------
r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bntseq.c
   A /branches/prog/bwa/bwtindex.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * fix a bug in generating .pac
 * index in one go

------------------------------------------------------------------------
r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwttop2.c

real coordinates can be ouput

------------------------------------------------------------------------
r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwttop2.c

add top2e which is similar to 1away

------------------------------------------------------------------------
r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwttop2.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * unified cmd-line interface for ungapped alignment
 * add two alternatives to top2 algorithm

------------------------------------------------------------------------
r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

add cmd-line interface to alntop2

------------------------------------------------------------------------
r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt1away.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   A /branches/prog/bwa/bwttop2.c

top2 algorithm seems to work. I need to change interface, though

------------------------------------------------------------------------
r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt1away.c

change the variable in the structure

------------------------------------------------------------------------
r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt1away.c

set a slightly better bound on the maximum allowed mismatches

------------------------------------------------------------------------
r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c

 * output time statistics

------------------------------------------------------------------------
r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   A /branches/prog/bwa/bwt1away.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h

 * presumably better way to make use of prefix. But for the moment I do
   not know whether it is correct or not.
 * a bit code clean up: separate alignment part

------------------------------------------------------------------------
r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt_gen/Makefile
   M /branches/prog/bwa/bwt_gen/bwt_gen.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/pac2bwt.c

 * a bit code clean up
 * put bwt_gen in bwa

------------------------------------------------------------------------
r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtio.c

 * improve cmd-line interface
 * fix a bug in loading .sa
 * change default sa interval to 32

------------------------------------------------------------------------
r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwtaln.c

 * fix memory leak (I know that. Just a bit lazy)
 * change to another method to do 1-away alignment

------------------------------------------------------------------------
r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

best unique match is partially finished

------------------------------------------------------------------------
r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

remove "ungapped" command and related codes

------------------------------------------------------------------------
r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h

change variable name thick to width

------------------------------------------------------------------------
r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/pac2bwt.c

revised algorithm for ungapped alignment. the old one can still be used.

------------------------------------------------------------------------
r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwt_gen/bwt_gen.c
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/pac2bwt.c

 * make commands more independent, but ungapped does not work at the moment

------------------------------------------------------------------------
r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt_gen/bwt_gen.c

little...

------------------------------------------------------------------------
r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt_gen/bwt_gen.c
   M /branches/prog/bwa/bwt_gen/bwt_gen.h

 * add CopyRight information from the original codes
 * do not dump .fmv files

------------------------------------------------------------------------
r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines
Changed paths:
   A /branches/prog/bwa/bwt_gen
   A /branches/prog/bwa/bwt_gen/Makefile
   A /branches/prog/bwa/bwt_gen/QSufSort.c
   A /branches/prog/bwa/bwt_gen/QSufSort.h
   A /branches/prog/bwa/bwt_gen/bwt_gen.c
   A /branches/prog/bwa/bwt_gen/bwt_gen.h

codes from BWT-SW, for building BWT from packed file

------------------------------------------------------------------------
r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
 * write Occ file as ".occ" as it is using a different interval from
   .fmv, the BWT-SW correspondance of .occ

------------------------------------------------------------------------
r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c

fix a bug

------------------------------------------------------------------------
r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c

add heuristics to improve the speed, but I have not tested whether the
results are correct or not.


------------------------------------------------------------------------
r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/bwtaln.c
   M /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * make ungapped alignment basically works...
 * but it is very slow in comparison to others...
 * also I need to improve the interface...
 * a lot of things to keep me busy today...

------------------------------------------------------------------------
r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwtaln.c

 * remove recursion
 * fixed a bug in bwt_occ()

------------------------------------------------------------------------
r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwtaln.c

 * bwa now tells whether a sequenced can be mapped with maximum allowed
   mismatches. ONLY ungapped.
 * this is a recursive version. I will remove recursion later.


------------------------------------------------------------------------
r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   A /branches/prog/bwa/bwtaln.c
   A /branches/prog/bwa/bwtaln.h
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/utils.c

 * load .sa and .fmv files
 * exact alignment now works

------------------------------------------------------------------------
r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/utils.c
   M /branches/prog/bwa/utils.h

add xassert and fix a bug

------------------------------------------------------------------------
r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwtio.c
   A /branches/prog/bwa/utils.c
   A /branches/prog/bwa/utils.h

improve error message and error handling

------------------------------------------------------------------------
r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c
   A /branches/prog/bwa/bwtio.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h

 * move I/O codes to bwtio.c
 * SA can be dumped and interestingly, it is identical to BWTSW
 * now, .fmv is still different from BWTSW

------------------------------------------------------------------------
r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c

generate/retrieve SA and Occ

------------------------------------------------------------------------
r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines
Changed paths:
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/bwt.c
   M /branches/prog/bwa/bwt.h
   M /branches/prog/bwa/bwt2fmv.c

 * retrieve occ value at any position
 * move bwt_cal_occ() to bwt.c

------------------------------------------------------------------------
r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   A /branches/prog/bwa/bwt.c
   A /branches/prog/bwa/bwt.h
   A /branches/prog/bwa/bwt2fmv.c
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   M /branches/prog/bwa/pac2bwt.c

 * add bwt2fmv. It works to some extend. However, I do not understand
   the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv
   could generate a file almost identical, but not exactly identical, to
   the .fmv file from BWT-SW.


------------------------------------------------------------------------
r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines
Changed paths:
   M /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bntseq.c
   M /branches/prog/bwa/bntseq.h
   M /branches/prog/bwa/main.c
   M /branches/prog/bwa/main.h
   A /branches/prog/bwa/pac2bwt.c

Burrows-Wheeler Transform now works. At least on one example, the
current code generates the same BWT as BWT-SW. Kind of magical, I would
say. :)


------------------------------------------------------------------------
r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines
Changed paths:
   A /branches/prog/bwa/Makefile
   M /branches/prog/bwa/bntseq.c
   A /branches/prog/bwa/main.c
   A /branches/prog/bwa/main.h

 * add Makefile and main.*
 * improve interface to fa2bns, a bit

------------------------------------------------------------------------
r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines
Changed paths:
   A /branches/prog/bwa
   A /branches/prog/bwa/bntseq.c
   A /branches/prog/bwa/bntseq.h
   A /branches/prog/bwa/seq.c
   A /branches/prog/bwa/seq.h

 * Burrow-Wheeler Alignment
 * initial codes

------------------------------------------------------------------------
bwa-0.7.3a/COPYING000644 000767 000024 00000104513 12120745361 013326 0ustar00lh3staff000000 000000                     GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

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bwa-0.7.3a/example.c000644 000767 000024 00000003055 12120745361 014071 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <zlib.h>
#include <string.h>
#include <assert.h>
#include "bwamem.h"
#include "kseq.h" // for the FASTA/Q parser
KSEQ_DECLARE(gzFile)

int main(int argc, char *argv[])
{
	bwaidx_t *idx;
	gzFile fp;
	kseq_t *ks;
	mem_opt_t *opt;

	if (argc < 3) {
		fprintf(stderr, "Usage: bwamem-lite <idx.base> <reads.fq>\n");
		return 1;
	}

	idx = bwa_idx_load(argv[1], BWA_IDX_ALL); // load the BWA index
	assert(idx);
	fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
	assert(fp);
	ks = kseq_init(fp); // initialize the FASTA/Q parser
	opt = mem_opt_init(); // initialize the BWA-MEM parameters to the default values

	while (kseq_read(ks) >= 0) { // read one sequence
		mem_alnreg_v ar;
		int i, k;
		ar = mem_align1(opt, idx->bwt, idx->bns, idx->pac, ks->seq.l, ks->seq.s); // get all the hits
		for (i = 0; i < ar.n; ++i) { // traverse each hit
			mem_aln_t a;
			if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
			a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
			// print alignment
			printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
			for (k = 0; k < a.n_cigar; ++k) // print CIGAR
				printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
			printf("\t%d\n", a.NM); // print edit distance
			free(a.cigar); // don't forget to deallocate CIGAR
		}
		free(ar.a); // and deallocate the hit list
	}

	free(opt);
	kseq_destroy(ks);
	gzclose(fp);
	bwa_idx_destroy(idx);
	return 0;
}
bwa-0.7.3a/fastmap.c000644 000767 000024 00000016777 12120745361 014110 0ustar00lh3staff000000 000000 #include <zlib.h>
#include <stdio.h>
#include <unistd.h>
#include <stdlib.h>
#include "bwa.h"
#include "bwamem.h"
#include "kvec.h"
#include "utils.h"
#include "kseq.h"
KSEQ_DECLARE(gzFile)

extern unsigned char nst_nt4_table[256];

void *kopen(const char *fn, int *_fd);
int kclose(void *a);

int main_mem(int argc, char *argv[])
{
	mem_opt_t *opt;
	int fd, fd2, i, c, n, copy_comment = 0;
	gzFile fp, fp2 = 0;
	kseq_t *ks, *ks2 = 0;
	bseq1_t *seqs;
	bwaidx_t *idx;
	char *rg_line = 0;
	void *ko = 0, *ko2 = 0;

	opt = mem_opt_init();
	while ((c = getopt(argc, argv, "paMCPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:")) >= 0) {
		if (c == 'k') opt->min_seed_len = atoi(optarg);
		else if (c == 'w') opt->w = atoi(optarg);
		else if (c == 'A') opt->a = atoi(optarg);
		else if (c == 'B') opt->b = atoi(optarg);
		else if (c == 'O') opt->q = atoi(optarg);
		else if (c == 'E') opt->r = atoi(optarg);
		else if (c == 'T') opt->T = atoi(optarg);
		else if (c == 'L') opt->pen_clip = atoi(optarg);
		else if (c == 'U') opt->pen_unpaired = atoi(optarg);
		else if (c == 't') opt->n_threads = atoi(optarg), opt->n_threads = opt->n_threads > 1? opt->n_threads : 1;
		else if (c == 'P') opt->flag |= MEM_F_NOPAIRING;
		else if (c == 'H') opt->flag |= MEM_F_HARDCLIP;
		else if (c == 'a') opt->flag |= MEM_F_ALL;
		else if (c == 'p') opt->flag |= MEM_F_PE;
		else if (c == 'M') opt->flag |= MEM_F_NO_MULTI;
		else if (c == 'c') opt->max_occ = atoi(optarg);
		else if (c == 'd') opt->zdrop = atoi(optarg);
		else if (c == 'v') bwa_verbose = atoi(optarg);
		else if (c == 'r') opt->split_factor = atof(optarg);
		else if (c == 'C') copy_comment = 1;
		else if (c == 'R') {
			if ((rg_line = bwa_set_rg(optarg)) == 0) return 1; // FIXME: memory leak
		} else if (c == 's') opt->split_width = atoi(optarg);
	}
	if (opt->n_threads < 1) opt->n_threads = 1;
	if (optind + 1 >= argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\n");
		fprintf(stderr, "Algorithm options:\n\n");
		fprintf(stderr, "       -t INT     number of threads [%d]\n", opt->n_threads);
		fprintf(stderr, "       -k INT     minimum seed length [%d]\n", opt->min_seed_len);
		fprintf(stderr, "       -w INT     band width for banded alignment [%d]\n", opt->w);
		fprintf(stderr, "       -d INT     off-diagonal X-dropoff [%d]\n", opt->zdrop);
		fprintf(stderr, "       -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
//		fprintf(stderr, "       -s INT     look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
		fprintf(stderr, "       -c INT     skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
		fprintf(stderr, "       -P         skip pairing; perform mate SW only\n");
		fprintf(stderr, "       -A INT     score for a sequence match [%d]\n", opt->a);
		fprintf(stderr, "       -B INT     penalty for a mismatch [%d]\n", opt->b);
		fprintf(stderr, "       -O INT     gap open penalty [%d]\n", opt->q);
		fprintf(stderr, "       -E INT     gap extension penalty; a gap of size k cost {-O} + {-E}*k [%d]\n", opt->r);
		fprintf(stderr, "       -L INT     penalty for clipping [%d]\n", opt->pen_clip);
		fprintf(stderr, "       -U INT     penalty for an unpaired read pair [%d]\n", opt->pen_unpaired);
		fprintf(stderr, "\nInput/output options:\n\n");
		fprintf(stderr, "       -p         first query file consists of interleaved paired-end sequences\n");
		fprintf(stderr, "       -R STR     read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
		fprintf(stderr, "\n");
		fprintf(stderr, "       -v INT     verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
		fprintf(stderr, "       -T INT     minimum score to output [%d]\n", opt->T);
		fprintf(stderr, "       -a         output all alignments for SE or unpaired PE\n");
		fprintf(stderr, "       -C         append FASTA/FASTQ comment to SAM output\n");
		fprintf(stderr, "       -H         hard clipping\n");
		fprintf(stderr, "       -M         mark shorter split hits as secondary (for Picard/GATK compatibility)\n");
		fprintf(stderr, "\nNote: Please read the man page for detailed description of the command line and options.\n");
		fprintf(stderr, "\n");
		free(opt);
		return 1;
	}

	bwa_fill_scmat(opt->a, opt->b, opt->mat);
	if ((idx = bwa_idx_load(argv[optind], BWA_IDX_ALL)) == 0) return 1; // FIXME: memory leak
	bwa_print_sam_hdr(idx->bns, rg_line);

	ko = kopen(argv[optind + 1], &fd);
	fp = gzdopen(fd, "r");
	ks = kseq_init(fp);
	if (optind + 2 < argc) {
		if (opt->flag&MEM_F_PE) {
			if (bwa_verbose >= 2)
				fprintf(stderr, "[W::%s] when '-p' is in use, the second query file will be ignored.\n", __func__);
		} else {
			ko2 = kopen(argv[optind + 2], &fd2);
			fp2 = gzdopen(fd2, "r");
			ks2 = kseq_init(fp2);
			opt->flag |= MEM_F_PE;
		}
	}
	while ((seqs = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
		int64_t size = 0;
		if ((opt->flag & MEM_F_PE) && (n&1) == 1) {
			if (bwa_verbose >= 2)
				fprintf(stderr, "[W::%s] odd number of reads in the PE mode; last read dropped\n", __func__);
			n = n>>1<<1;
		}
		if (!copy_comment)
			for (i = 0; i < n; ++i) {
				free(seqs[i].comment); seqs[i].comment = 0;
			}
		for (i = 0; i < n; ++i) size += seqs[i].l_seq;
		if (bwa_verbose >= 3)
			fprintf(stderr, "[M::%s] read %d sequences (%ld bp)...\n", __func__, n, (long)size);
		mem_process_seqs(opt, idx->bwt, idx->bns, idx->pac, n, seqs);
		free(seqs);
	}

	free(opt);
	bwa_idx_destroy(idx);
	kseq_destroy(ks);
	gzclose(fp); kclose(ko);
	if (ks2) {
		kseq_destroy(ks2);
		gzclose(fp2); kclose(ko2);
	}
	return 0;
}

int main_fastmap(int argc, char *argv[])
{
	int c, i, min_iwidth = 20, min_len = 17, print_seq = 0, split_width = 0;
	kseq_t *seq;
	bwtint_t k;
	gzFile fp;
	smem_i *itr;
	const bwtintv_v *a;
	bwaidx_t *idx;

	while ((c = getopt(argc, argv, "w:l:ps:")) >= 0) {
		switch (c) {
			case 's': split_width = atoi(optarg); break;
			case 'p': print_seq = 1; break;
			case 'w': min_iwidth = atoi(optarg); break;
			case 'l': min_len = atoi(optarg); break;
		}
	}
	if (optind + 1 >= argc) {
		fprintf(stderr, "Usage: bwa fastmap [-p] [-s splitWidth=%d] [-l minLen=%d] [-w maxSaSize=%d] <idxbase> <in.fq>\n", split_width, min_len, min_iwidth);
		return 1;
	}

	fp = gzopen(argv[optind + 1], "r");
	seq = kseq_init(fp);
	idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS);
	itr = smem_itr_init(idx->bwt);
	while (kseq_read(seq) >= 0) {
		printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
		if (print_seq) {
			putchar('\t');
			puts(seq->seq.s);
		} else putchar('\n');
		for (i = 0; i < seq->seq.l; ++i)
			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
		smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s);
		while ((a = smem_next(itr, min_len<<1, split_width)) != 0) {
			for (i = 0; i < a->n; ++i) {
				bwtintv_t *p = &a->a[i];
				if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
				printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
				if (p->x[2] <= min_iwidth) {
					for (k = 0; k < p->x[2]; ++k) {
						bwtint_t pos;
						int len, is_rev, ref_id;
						len  = (uint32_t)p->info - (p->info>>32);
						pos = bns_depos(idx->bns, bwt_sa(idx->bwt, p->x[0] + k), &is_rev);
						if (is_rev) pos -= len - 1;
						bns_cnt_ambi(idx->bns, pos, len, &ref_id);
						printf("\t%s:%c%ld", idx->bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - idx->bns->anns[ref_id].offset) + 1);
					}
				} else fputs("\t*", stdout);
				putchar('\n');
			}
		}
		puts("//");
	}

	smem_itr_destroy(itr);
	bwa_idx_destroy(idx);
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}
bwa-0.7.3a/is.c000644 000767 000024 00000014704 12120745361 013054 0ustar00lh3staff000000 000000 /*
 * sais.c for sais-lite
 * Copyright (c) 2008 Yuta Mori All Rights Reserved.
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */

#include <stdlib.h>

typedef unsigned char ubyte_t;
#define chr(i) (cs == sizeof(int) ? ((const int *)T)[i]:((const unsigned char *)T)[i])

/* find the start or end of each bucket */
static void getCounts(const unsigned char *T, int *C, int n, int k, int cs)
{
	int i;
	for (i = 0; i < k; ++i) C[i] = 0;
	for (i = 0; i < n; ++i) ++C[chr(i)];
}
static void getBuckets(const int *C, int *B, int k, int end)
{
	int i, sum = 0;
	if (end) {
		for (i = 0; i < k; ++i) {
			sum += C[i];
			B[i] = sum;
		}
	} else {
		for (i = 0; i < k; ++i) {
			sum += C[i];
			B[i] = sum - C[i];
		}
	}
}

/* compute SA */
static void induceSA(const unsigned char *T, int *SA, int *C, int *B, int n, int k, int cs)
{
	int *b, i, j;
	int  c0, c1;
	/* compute SAl */
	if (C == B) getCounts(T, C, n, k, cs);
	getBuckets(C, B, k, 0);	/* find starts of buckets */
	j = n - 1;
	b = SA + B[c1 = chr(j)];
	*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
	for (i = 0; i < n; ++i) {
		j = SA[i], SA[i] = ~j;
		if (0 < j) {
			--j;
			if ((c0 = chr(j)) != c1) {
				B[c1] = b - SA;
				b = SA + B[c1 = c0];
			}
			*b++ = ((0 < j) && (chr(j - 1) < c1)) ? ~j : j;
		}
	}
	/* compute SAs */
	if (C == B) getCounts(T, C, n, k, cs);
	getBuckets(C, B, k, 1);	/* find ends of buckets */
	for (i = n - 1, b = SA + B[c1 = 0]; 0 <= i; --i) {
		if (0 < (j = SA[i])) {
			--j;
			if ((c0 = chr(j)) != c1) {
				B[c1] = b - SA;
				b = SA + B[c1 = c0];
			}
			*--b = ((j == 0) || (chr(j - 1) > c1)) ? ~j : j;
		} else SA[i] = ~j;
	}
}

/*
 * find the suffix array SA of T[0..n-1] in {0..k-1}^n use a working
 * space (excluding T and SA) of at most 2n+O(1) for a constant alphabet
 */
static int sais_main(const unsigned char *T, int *SA, int fs, int n, int k, int cs)
{
	int *C, *B, *RA;
	int  i, j, c, m, p, q, plen, qlen, name;
	int  c0, c1;
	int  diff;

	/* stage 1: reduce the problem by at least 1/2 sort all the
	 * S-substrings */
	if (k <= fs) {
		C = SA + n;
		B = (k <= (fs - k)) ? C + k : C;
	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
	getCounts(T, C, n, k, cs);
	getBuckets(C, B, k, 1);	/* find ends of buckets */
	for (i = 0; i < n; ++i) SA[i] = 0;
	for (i = n - 2, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
		if ((c0 = chr(i)) < (c1 + c)) c = 1;
		else if (c != 0) SA[--B[c1]] = i + 1, c = 0;
	}
	induceSA(T, SA, C, B, n, k, cs);
	if (fs < k) free(C);
	/* compact all the sorted substrings into the first m items of SA
	 * 2*m must be not larger than n (proveable) */
	for (i = 0, m = 0; i < n; ++i) {
		p = SA[i];
		if ((0 < p) && (chr(p - 1) > (c0 = chr(p)))) {
			for (j = p + 1; (j < n) && (c0 == (c1 = chr(j))); ++j);
			if ((j < n) && (c0 < c1)) SA[m++] = p;
		}
	}
	for (i = m; i < n; ++i) SA[i] = 0;	/* init the name array buffer */
	/* store the length of all substrings */
	for (i = n - 2, j = n, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
		if ((c0 = chr(i)) < (c1 + c)) c = 1;
		else if (c != 0) {
			SA[m + ((i + 1) >> 1)] = j - i - 1;
			j = i + 1;
			c = 0;
		}
	}
	/* find the lexicographic names of all substrings */
	for (i = 0, name = 0, q = n, qlen = 0; i < m; ++i) {
		p = SA[i], plen = SA[m + (p >> 1)], diff = 1;
		if (plen == qlen) {
			for (j = 0; (j < plen) && (chr(p + j) == chr(q + j)); j++);
			if (j == plen) diff = 0;
		}
		if (diff != 0) ++name, q = p, qlen = plen;
		SA[m + (p >> 1)] = name;
	}

	/* stage 2: solve the reduced problem recurse if names are not yet
	 * unique */
	if (name < m) {
		RA = SA + n + fs - m;
		for (i = n - 1, j = m - 1; m <= i; --i) {
			if (SA[i] != 0) RA[j--] = SA[i] - 1;
		}
		if (sais_main((unsigned char *) RA, SA, fs + n - m * 2, m, name, sizeof(int)) != 0) return -2;
		for (i = n - 2, j = m - 1, c = 0, c1 = chr(n - 1); 0 <= i; --i, c1 = c0) {
			if ((c0 = chr(i)) < (c1 + c)) c = 1;
			else if (c != 0) RA[j--] = i + 1, c = 0; /* get p1 */
		}
		for (i = 0; i < m; ++i) SA[i] = RA[SA[i]]; /* get index */
	}
	/* stage 3: induce the result for the original problem */
	if (k <= fs) {
		C = SA + n;
		B = (k <= (fs - k)) ? C + k : C;
	} else if ((C = B = (int *) malloc(k * sizeof(int))) == NULL) return -2;
	/* put all left-most S characters into their buckets */
	getCounts(T, C, n, k, cs);
	getBuckets(C, B, k, 1);	/* find ends of buckets */
	for (i = m; i < n; ++i) SA[i] = 0; /* init SA[m..n-1] */
	for (i = m - 1; 0 <= i; --i) {
		j = SA[i], SA[i] = 0;
		SA[--B[chr(j)]] = j;
	}
	induceSA(T, SA, C, B, n, k, cs);
	if (fs < k) free(C);
	return 0;
}

/**
 * Constructs the suffix array of a given string.
 * @param T[0..n-1] The input string.
 * @param SA[0..n] The output array of suffixes.
 * @param n The length of the given string.
 * @return 0 if no error occurred
 */
int is_sa(const ubyte_t *T, int *SA, int n)
{
	if ((T == NULL) || (SA == NULL) || (n < 0)) return -1;
	SA[0] = n;
	if (n <= 1) {
		if (n == 1) SA[1] = 0;
		return 0;
	}
	return sais_main(T, SA+1, 0, n, 256, 1);
}

/**
 * Constructs the burrows-wheeler transformed string of a given string.
 * @param T[0..n-1] The input string.
 * @param n The length of the given string.
 * @return The primary index if no error occurred, -1 or -2 otherwise.
 */
int is_bwt(ubyte_t *T, int n)
{
	int *SA, i, primary = 0;
	SA = (int*)calloc(n+1, sizeof(int));
	is_sa(T, SA, n);

	for (i = 0; i <= n; ++i) {
		if (SA[i] == 0) primary = i;
		else SA[i] = T[SA[i] - 1];
	}
	for (i = 0; i < primary; ++i) T[i] = SA[i];
	for (; i < n; ++i) T[i] = SA[i + 1];
	free(SA);
	return primary;
}
bwa-0.7.3a/kbtree.h000644 000767 000024 00000036713 12120745361 013726 0ustar00lh3staff000000 000000 /*-
 * Copyright 1997-1999, 2001, John-Mark Gurney.
 *           2008-2009, Attractive Chaos <attractor@live.co.uk>
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
 * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
 * OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 * OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
 * SUCH DAMAGE.
 */

#ifndef __AC_KBTREE_H
#define __AC_KBTREE_H

#include <stdlib.h>
#include <string.h>
#include <stdint.h>

typedef struct {
	int32_t is_internal:1, n:31;
} kbnode_t;

#define	__KB_KEY(type, x)	((type*)((char*)x + 4))
#define __KB_PTR(btr, x)	((kbnode_t**)((char*)x + btr->off_ptr))

#define __KB_TREE_T(name)						\
	typedef struct {							\
		kbnode_t *root;							\
		int	off_key, off_ptr, ilen, elen;		\
		int	n, t;								\
		int	n_keys, n_nodes;					\
	} kbtree_##name##_t;

#define __KB_INIT(name, key_t)											\
	kbtree_##name##_t *kb_init_##name(int size)							\
	{																	\
		kbtree_##name##_t *b;											\
		b = (kbtree_##name##_t*)calloc(1, sizeof(kbtree_##name##_t));	\
		b->t = ((size - 4 - sizeof(void*)) / (sizeof(void*) + sizeof(key_t)) + 1) >> 1; \
		if (b->t < 2) {													\
			free(b); return 0;											\
		}																\
		b->n = 2 * b->t - 1;											\
		b->off_ptr = 4 + b->n * sizeof(key_t);							\
		b->ilen = (4 + sizeof(void*) + b->n * (sizeof(void*) + sizeof(key_t)) + 3) >> 2 << 2; \
		b->elen = (b->off_ptr + 3) >> 2 << 2;							\
		b->root = (kbnode_t*)calloc(1, b->ilen);						\
		++b->n_nodes;													\
		return b;														\
	}

#define __kb_destroy(b) do {											\
		int i, max = 8;													\
		kbnode_t *x, **top, **stack = 0;								\
		if (b) {														\
			top = stack = (kbnode_t**)calloc(max, sizeof(kbnode_t*));	\
			*top++ = (b)->root;											\
			while (top != stack) {										\
				x = *--top;												\
				if (x->is_internal == 0) { free(x); continue; }			\
				for (i = 0; i <= x->n; ++i)								\
					if (__KB_PTR(b, x)[i]) {							\
						if (top - stack == max) {						\
							max <<= 1;									\
							stack = (kbnode_t**)realloc(stack, max * sizeof(kbnode_t*)); \
							top = stack + (max>>1);						\
						}												\
						*top++ = __KB_PTR(b, x)[i];						\
					}													\
				free(x);												\
			}															\
		}																\
		free(b); free(stack);											\
	} while (0)

#define __kb_get_first(key_t, b, ret) do {	\
		kbnode_t *__x = (b)->root;			\
		while (__KB_PTR(b, __x)[0] != 0)	\
			__x = __KB_PTR(b, __x)[0];		\
		(ret) = __KB_KEY(key_t, __x)[0];	\
	} while (0)

#define __KB_GET_AUX0(name, key_t, __cmp)								\
	static inline int __kb_get_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
	{																	\
		int tr, *rr, begin, end, n = x->n >> 1;							\
		if (x->n == 0) return -1;										\
		if (__cmp(*k, __KB_KEY(key_t, x)[n]) < 0) {						\
			begin = 0; end = n;											\
		} else { begin = n; end = x->n - 1; }							\
		rr = r? r : &tr;												\
		n = end;														\
		while (n >= begin && (*rr = __cmp(*k, __KB_KEY(key_t, x)[n])) < 0) --n; \
		return n;														\
	}

#define __KB_GET_AUX1(name, key_t, __cmp)								\
	static inline int __kb_getp_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
	{																	\
		int tr, *rr, begin = 0, end = x->n;								\
		if (x->n == 0) return -1;										\
		rr = r? r : &tr;												\
		while (begin < end) {											\
			int mid = (begin + end) >> 1;								\
			if (__cmp(__KB_KEY(key_t, x)[mid], *k) < 0) begin = mid + 1; \
			else end = mid;												\
		}																\
		if (begin == x->n) { *rr = 1; return x->n - 1; }				\
		if ((*rr = __cmp(*k, __KB_KEY(key_t, x)[begin])) < 0) --begin;	\
		return begin;													\
	}

#define __KB_GET(name, key_t)											\
	static key_t *kb_getp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
	{																	\
		int i, r = 0;													\
		kbnode_t *x = b->root;											\
		while (x) {														\
			i = __kb_getp_aux_##name(x, k, &r);							\
			if (i >= 0 && r == 0) return &__KB_KEY(key_t, x)[i];		\
			if (x->is_internal == 0) return 0;							\
			x = __KB_PTR(b, x)[i + 1];									\
		}																\
		return 0;														\
	}																	\
	static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \
	{																	\
		return kb_getp_##name(b, &k);									\
	}

#define __KB_INTERVAL(name, key_t)										\
	static void kb_intervalp_##name(kbtree_##name##_t *b, const key_t * __restrict k, key_t **lower, key_t **upper)	\
	{																	\
		int i, r = 0;													\
		kbnode_t *x = b->root;											\
		*lower = *upper = 0;											\
		while (x) {														\
			i = __kb_getp_aux_##name(x, k, &r);							\
			if (i >= 0 && r == 0) {										\
				*lower = *upper = &__KB_KEY(key_t, x)[i];				\
				return;													\
			}															\
			if (i >= 0) *lower = &__KB_KEY(key_t, x)[i];				\
			if (i < x->n - 1) *upper = &__KB_KEY(key_t, x)[i + 1];		\
			if (x->is_internal == 0) return;							\
			x = __KB_PTR(b, x)[i + 1];									\
		}																\
	}																	\
	static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \
	{																	\
		kb_intervalp_##name(b, &k, lower, upper);						\
	}

#define __KB_PUT(name, key_t, __cmp)									\
	/* x must be an internal node */									\
	static void __kb_split_##name(kbtree_##name##_t *b, kbnode_t *x, int i, kbnode_t *y) \
	{																	\
		kbnode_t *z;													\
		z = (kbnode_t*)calloc(1, y->is_internal? b->ilen : b->elen);	\
		++b->n_nodes;													\
		z->is_internal = y->is_internal;								\
		z->n = b->t - 1;												\
		memcpy(__KB_KEY(key_t, z), __KB_KEY(key_t, y) + b->t, sizeof(key_t) * (b->t - 1)); \
		if (y->is_internal) memcpy(__KB_PTR(b, z), __KB_PTR(b, y) + b->t, sizeof(void*) * b->t); \
		y->n = b->t - 1;												\
		memmove(__KB_PTR(b, x) + i + 2, __KB_PTR(b, x) + i + 1, sizeof(void*) * (x->n - i)); \
		__KB_PTR(b, x)[i + 1] = z;										\
		memmove(__KB_KEY(key_t, x) + i + 1, __KB_KEY(key_t, x) + i, sizeof(key_t) * (x->n - i)); \
		__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[b->t - 1];			\
		++x->n;															\
	}																	\
	static void __kb_putp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k) \
	{																	\
		int i = x->n - 1;												\
		if (x->is_internal == 0) {										\
			i = __kb_getp_aux_##name(x, k, 0);							\
			if (i != x->n - 1)											\
				memmove(__KB_KEY(key_t, x) + i + 2, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
			__KB_KEY(key_t, x)[i + 1] = *k;								\
			++x->n;														\
		} else {														\
			i = __kb_getp_aux_##name(x, k, 0) + 1;						\
			if (__KB_PTR(b, x)[i]->n == 2 * b->t - 1) {					\
				__kb_split_##name(b, x, i, __KB_PTR(b, x)[i]);			\
				if (__cmp(*k, __KB_KEY(key_t, x)[i]) > 0) ++i;			\
			}															\
			__kb_putp_aux_##name(b, __KB_PTR(b, x)[i], k);				\
		}																\
	}																	\
	static void kb_putp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
	{																	\
		kbnode_t *r, *s;												\
		++b->n_keys;													\
		r = b->root;													\
		if (r->n == 2 * b->t - 1) {										\
			++b->n_nodes;												\
			s = (kbnode_t*)calloc(1, b->ilen);							\
			b->root = s; s->is_internal = 1; s->n = 0;					\
			__KB_PTR(b, s)[0] = r;										\
			__kb_split_##name(b, s, 0, r);								\
			r = s;														\
		}																\
		__kb_putp_aux_##name(b, r, k);									\
	}																	\
	static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \
	{																	\
		kb_putp_##name(b, &k);											\
	}


#define __KB_DEL(name, key_t)											\
	static key_t __kb_delp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k, int s) \
	{																	\
		int yn, zn, i, r = 0;											\
		kbnode_t *xp, *y, *z;											\
		key_t kp;														\
		if (x == 0) return *k;											\
		if (s) { /* s can only be 0, 1 or 2 */							\
			r = x->is_internal == 0? 0 : s == 1? 1 : -1;				\
			i = s == 1? x->n - 1 : -1;									\
		} else i = __kb_getp_aux_##name(x, k, &r);						\
		if (x->is_internal == 0) {										\
			if (s == 2) ++i;											\
			kp = __KB_KEY(key_t, x)[i];									\
			memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
			--x->n;														\
			return kp;													\
		}																\
		if (r == 0) {													\
			if ((yn = __KB_PTR(b, x)[i]->n) >= b->t) {					\
				xp = __KB_PTR(b, x)[i];									\
				kp = __KB_KEY(key_t, x)[i];								\
				__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 1); \
				return kp;												\
			} else if ((zn = __KB_PTR(b, x)[i + 1]->n) >= b->t) {		\
				xp = __KB_PTR(b, x)[i + 1];								\
				kp = __KB_KEY(key_t, x)[i];								\
				__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 2); \
				return kp;												\
			} else if (yn == b->t - 1 && zn == b->t - 1) {				\
				y = __KB_PTR(b, x)[i]; z = __KB_PTR(b, x)[i + 1];		\
				__KB_KEY(key_t, y)[y->n++] = *k;						\
				memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, z), z->n * sizeof(key_t)); \
				if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, z), (z->n + 1) * sizeof(void*)); \
				y->n += z->n;											\
				memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
				memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
				--x->n;													\
				free(z);												\
				return __kb_delp_aux_##name(b, y, k, s);				\
			}															\
		}																\
		++i;															\
		if ((xp = __KB_PTR(b, x)[i])->n == b->t - 1) {					\
			if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n >= b->t) {		\
				memmove(__KB_KEY(key_t, xp) + 1, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
				if (xp->is_internal) memmove(__KB_PTR(b, xp) + 1, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
				__KB_KEY(key_t, xp)[0] = __KB_KEY(key_t, x)[i - 1];		\
				__KB_KEY(key_t, x)[i - 1] = __KB_KEY(key_t, y)[y->n - 1]; \
				if (xp->is_internal) __KB_PTR(b, xp)[0] = __KB_PTR(b, y)[y->n]; \
				--y->n; ++xp->n;										\
			} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n >= b->t) { \
				__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i];	\
				__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[0];			\
				if (xp->is_internal) __KB_PTR(b, xp)[xp->n] = __KB_PTR(b, y)[0]; \
				--y->n;													\
				memmove(__KB_KEY(key_t, y), __KB_KEY(key_t, y) + 1, y->n * sizeof(key_t)); \
				if (y->is_internal) memmove(__KB_PTR(b, y), __KB_PTR(b, y) + 1, (y->n + 1) * sizeof(void*)); \
			} else if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n == b->t - 1) { \
				__KB_KEY(key_t, y)[y->n++] = __KB_KEY(key_t, x)[i - 1];	\
				memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, xp), xp->n * sizeof(key_t));	\
				if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
				y->n += xp->n;											\
				memmove(__KB_KEY(key_t, x) + i - 1, __KB_KEY(key_t, x) + i, (x->n - i) * sizeof(key_t)); \
				memmove(__KB_PTR(b, x) + i, __KB_PTR(b, x) + i + 1, (x->n - i) * sizeof(void*)); \
				--x->n;													\
				free(xp);												\
				xp = y;													\
			} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n == b->t - 1) { \
				__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i];	\
				memmove(__KB_KEY(key_t, xp) + xp->n, __KB_KEY(key_t, y), y->n * sizeof(key_t));	\
				if (xp->is_internal) memmove(__KB_PTR(b, xp) + xp->n, __KB_PTR(b, y), (y->n + 1) * sizeof(void*)); \
				xp->n += y->n;											\
				memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
				memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
				--x->n;													\
				free(y);												\
			}															\
		}																\
		return __kb_delp_aux_##name(b, xp, k, s);						\
	}																	\
	static key_t kb_delp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
	{																	\
		kbnode_t *x;													\
		key_t ret;														\
		ret = __kb_delp_aux_##name(b, b->root, k, 0);					\
		--b->n_keys;													\
		if (b->root->n == 0 && b->root->is_internal) {					\
			--b->n_nodes;												\
			x = b->root;												\
			b->root = __KB_PTR(b, x)[0];								\
			free(x);													\
		}																\
		return ret;														\
	}																	\
	static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \
	{																	\
		return kb_delp_##name(b, &k);									\
	}

typedef struct {
	kbnode_t *x;
	int i;
} __kbstack_t;

#define __kb_traverse(key_t, b, __func) do {							\
		int __kmax = 8;													\
		__kbstack_t *__kstack, *__kp;									\
		__kp = __kstack = (__kbstack_t*)calloc(__kmax, sizeof(__kbstack_t)); \
		__kp->x = (b)->root; __kp->i = 0;								\
		for (;;) {														\
			while (__kp->x && __kp->i <= __kp->x->n) {					\
				if (__kp - __kstack == __kmax - 1) {					\
					__kmax <<= 1;										\
					__kstack = (__kbstack_t*)realloc(__kstack, __kmax * sizeof(__kbstack_t)); \
					__kp = __kstack + (__kmax>>1) - 1;					\
				}														\
				(__kp+1)->i = 0; (__kp+1)->x = __kp->x->is_internal? __KB_PTR(b, __kp->x)[__kp->i] : 0; \
				++__kp;													\
			}															\
			--__kp;														\
			if (__kp >= __kstack) {										\
				if (__kp->x && __kp->i < __kp->x->n) __func(&__KB_KEY(key_t, __kp->x)[__kp->i]); \
				++__kp->i;												\
			} else break;												\
		}																\
		free(__kstack);													\
	} while (0)

#define KBTREE_INIT(name, key_t, __cmp)			\
	__KB_TREE_T(name)							\
	__KB_INIT(name, key_t)						\
	__KB_GET_AUX1(name, key_t, __cmp)			\
	__KB_GET(name, key_t)						\
	__KB_INTERVAL(name, key_t)					\
	__KB_PUT(name, key_t, __cmp)				\
	__KB_DEL(name, key_t)

#define KB_DEFAULT_SIZE 512

#define kbtree_t(name) kbtree_##name##_t
#define kb_init(name, s) kb_init_##name(s)
#define kb_destroy(name, b) __kb_destroy(b)
#define kb_get(name, b, k) kb_get_##name(b, k)
#define kb_put(name, b, k) kb_put_##name(b, k)
#define kb_del(name, b, k) kb_del_##name(b, k)
#define kb_interval(name, b, k, l, u) kb_interval_##name(b, k, l, u)
#define kb_getp(name, b, k) kb_getp_##name(b, k)
#define kb_putp(name, b, k) kb_putp_##name(b, k)
#define kb_delp(name, b, k) kb_delp_##name(b, k)
#define kb_intervalp(name, b, k, l, u) kb_intervalp_##name(b, k, l, u)

#define kb_size(b) ((b)->n_keys)

#define kb_generic_cmp(a, b) (((b) < (a)) - ((a) < (b)))
#define kb_str_cmp(a, b) strcmp(a, b)

#endif
bwa-0.7.3a/khash.h000644 000767 000024 00000050532 12120745361 013543 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor@live.co.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/*
  An example:

#include "khash.h"
KHASH_MAP_INIT_INT(32, char)
int main() {
	int ret, is_missing;
	khiter_t k;
	khash_t(32) *h = kh_init(32);
	k = kh_put(32, h, 5, &ret);
	kh_value(h, k) = 10;
	k = kh_get(32, h, 10);
	is_missing = (k == kh_end(h));
	k = kh_get(32, h, 5);
	kh_del(32, h, k);
	for (k = kh_begin(h); k != kh_end(h); ++k)
		if (kh_exist(h, k)) kh_value(h, k) = 1;
	kh_destroy(32, h);
	return 0;
}
*/

/*
  2011-12-29 (0.2.7):

    * Minor code clean up; no actual effect.

  2011-09-16 (0.2.6):

	* The capacity is a power of 2. This seems to dramatically improve the
	  speed for simple keys. Thank Zilong Tan for the suggestion. Reference:

	   - http://code.google.com/p/ulib/
	   - http://nothings.org/computer/judy/

	* Allow to optionally use linear probing which usually has better
	  performance for random input. Double hashing is still the default as it
	  is more robust to certain non-random input.

	* Added Wang's integer hash function (not used by default). This hash
	  function is more robust to certain non-random input.

  2011-02-14 (0.2.5):

    * Allow to declare global functions.

  2009-09-26 (0.2.4):

    * Improve portability

  2008-09-19 (0.2.3):

	* Corrected the example
	* Improved interfaces

  2008-09-11 (0.2.2):

	* Improved speed a little in kh_put()

  2008-09-10 (0.2.1):

	* Added kh_clear()
	* Fixed a compiling error

  2008-09-02 (0.2.0):

	* Changed to token concatenation which increases flexibility.

  2008-08-31 (0.1.2):

	* Fixed a bug in kh_get(), which has not been tested previously.

  2008-08-31 (0.1.1):

	* Added destructor
*/


#ifndef __AC_KHASH_H
#define __AC_KHASH_H

/*!
  @header

  Generic hash table library.
 */

#define AC_VERSION_KHASH_H "0.2.6"

#include <stdlib.h>
#include <string.h>
#include <limits.h>

/* compipler specific configuration */

#if UINT_MAX == 0xffffffffu
typedef unsigned int khint32_t;
#elif ULONG_MAX == 0xffffffffu
typedef unsigned long khint32_t;
#endif

#if ULONG_MAX == ULLONG_MAX
typedef unsigned long khint64_t;
#else
typedef unsigned long long khint64_t;
#endif

#ifdef _MSC_VER
#define kh_inline __inline
#else
#define kh_inline inline
#endif

typedef khint32_t khint_t;
typedef khint_t khiter_t;

#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))

#ifdef KHASH_LINEAR
#define __ac_inc(k, m) 1
#else
#define __ac_inc(k, m) (((k)>>3 ^ (k)<<3) | 1) & (m)
#endif

#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4)

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#ifndef kcalloc
#define kcalloc(N,Z) calloc(N,Z)
#endif
#ifndef kmalloc
#define kmalloc(Z) malloc(Z)
#endif
#ifndef krealloc
#define krealloc(P,Z) realloc(P,Z)
#endif
#ifndef kfree
#define kfree(P) free(P)
#endif

static const double __ac_HASH_UPPER = 0.77;

#define __KHASH_TYPE(name, khkey_t, khval_t) \
	typedef struct { \
		khint_t n_buckets, size, n_occupied, upper_bound; \
		khint32_t *flags; \
		khkey_t *keys; \
		khval_t *vals; \
	} kh_##name##_t;

#define __KHASH_PROTOTYPES(name, khkey_t, khval_t)	 					\
	extern kh_##name##_t *kh_init_##name(void);							\
	extern void kh_destroy_##name(kh_##name##_t *h);					\
	extern void kh_clear_##name(kh_##name##_t *h);						\
	extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); 	\
	extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
	extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
	extern void kh_del_##name(kh_##name##_t *h, khint_t x);

#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
	SCOPE kh_##name##_t *kh_init_##name(void) {							\
		return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t));		\
	}																	\
	SCOPE void kh_destroy_##name(kh_##name##_t *h)						\
	{																	\
		if (h) {														\
			kfree((void *)h->keys); kfree(h->flags);					\
			kfree((void *)h->vals);										\
			kfree(h);													\
		}																\
	}																	\
	SCOPE void kh_clear_##name(kh_##name##_t *h)						\
	{																	\
		if (h && h->flags) {											\
			memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \
			h->size = h->n_occupied = 0;								\
		}																\
	}																	\
	SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) 	\
	{																	\
		if (h->n_buckets) {												\
			khint_t inc, k, i, last, mask;								\
			mask = h->n_buckets - 1;									\
			k = __hash_func(key); i = k & mask;							\
			inc = __ac_inc(k, mask); last = i; /* inc==1 for linear probing */ \
			while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
				i = (i + inc) & mask; 									\
				if (i == last) return h->n_buckets;						\
			}															\
			return __ac_iseither(h->flags, i)? h->n_buckets : i;		\
		} else return 0;												\
	}																	\
	SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
	{ /* This function uses 0.25*n_bucktes bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \
		khint32_t *new_flags = 0;										\
		khint_t j = 1;													\
		{																\
			kroundup32(new_n_buckets); 									\
			if (new_n_buckets < 4) new_n_buckets = 4;					\
			if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0;	/* requested size is too small */ \
			else { /* hash table size to be changed (shrink or expand); rehash */ \
				new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t));	\
				if (!new_flags) return -1;								\
				memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \
				if (h->n_buckets < new_n_buckets) {	/* expand */		\
					khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
					if (!new_keys) return -1;							\
					h->keys = new_keys;									\
					if (kh_is_map) {									\
						khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
						if (!new_vals) return -1;						\
						h->vals = new_vals;								\
					}													\
				} /* otherwise shrink */								\
			}															\
		}																\
		if (j) { /* rehashing is needed */								\
			for (j = 0; j != h->n_buckets; ++j) {						\
				if (__ac_iseither(h->flags, j) == 0) {					\
					khkey_t key = h->keys[j];							\
					khval_t val;										\
					khint_t new_mask;									\
					new_mask = new_n_buckets - 1; 						\
					if (kh_is_map) val = h->vals[j];					\
					__ac_set_isdel_true(h->flags, j);					\
					while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \
						khint_t inc, k, i;								\
						k = __hash_func(key);							\
						i = k & new_mask;								\
						inc = __ac_inc(k, new_mask);					\
						while (!__ac_isempty(new_flags, i)) i = (i + inc) & new_mask; \
						__ac_set_isempty_false(new_flags, i);			\
						if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \
							{ khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
							if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
							__ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \
						} else { /* write the element and jump out of the loop */ \
							h->keys[i] = key;							\
							if (kh_is_map) h->vals[i] = val;			\
							break;										\
						}												\
					}													\
				}														\
			}															\
			if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \
				h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
				if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
			}															\
			kfree(h->flags); /* free the working space */				\
			h->flags = new_flags;										\
			h->n_buckets = new_n_buckets;								\
			h->n_occupied = h->size;									\
			h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
		}																\
		return 0;														\
	}																	\
	SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
	{																	\
		khint_t x;														\
		if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \
			if (h->n_buckets > (h->size<<1)) {							\
				if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \
					*ret = -1; return h->n_buckets;						\
				}														\
			} else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \
				*ret = -1; return h->n_buckets;							\
			}															\
		} /* TODO: to implement automatically shrinking; resize() already support shrinking */ \
		{																\
			khint_t inc, k, i, site, last, mask = h->n_buckets - 1;		\
			x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \
			if (__ac_isempty(h->flags, i)) x = i; /* for speed up */	\
			else {														\
				inc = __ac_inc(k, mask); last = i;						\
				while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
					if (__ac_isdel(h->flags, i)) site = i;				\
					i = (i + inc) & mask; 								\
					if (i == last) { x = site; break; }					\
				}														\
				if (x == h->n_buckets) {								\
					if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
					else x = i;											\
				}														\
			}															\
		}																\
		if (__ac_isempty(h->flags, x)) { /* not present at all */		\
			h->keys[x] = key;											\
			__ac_set_isboth_false(h->flags, x);							\
			++h->size; ++h->n_occupied;									\
			*ret = 1;													\
		} else if (__ac_isdel(h->flags, x)) { /* deleted */				\
			h->keys[x] = key;											\
			__ac_set_isboth_false(h->flags, x);							\
			++h->size;													\
			*ret = 2;													\
		} else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \
		return x;														\
	}																	\
	SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)				\
	{																	\
		if (x != h->n_buckets && !__ac_iseither(h->flags, x)) {			\
			__ac_set_isdel_true(h->flags, x);							\
			--h->size;													\
		}																\
	}

#define KHASH_DECLARE(name, khkey_t, khval_t)		 					\
	__KHASH_TYPE(name, khkey_t, khval_t) 								\
	__KHASH_PROTOTYPES(name, khkey_t, khval_t)

#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
	__KHASH_TYPE(name, khkey_t, khval_t) 								\
	__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)

#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
	KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)

/* --- BEGIN OF HASH FUNCTIONS --- */

/*! @function
  @abstract     Integer hash function
  @param  key   The integer [khint32_t]
  @return       The hash value [khint_t]
 */
#define kh_int_hash_func(key) (khint32_t)(key)
/*! @function
  @abstract     Integer comparison function
 */
#define kh_int_hash_equal(a, b) ((a) == (b))
/*! @function
  @abstract     64-bit integer hash function
  @param  key   The integer [khint64_t]
  @return       The hash value [khint_t]
 */
#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
/*! @function
  @abstract     64-bit integer comparison function
 */
#define kh_int64_hash_equal(a, b) ((a) == (b))
/*! @function
  @abstract     const char* hash function
  @param  s     Pointer to a null terminated string
  @return       The hash value
 */
static kh_inline khint_t __ac_X31_hash_string(const char *s)
{
	khint_t h = (khint_t)*s;
	if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s;
	return h;
}
/*! @function
  @abstract     Another interface to const char* hash function
  @param  key   Pointer to a null terminated string [const char*]
  @return       The hash value [khint_t]
 */
#define kh_str_hash_func(key) __ac_X31_hash_string(key)
/*! @function
  @abstract     Const char* comparison function
 */
#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)

static kh_inline khint_t __ac_Wang_hash(khint_t key)
{
    key += ~(key << 15);
    key ^=  (key >> 10);
    key +=  (key << 3);
    key ^=  (key >> 6);
    key += ~(key << 11);
    key ^=  (key >> 16);
    return key;
}
#define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key)

/* --- END OF HASH FUNCTIONS --- */

/* Other convenient macros... */

/*!
  @abstract Type of the hash table.
  @param  name  Name of the hash table [symbol]
 */
#define khash_t(name) kh_##name##_t

/*! @function
  @abstract     Initiate a hash table.
  @param  name  Name of the hash table [symbol]
  @return       Pointer to the hash table [khash_t(name)*]
 */
#define kh_init(name) kh_init_##name()

/*! @function
  @abstract     Destroy a hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
 */
#define kh_destroy(name, h) kh_destroy_##name(h)

/*! @function
  @abstract     Reset a hash table without deallocating memory.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
 */
#define kh_clear(name, h) kh_clear_##name(h)

/*! @function
  @abstract     Resize a hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  s     New size [khint_t]
 */
#define kh_resize(name, h, s) kh_resize_##name(h, s)

/*! @function
  @abstract     Insert a key to the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Key [type of keys]
  @param  r     Extra return code: 0 if the key is present in the hash table;
                1 if the bucket is empty (never used); 2 if the element in
				the bucket has been deleted [int*]
  @return       Iterator to the inserted element [khint_t]
 */
#define kh_put(name, h, k, r) kh_put_##name(h, k, r)

/*! @function
  @abstract     Retrieve a key from the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Key [type of keys]
  @return       Iterator to the found element, or kh_end(h) is the element is absent [khint_t]
 */
#define kh_get(name, h, k) kh_get_##name(h, k)

/*! @function
  @abstract     Remove a key from the hash table.
  @param  name  Name of the hash table [symbol]
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  k     Iterator to the element to be deleted [khint_t]
 */
#define kh_del(name, h, k) kh_del_##name(h, k)

/*! @function
  @abstract     Test whether a bucket contains data.
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       1 if containing data; 0 otherwise [int]
 */
#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))

/*! @function
  @abstract     Get key given an iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       Key [type of keys]
 */
#define kh_key(h, x) ((h)->keys[x])

/*! @function
  @abstract     Get value given an iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  x     Iterator to the bucket [khint_t]
  @return       Value [type of values]
  @discussion   For hash sets, calling this results in segfault.
 */
#define kh_val(h, x) ((h)->vals[x])

/*! @function
  @abstract     Alias of kh_val()
 */
#define kh_value(h, x) ((h)->vals[x])

/*! @function
  @abstract     Get the start iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       The start iterator [khint_t]
 */
#define kh_begin(h) (khint_t)(0)

/*! @function
  @abstract     Get the end iterator
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       The end iterator [khint_t]
 */
#define kh_end(h) ((h)->n_buckets)

/*! @function
  @abstract     Get the number of elements in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       Number of elements in the hash table [khint_t]
 */
#define kh_size(h) ((h)->size)

/*! @function
  @abstract     Get the number of buckets in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @return       Number of buckets in the hash table [khint_t]
 */
#define kh_n_buckets(h) ((h)->n_buckets)

/*! @function
  @abstract     Iterate over the entries in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  kvar  Variable to which key will be assigned
  @param  vvar  Variable to which value will be assigned
  @param  code  Block of code to execute
 */
#define kh_foreach(h, kvar, vvar, code) { khint_t __i;		\
	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
		if (!kh_exist(h,__i)) continue;						\
		(kvar) = kh_key(h,__i);								\
		(vvar) = kh_val(h,__i);								\
		code;												\
	} }

/*! @function
  @abstract     Iterate over the values in the hash table
  @param  h     Pointer to the hash table [khash_t(name)*]
  @param  vvar  Variable to which value will be assigned
  @param  code  Block of code to execute
 */
#define kh_foreach_value(h, vvar, code) { khint_t __i;		\
	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
		if (!kh_exist(h,__i)) continue;						\
		(vvar) = kh_val(h,__i);								\
		code;												\
	} }

/* More conenient interfaces */

/*! @function
  @abstract     Instantiate a hash set containing integer keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_INT(name)										\
	KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing integer keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_INT(name, khval_t)								\
	KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing 64-bit integer keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_INT64(name)										\
	KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing 64-bit integer keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_INT64(name, khval_t)								\
	KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)

typedef const char *kh_cstr_t;
/*! @function
  @abstract     Instantiate a hash map containing const char* keys
  @param  name  Name of the hash table [symbol]
 */
#define KHASH_SET_INIT_STR(name)										\
	KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)

/*! @function
  @abstract     Instantiate a hash map containing const char* keys
  @param  name  Name of the hash table [symbol]
  @param  khval_t  Type of values [type]
 */
#define KHASH_MAP_INIT_STR(name, khval_t)								\
	KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)

#endif /* __AC_KHASH_H */
bwa-0.7.3a/kopen.c000644 000767 000024 00000021570 12120745361 013554 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <fcntl.h>
#include <errno.h>
#include <ctype.h>
#include <unistd.h>
#include <string.h>
#include <stdlib.h>
#include <signal.h>
#include <sys/wait.h>
#include <sys/types.h>
#ifndef _WIN32
#include <netdb.h>
#include <arpa/inet.h>
#include <sys/socket.h>
#endif

#ifdef _WIN32
#define _KO_NO_NET
#endif

#ifndef _KO_NO_NET
static int socket_wait(int fd, int is_read)
{
	fd_set fds, *fdr = 0, *fdw = 0;
	struct timeval tv;
	int ret;
	tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
	FD_ZERO(&fds);
	FD_SET(fd, &fds);
	if (is_read) fdr = &fds;
	else fdw = &fds;
	ret = select(fd+1, fdr, fdw, 0, &tv);
	if (ret == -1) perror("select");
	return ret;
}

static int socket_connect(const char *host, const char *port)
{
#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)

	int on = 1, fd;
	struct linger lng = { 0, 0 };
	struct addrinfo hints, *res = 0;
	memset(&hints, 0, sizeof(struct addrinfo));
	hints.ai_family = AF_UNSPEC;
	hints.ai_socktype = SOCK_STREAM;
	if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
	if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
	if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
	freeaddrinfo(res);
	return fd;
#undef __err_connect
}

static int http_open(const char *fn)
{
	char *p, *proxy, *q, *http_host, *host, *port, *path, *buf;
	int fd, ret, l;

	/* parse URL; adapted from khttp_parse_url() in knetfile.c */
	if (strstr(fn, "http://") != fn) return 0;
	// set ->http_host
	for (p = (char*)fn + 7; *p && *p != '/'; ++p);
	l = p - fn - 7;
	http_host = calloc(l + 1, 1);
	strncpy(http_host, fn + 7, l);
	http_host[l] = 0;
	for (q = http_host; *q && *q != ':'; ++q);
	if (*q == ':') *q++ = 0;
	// get http_proxy
	proxy = getenv("http_proxy");
	// set host, port and path
	if (proxy == 0) {
		host = strdup(http_host); // when there is no proxy, server name is identical to http_host name.
		port = strdup(*q? q : "80");
		path = strdup(*p? p : "/");
	} else {
		host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
		for (q = host; *q && *q != ':'; ++q);
		if (*q == ':') *q++ = 0; 
		port = strdup(*q? q : "80");
		path = strdup(fn);
	}

	/* connect; adapted from khttp_connect() in knetfile.c */
	l = 0;
	fd = socket_connect(host, port);
	buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
	l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", path, http_host);
	l += sprintf(buf + l, "\r\n");
	write(fd, buf, l);
	l = 0;
	while (read(fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
		if (buf[l] == '\n' && l >= 3)
			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
		++l;
	}
	buf[l] = 0;
	if (l < 14) { // prematured header
		close(fd);
		fd = -1;
	}
	ret = strtol(buf + 8, &p, 0); // HTTP return code
	if (ret != 200) {
		close(fd);
		fd = -1;
	}
	free(buf); free(http_host); free(host); free(port); free(path);
	return fd;
}

typedef struct {
	int max_response, ctrl_fd;
	char *response;
} ftpaux_t;

static int kftp_get_response(ftpaux_t *aux)
{
	unsigned char c;
	int n = 0;
	char *p;
	if (socket_wait(aux->ctrl_fd, 1) <= 0) return 0;
	while (read(aux->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
		if (n >= aux->max_response) {
			aux->max_response = aux->max_response? aux->max_response<<1 : 256;
			aux->response = realloc(aux->response, aux->max_response);
		}
		aux->response[n++] = c;
		if (c == '\n') {
			if (n >= 4 && isdigit(aux->response[0]) && isdigit(aux->response[1]) && isdigit(aux->response[2])
				&& aux->response[3] != '-') break;
			n = 0;
			continue;
		}
	}
	if (n < 2) return -1;
	aux->response[n-2] = 0;
	return strtol(aux->response, &p, 0);
}

static int kftp_send_cmd(ftpaux_t *aux, const char *cmd, int is_get)
{
	if (socket_wait(aux->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
	write(aux->ctrl_fd, cmd, strlen(cmd));
	return is_get? kftp_get_response(aux) : 0;
}

static int ftp_open(const char *fn)
{
	char *p, *host = 0, *port = 0, *retr = 0;
	char host2[80], port2[10];
	int v[6], l, fd = -1, ret, pasv_port, pasv_ip[4];
	ftpaux_t aux;
	
	/* parse URL */
	if (strstr(fn, "ftp://") != fn) return 0;
	for (p = (char*)fn + 6; *p && *p != '/'; ++p);
	if (*p != '/') return 0;
	l = p - fn - 6;
	port = strdup("21");
	host = calloc(l + 1, 1);
	strncpy(host, fn + 6, l);
	retr = calloc(strlen(p) + 8, 1);
	sprintf(retr, "RETR %s\r\n", p);
	
	/* connect to ctrl */
	memset(&aux, 0, sizeof(ftpaux_t));
	aux.ctrl_fd = socket_connect(host, port);
	if (aux.ctrl_fd == -1) goto ftp_open_end; /* fail to connect ctrl */

	/* connect to the data stream */
	kftp_get_response(&aux);
	kftp_send_cmd(&aux, "USER anonymous\r\n", 1);
	kftp_send_cmd(&aux, "PASS kopen@\r\n", 1);
	kftp_send_cmd(&aux, "TYPE I\r\n", 1);
	kftp_send_cmd(&aux, "PASV\r\n", 1);
	for (p = aux.response; *p && *p != '('; ++p);
	if (*p != '(') goto ftp_open_end;
	++p;
	sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
	memcpy(pasv_ip, v, 4 * sizeof(int));
	pasv_port = (v[4]<<8&0xff00) + v[5];
	kftp_send_cmd(&aux, retr, 0);
	sprintf(host2, "%d.%d.%d.%d", pasv_ip[0], pasv_ip[1], pasv_ip[2], pasv_ip[3]);
	sprintf(port2, "%d", pasv_port);
	fd = socket_connect(host2, port2);
	if (fd == -1) goto ftp_open_end;
	ret = kftp_get_response(&aux);
	if (ret != 150) {
		close(fd);
		fd = -1;
	}
	close(aux.ctrl_fd);

ftp_open_end:
	free(host); free(port); free(retr); free(aux.response);
	return fd;
}
#endif /* !defined(_KO_NO_NET) */

static char **cmd2argv(const char *cmd)
{
	int i, beg, end, argc;
	char **argv, *str;
	end = strlen(cmd);
	for (i = end - 1; i >= 0; --i)
		if (!isspace(cmd[i])) break;
	end = i + 1;
	for (beg = 0; beg < end; ++beg)
		if (!isspace(cmd[beg])) break;
	if (beg == end) return 0;
	for (i = beg + 1, argc = 0; i < end; ++i)
		if (isspace(cmd[i]) && !isspace(cmd[i-1]))
			++argc;
	argv = (char**)calloc(argc + 2, sizeof(void*));
	argv[0] = str = (char*)calloc(end - beg + 1, 1);
	strncpy(argv[0], cmd + beg, end - beg);
	for (i = argc = 1; i < end - beg; ++i)
		if (isspace(str[i])) str[i] = 0;
		else if (str[i] && str[i-1] == 0) argv[argc++] = &str[i];
	return argv;
}

#define KO_STDIN    1
#define KO_FILE     2
#define KO_PIPE     3
#define KO_HTTP     4
#define KO_FTP      5

typedef struct {
	int type, fd;
	pid_t pid;
} koaux_t;

void *kopen(const char *fn, int *_fd)
{
	koaux_t *aux = 0;
	*_fd = -1;
	if (strstr(fn, "http://") == fn) {
		aux = calloc(1, sizeof(koaux_t));
		aux->type = KO_HTTP;
		aux->fd = http_open(fn);
	} else if (strstr(fn, "ftp://") == fn) {
		aux = calloc(1, sizeof(koaux_t));
		aux->type = KO_FTP;
		aux->fd = ftp_open(fn);
	} else if (strcmp(fn, "-") == 0) {
		aux = calloc(1, sizeof(koaux_t));
		aux->type = KO_STDIN;
		aux->fd = STDIN_FILENO;
	} else {
		const char *p, *q;
		for (p = fn; *p; ++p)
			if (!isspace(*p)) break;
		if (*p == '<') { // pipe open
			int need_shell, pfd[2];
			pid_t pid;
			// a simple check to see if we need to invoke a shell; not always working
			for (q = p + 1; *q; ++q)
				if (ispunct(*q) && *q != '.' && *q != '_' && *q != '-' && *q != ':')
					break;
			need_shell = (*q != 0);
			pipe(pfd);
			pid = vfork();
			if (pid == -1) { /* vfork() error */
				close(pfd[0]); close(pfd[1]);
				return 0;
			}
			if (pid == 0) { /* the child process */
				char **argv; /* FIXME: I do not know if this will lead to a memory leak */
				close(pfd[0]);
				dup2(pfd[1], STDOUT_FILENO);
				close(pfd[1]);
				if (!need_shell) {
					argv = cmd2argv(p + 1);
					execvp(argv[0], argv);
					free(argv[0]); free(argv);
				} else execl("/bin/sh", "sh", "-c", p + 1, NULL);
				exit(1);
			} else { /* parent process */
				close(pfd[1]);
				aux = calloc(1, sizeof(koaux_t));
				aux->type = KO_PIPE;
				aux->fd = pfd[0];
				aux->pid = pid;
			}
		} else {
#ifdef _WIN32
			*_fd = open(fn, O_RDONLY | O_BINARY);
#else
			*_fd = open(fn, O_RDONLY);
#endif
			if (*_fd) {
				aux = calloc(1, sizeof(koaux_t));
				aux->type = KO_FILE;
				aux->fd = *_fd;
			}
		}
	}
	*_fd = aux->fd;
	return aux;
}

int kclose(void *a)
{
	koaux_t *aux = (koaux_t*)a;
	if (aux->type == KO_PIPE) {
		int status;
		pid_t pid;
		pid = waitpid(aux->pid, &status, WNOHANG);
		if (pid != aux->pid) kill(aux->pid, 15);
	}
	free(aux);
	return 0;
}

#ifdef _KO_MAIN
#define BUF_SIZE 0x10000
int main(int argc, char *argv[])
{
	void *x;
	int l, fd;
	unsigned char buf[BUF_SIZE];
	FILE *fp;
	if (argc == 1) {
		fprintf(stderr, "Usage: kopen <file>\n");
		return 1;
	}
	x = kopen(argv[1], &fd);
	fp = fdopen(fd, "r");
	if (fp == 0) {
		fprintf(stderr, "ERROR: fail to open the input\n");
		return 1;
	}
	do {
		if ((l = fread(buf, 1, BUF_SIZE, fp)) != 0)
			fwrite(buf, 1, l, stdout);
	} while (l == BUF_SIZE);
	fclose(fp);
	kclose(x);
	return 0;
}
#endif
bwa-0.7.3a/kseq.h000644 000767 000024 00000021153 12120745361 013405 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor@live.co.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Last Modified: 05MAR2012 */

#ifndef AC_KSEQ_H
#define AC_KSEQ_H

#include <ctype.h>
#include <string.h>
#include <stdlib.h>

#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
#define KS_SEP_TAB   1 // isspace() && !' '
#define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
#define KS_SEP_MAX   2

#define __KS_TYPE(type_t)						\
	typedef struct __kstream_t {				\
		unsigned char *buf;						\
		int begin, end, is_eof;					\
		type_t f;								\
	} kstream_t;

#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)

#define __KS_BASIC(type_t, __bufsize)								\
	static inline kstream_t *ks_init(type_t f)						\
	{																\
		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
		ks->f = f;													\
		ks->buf = (unsigned char*)malloc(__bufsize);				\
		return ks;													\
	}																\
	static inline void ks_destroy(kstream_t *ks)					\
	{																\
		if (ks) {													\
			free(ks->buf);											\
			free(ks);												\
		}															\
	}

#define __KS_GETC(__read, __bufsize)						\
	static inline int ks_getc(kstream_t *ks)				\
	{														\
		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
		if (ks->begin >= ks->end) {							\
			ks->begin = 0;									\
			ks->end = __read(ks->f, ks->buf, __bufsize);	\
			if (ks->end < __bufsize) ks->is_eof = 1;		\
			if (ks->end == 0) return -1;					\
		}													\
		return (int)ks->buf[ks->begin++];					\
	}

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
	size_t l, m;
	char *s;
} kstring_t;
#endif

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#define __KS_GETUNTIL(__read, __bufsize)								\
	static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
	{																	\
		if (dret) *dret = 0;											\
		str->l = append? str->l : 0;									\
		if (ks->begin >= ks->end && ks->is_eof) return -1;				\
		for (;;) {														\
			int i;														\
			if (ks->begin >= ks->end) {									\
				if (!ks->is_eof) {										\
					ks->begin = 0;										\
					ks->end = __read(ks->f, ks->buf, __bufsize);		\
					if (ks->end < __bufsize) ks->is_eof = 1;			\
					if (ks->end == 0) break;							\
				} else break;											\
			}															\
			if (delimiter == KS_SEP_LINE) { \
				for (i = ks->begin; i < ks->end; ++i) \
					if (ks->buf[i] == '\n') break; \
			} else if (delimiter > KS_SEP_MAX) {						\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (ks->buf[i] == delimiter) break;					\
			} else if (delimiter == KS_SEP_SPACE) {						\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (isspace(ks->buf[i])) break;						\
			} else if (delimiter == KS_SEP_TAB) {						\
				for (i = ks->begin; i < ks->end; ++i)					\
					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
			} else i = 0; /* never come to here! */						\
			if (str->m - str->l < (size_t)(i - ks->begin + 1)) {		\
				str->m = str->l + (i - ks->begin) + 1;					\
				kroundup32(str->m);										\
				str->s = (char*)realloc(str->s, str->m);				\
			}															\
			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
			str->l = str->l + (i - ks->begin);							\
			ks->begin = i + 1;											\
			if (i < ks->end) {											\
				if (dret) *dret = ks->buf[i];							\
				break;													\
			}															\
		}																\
		if (str->s == 0) {												\
			str->m = 1;													\
			str->s = (char*)calloc(1, 1);								\
		} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
		str->s[str->l] = '\0';											\
		return str->l;													\
	} \
	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }

#define KSTREAM_INIT(type_t, __read, __bufsize) \
	__KS_TYPE(type_t)							\
	__KS_BASIC(type_t, __bufsize)				\
	__KS_GETC(__read, __bufsize)				\
	__KS_GETUNTIL(__read, __bufsize)

#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)

#define __KSEQ_BASIC(SCOPE, type_t)										\
	SCOPE kseq_t *kseq_init(type_t fd)									\
	{																	\
		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
		s->f = ks_init(fd);												\
		return s;														\
	}																	\
	SCOPE void kseq_destroy(kseq_t *ks)									\
	{																	\
		if (!ks) return;												\
		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
		ks_destroy(ks->f);												\
		free(ks);														\
	}

/* Return value:
   >=0  length of the sequence (normal)
   -1   end-of-file
   -2   truncated quality string
 */
#define __KSEQ_READ(SCOPE) \
	SCOPE int kseq_read(kseq_t *seq) \
	{ \
		int c; \
		kstream_t *ks = seq->f; \
		if (seq->last_char == 0) { /* then jump to the next header line */ \
			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
			if (c == -1) return -1; /* end of file */ \
			seq->last_char = c; \
		} /* else: the first header char has been read in the previous call */ \
		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
			seq->seq.m = 256; \
			seq->seq.s = (char*)malloc(seq->seq.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
			if (c == '\n') continue; /* skip empty lines */ \
			seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
		} \
		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
			seq->seq.m = seq->seq.l + 2; \
			kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
			seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
		} \
		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */ \
		if (c != '+') return seq->seq.l; /* FASTA */ \
		if (seq->qual.m < seq->seq.m) {	/* allocate memory for qual in case insufficient */ \
			seq->qual.m = seq->seq.m; \
			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
		} \
		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
		if (c == -1) return -2; /* error: no quality string */ \
		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
		seq->last_char = 0;	/* we have not come to the next header line */ \
		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
		return seq->seq.l; \
	}

#define __KSEQ_TYPE(type_t)						\
	typedef struct {							\
		kstring_t name, comment, seq, qual;		\
		int last_char;							\
		kstream_t *f;							\
	} kseq_t;

#define KSEQ_INIT2(SCOPE, type_t, __read)		\
	KSTREAM_INIT(type_t, __read, 16384)			\
	__KSEQ_TYPE(type_t)							\
	__KSEQ_BASIC(SCOPE, type_t)					\
	__KSEQ_READ(SCOPE)

#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)

#define KSEQ_DECLARE(type_t) \
	__KS_TYPE(type_t) \
	__KSEQ_TYPE(type_t) \
	extern kseq_t *kseq_init(type_t fd); \
	void kseq_destroy(kseq_t *ks); \
	int kseq_read(kseq_t *seq);

#endif
bwa-0.7.3a/ksort.h000644 000767 000024 00000022671 12120745361 013612 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008, by Attractive Chaos <attractivechaos@aol.co.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/*
  2008-11-16 (0.1.4):

    * Fixed a bug in introsort() that happens in rare cases.

  2008-11-05 (0.1.3):

    * Fixed a bug in introsort() for complex comparisons.

	* Fixed a bug in mergesort(). The previous version is not stable.

  2008-09-15 (0.1.2):

	* Accelerated introsort. On my Mac (not on another Linux machine),
	  my implementation is as fast as std::sort on random input.

	* Added combsort and in introsort, switch to combsort if the
	  recursion is too deep.

  2008-09-13 (0.1.1):

	* Added k-small algorithm

  2008-09-05 (0.1.0):

	* Initial version

*/

#ifndef AC_KSORT_H
#define AC_KSORT_H

#include <stdlib.h>
#include <string.h>

typedef struct {
	void *left, *right;
	int depth;
} ks_isort_stack_t;

#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }

#define KSORT_INIT(name, type_t, __sort_lt)								\
	void ks_mergesort_##name(size_t n, type_t array[], type_t temp[])	\
	{																	\
		type_t *a2[2], *a, *b;											\
		int curr, shift;												\
																		\
		a2[0] = array;													\
		a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);		\
		for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) {			\
			a = a2[curr]; b = a2[1-curr];								\
			if (shift == 0) {											\
				type_t *p = b, *i, *eb = a + n;							\
				for (i = a; i < eb; i += 2) {							\
					if (i == eb - 1) *p++ = *i;							\
					else {												\
						if (__sort_lt(*(i+1), *i)) {					\
							*p++ = *(i+1); *p++ = *i;					\
						} else {										\
							*p++ = *i; *p++ = *(i+1);					\
						}												\
					}													\
				}														\
			} else {													\
				size_t i, step = 1ul<<shift;							\
				for (i = 0; i < n; i += step<<1) {						\
					type_t *p, *j, *k, *ea, *eb;						\
					if (n < i + step) {									\
						ea = a + n; eb = a;								\
					} else {											\
						ea = a + i + step;								\
						eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
					}													\
					j = a + i; k = a + i + step; p = b + i;				\
					while (j < ea && k < eb) {							\
						if (__sort_lt(*k, *j)) *p++ = *k++;				\
						else *p++ = *j++;								\
					}													\
					while (j < ea) *p++ = *j++;							\
					while (k < eb) *p++ = *k++;							\
				}														\
			}															\
			curr = 1 - curr;											\
		}																\
		if (curr == 1) {												\
			type_t *p = a2[0], *i = a2[1], *eb = array + n;				\
			for (; p < eb; ++i) *p++ = *i;								\
		}																\
		if (temp == 0) free(a2[1]);										\
	}																	\
	void ks_heapadjust_##name(size_t i, size_t n, type_t l[])			\
	{																	\
		size_t k = i;													\
		type_t tmp = l[i];												\
		while ((k = (k << 1) + 1) < n) {								\
			if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k;				\
			if (__sort_lt(l[k], tmp)) break;							\
			l[i] = l[k]; i = k;											\
		}																\
		l[i] = tmp;														\
	}																	\
	void ks_heapmake_##name(size_t lsize, type_t l[])					\
	{																	\
		size_t i;														\
		for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i)				\
			ks_heapadjust_##name(i, lsize, l);							\
	}																	\
	void ks_heapsort_##name(size_t lsize, type_t l[])					\
	{																	\
		size_t i;														\
		for (i = lsize - 1; i > 0; --i) {								\
			type_t tmp;													\
			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
		}																\
	}																	\
	static inline void __ks_insertsort_##name(type_t *s, type_t *t)		\
	{																	\
		type_t *i, *j, swap_tmp;										\
		for (i = s + 1; i < t; ++i)										\
			for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {			\
				swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;			\
			}															\
	}																	\
	void ks_combsort_##name(size_t n, type_t a[])						\
	{																	\
		const double shrink_factor = 1.2473309501039786540366528676643; \
		int do_swap;													\
		size_t gap = n;													\
		type_t tmp, *i, *j;												\
		do {															\
			if (gap > 2) {												\
				gap = (size_t)(gap / shrink_factor);					\
				if (gap == 9 || gap == 10) gap = 11;					\
			}															\
			do_swap = 0;												\
			for (i = a; i < a + n - gap; ++i) {							\
				j = i + gap;											\
				if (__sort_lt(*j, *i)) {								\
					tmp = *i; *i = *j; *j = tmp;						\
					do_swap = 1;										\
				}														\
			}															\
		} while (do_swap || gap > 2);									\
		if (gap != 1) __ks_insertsort_##name(a, a + n);					\
	}																	\
	void ks_introsort_##name(size_t n, type_t a[])						\
	{																	\
		int d;															\
		ks_isort_stack_t *top, *stack;									\
		type_t rp, swap_tmp;											\
		type_t *s, *t, *i, *j, *k;										\
																		\
		if (n < 1) return;												\
		else if (n == 2) {												\
			if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
			return;														\
		}																\
		for (d = 2; 1ul<<d < n; ++d);									\
		stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
		top = stack; s = a; t = a + (n-1); d <<= 1;						\
		while (1) {														\
			if (s < t) {												\
				if (--d == 0) {											\
					ks_combsort_##name(t - s + 1, s);					\
					t = s;												\
					continue;											\
				}														\
				i = s; j = t; k = i + ((j-i)>>1) + 1;					\
				if (__sort_lt(*k, *i)) {								\
					if (__sort_lt(*k, *j)) k = j;						\
				} else k = __sort_lt(*j, *i)? i : j;					\
				rp = *k;												\
				if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }	\
				for (;;) {												\
					do ++i; while (__sort_lt(*i, rp));					\
					do --j; while (i <= j && __sort_lt(rp, *j));		\
					if (j <= i) break;									\
					swap_tmp = *i; *i = *j; *j = swap_tmp;				\
				}														\
				swap_tmp = *i; *i = *t; *t = swap_tmp;					\
				if (i-s > t-i) {										\
					if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
					s = t-i > 16? i+1 : t;								\
				} else {												\
					if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
					t = i-s > 16? i-1 : s;								\
				}														\
			} else {													\
				if (top == stack) {										\
					free(stack);										\
					__ks_insertsort_##name(a, a+n);						\
					return;												\
				} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
			}															\
		}																\
	}																	\
	/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
	/* 0 <= kk < n */													\
	type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk)			\
	{																	\
		type_t *low, *high, *k, *ll, *hh, *mid;							\
		low = arr; high = arr + n - 1; k = arr + kk;					\
		for (;;) {														\
			if (high <= low) return *k;									\
			if (high == low + 1) {										\
				if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
				return *k;												\
			}															\
			mid = low + (high - low) / 2;								\
			if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
			if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
			if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);	\
			KSORT_SWAP(type_t, *mid, *(low+1));							\
			ll = low + 1; hh = high;									\
			for (;;) {													\
				do ++ll; while (__sort_lt(*ll, *low));					\
				do --hh; while (__sort_lt(*low, *hh));					\
				if (hh < ll) break;										\
				KSORT_SWAP(type_t, *ll, *hh);							\
			}															\
			KSORT_SWAP(type_t, *low, *hh);								\
			if (hh <= k) low = ll;										\
			if (hh >= k) high = hh - 1;									\
		}																\
	}

#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)

#define ks_lt_generic(a, b) ((a) < (b))
#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)

typedef const char *ksstr_t;

#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)

#endif
bwa-0.7.3a/kstring.c000644 000767 000024 00000001201 12120745361 014106 0ustar00lh3staff000000 000000 #include <stdarg.h>
#include <stdio.h>
#include "kstring.h"

int ksprintf(kstring_t *s, const char *fmt, ...)
{
	va_list ap;
	int l;
	va_start(ap, fmt);
	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
	va_end(ap);
	if (l + 1 > s->m - s->l) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
		va_start(ap, fmt);
		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
	}
	va_end(ap);
	s->l += l;
	return l;
}

#ifdef KSTRING_MAIN
#include <stdio.h>
int main()
{
	kstring_t *s;
	s = (kstring_t*)calloc(1, sizeof(kstring_t));
	ksprintf(s, "abcdefg: %d", 100);
	printf("%s\n", s->s);
	free(s);
	return 0;
}
#endif
bwa-0.7.3a/kstring.h000644 000767 000024 00000004336 12120745361 014127 0ustar00lh3staff000000 000000 #ifndef KSTRING_H
#define KSTRING_H

#include <stdlib.h>
#include <string.h>

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
	size_t l, m;
	char *s;
} kstring_t;
#endif

static inline void ks_resize(kstring_t *s, size_t size)
{
	if (s->m < size) {
		s->m = size;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
}

static inline int kputsn(const char *p, int l, kstring_t *s)
{
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	memcpy(s->s + s->l, p, l);
	s->l += l;
	s->s[s->l] = 0;
	return l;
}

static inline int kputs(const char *p, kstring_t *s)
{
	return kputsn(p, strlen(p), s);
}

static inline int kputc(int c, kstring_t *s)
{
	if (s->l + 1 >= s->m) {
		s->m = s->l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	s->s[s->l++] = c;
	s->s[s->l] = 0;
	return c;
}

static inline int kputw(int c, kstring_t *s)
{
	char buf[16];
	int l, x;
	if (c == 0) return kputc('0', s);
	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (c < 0) buf[l++] = '-';
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
	s->s[s->l] = 0;
	return 0;
}

static inline int kputuw(unsigned c, kstring_t *s)
{
	char buf[16];
	int l, i;
	unsigned x;
	if (c == 0) return kputc('0', s);
	for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
	s->s[s->l] = 0;
	return 0;
}

static inline int kputl(long c, kstring_t *s)
{
	char buf[32];
	long l, x;
	if (c == 0) return kputc('0', s);
	for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
	if (c < 0) buf[l++] = '-';
	if (s->l + l + 1 >= s->m) {
		s->m = s->l + l + 2;
		kroundup32(s->m);
		s->s = (char*)realloc(s->s, s->m);
	}
	for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
	s->s[s->l] = 0;
	return 0;
}

int ksprintf(kstring_t *s, const char *fmt, ...);

#endif
bwa-0.7.3a/ksw.c000644 000767 000024 00000054351 12120745361 013247 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#include <stdlib.h>
#include <stdint.h>
#include <emmintrin.h>
#include "ksw.h"

#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1)
#define UNLIKELY(x) __builtin_expect((x),0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif

const kswr_t g_defr = { 0, -1, -1, -1, -1, -1, -1 };

struct _kswq_t {
	int qlen, slen;
	uint8_t shift, mdiff, max, size;
	__m128i *qp, *H0, *H1, *E, *Hmax;
};

/**
 * Initialize the query data structure
 *
 * @param size   Number of bytes used to store a score; valid valures are 1 or 2
 * @param qlen   Length of the query sequence
 * @param query  Query sequence
 * @param m      Size of the alphabet
 * @param mat    Scoring matrix in a one-dimension array
 *
 * @return       Query data structure
 */
kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)
{
	kswq_t *q;
	int slen, a, tmp, p;

	size = size > 1? 2 : 1;
	p = 8 * (3 - size); // # values per __m128i
	slen = (qlen + p - 1) / p; // segmented length
	q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory
	q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory
	q->H0 = q->qp + slen * m;
	q->H1 = q->H0 + slen;
	q->E  = q->H1 + slen;
	q->Hmax = q->E + slen;
	q->slen = slen; q->qlen = qlen; q->size = size;
	// compute shift
	tmp = m * m;
	for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score
		if (mat[a] < (int8_t)q->shift) q->shift = mat[a];
		if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];
	}
	q->max = q->mdiff;
	q->shift = 256 - q->shift; // NB: q->shift is uint8_t
	q->mdiff += q->shift; // this is the difference between the min and max scores
	// An example: p=8, qlen=19, slen=3 and segmentation:
	//  {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}
	if (size == 1) {
		int8_t *t = (int8_t*)q->qp;
		for (a = 0; a < m; ++a) {
			int i, k, nlen = slen * p;
			const int8_t *ma = mat + a * m;
			for (i = 0; i < slen; ++i)
				for (k = i; k < nlen; k += slen) // p iterations
					*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
		}
	} else {
		int16_t *t = (int16_t*)q->qp;
		for (a = 0; a < m; ++a) {
			int i, k, nlen = slen * p;
			const int8_t *ma = mat + a * m;
			for (i = 0; i < slen; ++i)
				for (k = i; k < nlen; k += slen) // p iterations
					*t++ = (k >= qlen? 0 : ma[query[k]]);
		}
	}
	return q;
}

kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)
{
	int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
	uint64_t *b;
	__m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax;
	kswr_t r;

#define __max_16(ret, xx) do { \
		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \
		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \
		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \
		(xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \
    	(ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \
	} while (0)

	// initialization
	r = g_defr;
	minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
	endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
	m_b = n_b = 0; b = 0;
	zero = _mm_set1_epi32(0);
	gapoe = _mm_set1_epi8(_gapo + _gape);
	gape = _mm_set1_epi8(_gape);
	shift = _mm_set1_epi8(q->shift);
	H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
	slen = q->slen;
	for (i = 0; i < slen; ++i) {
		_mm_store_si128(E + i, zero);
		_mm_store_si128(H0 + i, zero);
		_mm_store_si128(Hmax + i, zero);
	}
	// the core loop
	for (i = 0; i < tlen; ++i) {
		int j, k, cmp, imax;
		__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
		h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
		h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian
		for (j = 0; LIKELY(j < slen); ++j) {
			/* SW cells are computed in the following order:
			 *   H(i,j)   = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
			 *   E(i+1,j) = max{H(i,j)-q, E(i,j)-r}
			 *   F(i,j+1) = max{H(i,j)-q, F(i,j)-r}
			 */
			// compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)
			h = _mm_adds_epu8(h, _mm_load_si128(S + j));
			h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)
			e = _mm_load_si128(E + j); // e=E'(i,j)
			h = _mm_max_epu8(h, e);
			h = _mm_max_epu8(h, f); // h=H'(i,j)
			max = _mm_max_epu8(max, h); // set max
			_mm_store_si128(H1 + j, h); // save to H'(i,j)
			// now compute E'(i+1,j)
			h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo
			e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape
			e = _mm_max_epu8(e, h); // e=E'(i+1,j)
			_mm_store_si128(E + j, e); // save to E'(i+1,j)
			// now compute F'(i,j+1)
			f = _mm_subs_epu8(f, gape);
			f = _mm_max_epu8(f, h);
			// get H'(i-1,j) and prepare for the next j
			h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
		}
		// NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
		for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max
			f = _mm_slli_si128(f, 1);
			for (j = 0; LIKELY(j < slen); ++j) {
				h = _mm_load_si128(H1 + j);
				h = _mm_max_epu8(h, f); // h=H'(i,j)
				_mm_store_si128(H1 + j, h);
				h = _mm_subs_epu8(h, gapoe);
				f = _mm_subs_epu8(f, gape);
				cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));
				if (UNLIKELY(cmp == 0xffff)) goto end_loop16;
			}
		}
end_loop16:
		//int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");
		__max_16(imax, max); // imax is the maximum number in max
		if (imax >= minsc) { // write the b array; this condition adds branching unfornately
			if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append
				if (n_b == m_b) {
					m_b = m_b? m_b<<1 : 8;
					b = (uint64_t*)realloc(b, 8 * m_b);
				}
				b[n_b++] = (uint64_t)imax<<32 | i;
			} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
		}
		if (imax > gmax) {
			gmax = imax; te = i; // te is the end position on the target
			for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector
				_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
			if (gmax + q->shift >= 255 || gmax >= endsc) break;
		}
		S = H1; H1 = H0; H0 = S; // swap H0 and H1
	}
	r.score = gmax + q->shift < 255? gmax : 255;
	r.te = te;
	if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score
		int max = -1, low, high, qlen = slen * 16;
		uint8_t *t = (uint8_t*)Hmax;
		for (i = 0; i < qlen; ++i, ++t)
			if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;
		//printf("%d,%d\n", max, gmax);
		if (b) {
			i = (r.score + q->max - 1) / q->max;
			low = te - i; high = te + i;
			for (i = 0; i < n_b; ++i) {
				int e = (int32_t)b[i];
				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
					r.score2 = b[i]>>32, r.te2 = e;
			}
		}
	}
	free(b);
	return r;
}

kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)
{
	int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;
	uint64_t *b;
	__m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;
	kswr_t r;

#define __max_8(ret, xx) do { \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \
		(xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \
    	(ret) = _mm_extract_epi16((xx), 0); \
	} while (0)

	// initialization
	r = g_defr;
	minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;
	endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;
	m_b = n_b = 0; b = 0;
	zero = _mm_set1_epi32(0);
	gapoe = _mm_set1_epi16(_gapo + _gape);
	gape = _mm_set1_epi16(_gape);
	H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;
	slen = q->slen;
	for (i = 0; i < slen; ++i) {
		_mm_store_si128(E + i, zero);
		_mm_store_si128(H0 + i, zero);
		_mm_store_si128(Hmax + i, zero);
	}
	// the core loop
	for (i = 0; i < tlen; ++i) {
		int j, k, imax;
		__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
		h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
		h = _mm_slli_si128(h, 2);
		for (j = 0; LIKELY(j < slen); ++j) {
			h = _mm_adds_epi16(h, *S++);
			e = _mm_load_si128(E + j);
			h = _mm_max_epi16(h, e);
			h = _mm_max_epi16(h, f);
			max = _mm_max_epi16(max, h);
			_mm_store_si128(H1 + j, h);
			h = _mm_subs_epu16(h, gapoe);
			e = _mm_subs_epu16(e, gape);
			e = _mm_max_epi16(e, h);
			_mm_store_si128(E + j, e);
			f = _mm_subs_epu16(f, gape);
			f = _mm_max_epi16(f, h);
			h = _mm_load_si128(H0 + j);
		}
		for (k = 0; LIKELY(k < 16); ++k) {
			f = _mm_slli_si128(f, 2);
			for (j = 0; LIKELY(j < slen); ++j) {
				h = _mm_load_si128(H1 + j);
				h = _mm_max_epi16(h, f);
				_mm_store_si128(H1 + j, h);
				h = _mm_subs_epu16(h, gapoe);
				f = _mm_subs_epu16(f, gape);
				if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;
			}
		}
end_loop8:
		__max_8(imax, max);
		if (imax >= minsc) {
			if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {
				if (n_b == m_b) {
					m_b = m_b? m_b<<1 : 8;
					b = (uint64_t*)realloc(b, 8 * m_b);
				}
				b[n_b++] = (uint64_t)imax<<32 | i;
			} else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last
		}
		if (imax > gmax) {
			gmax = imax; te = i;
			for (j = 0; LIKELY(j < slen); ++j)
				_mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));
			if (gmax >= endsc) break;
		}
		S = H1; H1 = H0; H0 = S;
	}
	r.score = gmax; r.te = te;
	{
		int max = -1, low, high, qlen = slen * 8;
		uint16_t *t = (uint16_t*)Hmax;
		for (i = 0, r.qe = -1; i < qlen; ++i, ++t)
			if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;
		if (b) {
			i = (r.score + q->max - 1) / q->max;
			low = te - i; high = te + i;
			for (i = 0; i < n_b; ++i) {
				int e = (int32_t)b[i];
				if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)
					r.score2 = b[i]>>32, r.te2 = e;
			}
		}
	}
	free(b);
	return r;
}

static void revseq(int l, uint8_t *s)
{
	int i, t;
	for (i = 0; i < l>>1; ++i)
		t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;
}

kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)
{
	int size;
	kswq_t *q;
	kswr_t r, rr;
	kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int);

	q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);
	if (qry && *qry == 0) *qry = q;
	func = q->size == 2? ksw_i16 : ksw_u8;
	size = q->size;
	r = func(q, tlen, target, gapo, gape, xtra);
	if (qry == 0) free(q);
	if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;
	revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end
	q = ksw_qinit(size, r.qe + 1, query, m, mat);
	rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score);
	revseq(r.qe + 1, query); revseq(r.te + 1, target);
	free(q);
	if (r.score == rr.score)
		r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;
	return r;
}

/********************
 *** SW extension ***
 ********************/

typedef struct {
	int32_t h, e;
} eh_t;

int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off)
{
	eh_t *eh; // score array
	int8_t *qp; // query profile
	int i, j, k, gapoe = gapo + gape, beg, end, max, max_i, max_j, max_gap, max_ie, gscore, max_off;
	if (h0 < 0) h0 = 0;
	// allocate memory
	qp = malloc(qlen * m);
	eh = calloc(qlen + 1, 8);
	// generate the query profile
	for (k = i = 0; k < m; ++k) {
		const int8_t *p = &mat[k * m];
		for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
	}
	// fill the first row
	eh[0].h = h0; eh[1].h = h0 > gapoe? h0 - gapoe : 0;
	for (j = 2; j <= qlen && eh[j-1].h > gape; ++j)
		eh[j].h = eh[j-1].h - gape;
	// adjust $w if it is too large
	k = m * m;
	for (i = 0, max = 0; i < k; ++i) // get the max score
		max = max > mat[i]? max : mat[i];
	max_gap = (int)((double)(qlen * max - gapo) / gape + 1.);
	max_gap = max_gap > 1? max_gap : 1;
	w = w < max_gap? w : max_gap;
	// DP loop
	max = h0, max_i = max_j = -1; max_ie = -1, gscore = -1;
	max_off = 0;
	beg = 0, end = qlen;
	for (i = 0; LIKELY(i < tlen); ++i) {
		int f = 0, h1, m = 0, mj = -1;
		int8_t *q = &qp[target[i] * qlen];
		// compute the first column
		h1 = h0 - (gapo + gape * (i + 1));
		if (h1 < 0) h1 = 0;
		// apply the band and the constraint (if provided)
		if (beg < i - w) beg = i - w;
		if (end > i + w + 1) end = i + w + 1;
		if (end > qlen) end = qlen;
		for (j = beg; LIKELY(j < end); ++j) {
			// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
			// Similar to SSE2-SW, cells are computed in the following order:
			//   H(i,j)   = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
			//   E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
			//   F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
			eh_t *p = &eh[j];
			int h = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
			p->h = h1;          // set H(i,j-1) for the next row
			h += q[j];
			h = h > e? h : e;
			h = h > f? h : f;
			h1 = h;             // save H(i,j) to h1 for the next column
			mj = m > h? mj : j; // record the position where max score is achieved
			m = m > h? m : h;   // m is stored at eh[mj+1]
			h -= gapoe;
			h = h > 0? h : 0;
			e -= gape;
			e = e > h? e : h;   // computed E(i+1,j)
			p->e = e;           // save E(i+1,j) for the next row
			f -= gape;
			f = f > h? f : h;   // computed F(i,j+1)
		}
		eh[end].h = h1; eh[end].e = 0;
		if (j == qlen) {
			max_ie = gscore > h1? max_ie : i;
			gscore = gscore > h1? gscore : h1;
		}
		if (m == 0 || (zdrop > 0 && max - m - abs((i - max_i) - (j - max_j)) * gape > zdrop)) break; // drop to zero, or below Z-dropoff
		if (m > max) {
			max = m, max_i = i, max_j = mj;
			max_off = max_off > abs(mj - i)? max_off : abs(mj - i);
		}
		// update beg and end for the next round
		for (j = mj; j >= beg && eh[j].h; --j);
		beg = j + 1;
		for (j = mj + 2; j <= end && eh[j].h; ++j);
		end = j;
		//beg = 0; end = qlen; // uncomment this line for debugging
	}
	free(eh); free(qp);
	if (_qle) *_qle = max_j + 1;
	if (_tle) *_tle = max_i + 1;
	if (_gtle) *_gtle = max_ie + 1;
	if (_gscore) *_gscore = gscore;
	if (_max_off) *_max_off = max_off;
	return max;
}

/********************
 * Global alignment *
 ********************/

#define MINUS_INF -0x40000000

static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
{
	if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
		if (*n_cigar == *m_cigar) {
			*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
			cigar = realloc(cigar, (*m_cigar) << 2);
		}
		cigar[(*n_cigar)++] = len<<4 | op;
	} else cigar[(*n_cigar)-1] += len<<4;
	return cigar;
}

int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_)
{
	eh_t *eh;
	int8_t *qp; // query profile
	int i, j, k, gapoe = gapo + gape, score, n_col;
	uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex
	if (n_cigar_) *n_cigar_ = 0;
	// allocate memory
	n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
	z = malloc(n_col * tlen);
	qp = malloc(qlen * m);
	eh = calloc(qlen + 1, 8);
	// generate the query profile
	for (k = i = 0; k < m; ++k) {
		const int8_t *p = &mat[k * m];
		for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
	}
	// fill the first row
	eh[0].h = 0; eh[0].e = MINUS_INF;
	for (j = 1; j <= qlen && j <= w; ++j)
		eh[j].h = -(gapo + gape * j), eh[j].e = MINUS_INF;
	for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band
	// DP loop
	for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop
		int32_t f = MINUS_INF, h1, beg, end;
		int8_t *q = &qp[target[i] * qlen];
		uint8_t *zi = &z[i * n_col];
		beg = i > w? i - w : 0;
		end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
		h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF;
		for (j = beg; LIKELY(j < end); ++j) {
			// This loop is organized in a similar way to ksw_extend() and ksw_sse2(), except:
			// 1) not checking h>0; 2) recording direction for backtracking
			eh_t *p = &eh[j];
			int32_t h = p->h, e = p->e;
			uint8_t d; // direction
			p->h = h1;
			h += q[j];
			d = h >= e? 0 : 1;
			h = h >= e? h : e;
			d = h >= f? d : 2;
			h = h >= f? h : f;
			h1 = h;
			h -= gapoe;
			e -= gape;
			d |= e > h? 1<<2 : 0;
			e = e > h? e : h;
			p->e = e;
			f -= gape;
			d |= f > h? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two
			f = f > h? f : h;
			zi[j - beg] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
		}
		eh[end].h = h1; eh[end].e = MINUS_INF;
	}
	score = eh[qlen].h;
	if (n_cigar_ && cigar_) { // backtrack
		int n_cigar = 0, m_cigar = 0, which = 0;
		uint32_t *cigar = 0, tmp;
		i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
		while (i >= 0 && k >= 0) {
			which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
			if (which == 0)      cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
			else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
			else                 cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
		}
		if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
		if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
		for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
			tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
		*n_cigar_ = n_cigar, *cigar_ = cigar;
	}
	free(eh); free(qp); free(z);
	return score;
}

/*******************************************
 * Main function (not compiled by default) *
 *******************************************/

#ifdef _KSW_MAIN

#include <unistd.h>
#include <stdio.h>
#include <zlib.h>
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

unsigned char seq_nt4_table[256] = {
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 0, 4, 1,  4, 4, 4, 2,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  3, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4
};

int main(int argc, char *argv[])
{
	int c, sa = 1, sb = 3, i, j, k, forward_only = 0, max_rseq = 0;
	int8_t mat[25];
	int gapo = 5, gape = 2, minsc = 0, xtra = KSW_XSTART;
	uint8_t *rseq = 0;
	gzFile fpt, fpq;
	kseq_t *kst, *ksq;

	// parse command line
	while ((c = getopt(argc, argv, "a:b:q:r:ft:1")) >= 0) {
		switch (c) {
			case 'a': sa = atoi(optarg); break;
			case 'b': sb = atoi(optarg); break;
			case 'q': gapo = atoi(optarg); break;
			case 'r': gape = atoi(optarg); break;
			case 't': minsc = atoi(optarg); break;
			case 'f': forward_only = 1; break;
			case '1': xtra |= KSW_XBYTE; break;
		}
	}
	if (optind + 2 > argc) {
		fprintf(stderr, "Usage: ksw [-1] [-f] [-a%d] [-b%d] [-q%d] [-r%d] [-t%d] <target.fa> <query.fa>\n", sa, sb, gapo, gape, minsc);
		return 1;
	}
	if (minsc > 0xffff) minsc = 0xffff;
	xtra |= KSW_XSUBO | minsc;
	// initialize scoring matrix
	for (i = k = 0; i < 4; ++i) {
		for (j = 0; j < 4; ++j)
			mat[k++] = i == j? sa : -sb;
		mat[k++] = 0; // ambiguous base
	}
	for (j = 0; j < 5; ++j) mat[k++] = 0;
	// open file
	fpt = gzopen(argv[optind],   "r"); kst = kseq_init(fpt);
	fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);
	// all-pair alignment
	while (kseq_read(ksq) > 0) {
		kswq_t *q[2] = {0, 0};
		kswr_t r;
		for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
		if (!forward_only) { // reverse
			if ((int)ksq->seq.m > max_rseq) {
				max_rseq = ksq->seq.m;
				rseq = (uint8_t*)realloc(rseq, max_rseq);
			}
			for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j)
				rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];
		}
		gzrewind(fpt); kseq_rewind(kst);
		while (kseq_read(kst) > 0) {
			for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];
			r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);
			if (r.score >= minsc)
				printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);
			if (rseq) {
				r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);
				if (r.score >= minsc)
					printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);
			}
		}
		free(q[0]); free(q[1]);
	}
	free(rseq);
	kseq_destroy(kst); gzclose(fpt);
	kseq_destroy(ksq); gzclose(fpq);
	return 0;
}
#endif
bwa-0.7.3a/ksw.h000644 000767 000024 00000010561 12120745361 013247 0ustar00lh3staff000000 000000 #ifndef __AC_KSW_H
#define __AC_KSW_H

#include <stdint.h>

#define KSW_XBYTE  0x10000
#define KSW_XSTOP  0x20000
#define KSW_XSUBO  0x40000
#define KSW_XSTART 0x80000

struct _kswq_t;
typedef struct _kswq_t kswq_t;

typedef struct {
	int score; // best score
	int te, qe; // target end and query end
	int score2, te2; // second best score and ending position on the target
	int tb, qb; // target start and query start
} kswr_t;

#ifdef __cplusplus
extern "C" {
#endif

	/**
	 * Aligning two sequences
	 *
	 * @param qlen    length of the query sequence (typically <tlen)
	 * @param query   query sequence with 0 <= query[i] < m
	 * @param tlen    length of the target sequence
	 * @param target  target sequence
	 * @param m       number of residue types
	 * @param mat     m*m scoring matrix in one-dimension array
	 * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
	 * @param gape    gap extension penalty
	 * @param xtra    extra information (see below)
	 * @param qry     query profile (see below)
	 *
	 * @return        alignment information in a struct; unset values to -1
	 *
	 * When xtra==0, ksw_align() uses a signed two-byte integer to store a
	 * score and only finds the best score and the end positions. The 2nd best
	 * score or the start positions are not attempted. The default behavior can
	 * be tuned by setting KSW_X* flags:
	 *
	 *   KSW_XBYTE:  use an unsigned byte to store a score. If overflow occurs,
	 *               kswr_t::score will be set to 255
	 *
	 *   KSW_XSUBO:  track the 2nd best score and the ending position on the
	 *               target if the 2nd best is higher than (xtra&0xffff)
	 *
	 *   KSW_XSTOP:  stop if the maximum score is above (xtra&0xffff)
	 *
	 *   KSW_XSTART: find the start positions
	 *
	 * When *qry==NULL, ksw_align() will compute and allocate the query profile
	 * and when the function returns, *qry will point to the profile, which can
	 * be deallocated simply by free(). If one query is aligned against multiple
	 * target sequences, *qry should be set to NULL during the first call and
	 * freed after the last call. Note that qry can equal 0. In this case, the
	 * query profile will be deallocated in ksw_align().
	 */
	kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);

	/**
	 * Banded global alignment
	 *
	 * @param qlen    query length
	 * @param query   query sequence with 0 <= query[i] < m
	 * @param tlen    target length
	 * @param target  target sequence with 0 <= target[i] < m
	 * @param m       number of residue types
	 * @param mat     m*m scoring mattrix in one-dimension array
	 * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
	 * @param gape    gap extension penalty
	 * @param w       band width
	 * @param n_cigar (out) number of CIGAR elements
	 * @param cigar   (out) BAM-encoded CIGAR; caller need to deallocate with free()
	 *
	 * @return        score of the alignment
	 */
	int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar);

	/**
	 * Extend alignment
	 *
	 * The routine aligns $query and $target, assuming their upstream sequences,
	 * which are not provided, have been aligned with score $h0. In return,
	 * region [0,*qle) on the query and [0,*tle) on the target sequences are
	 * aligned together. If *gscore>=0, *gscore keeps the best score such that
	 * the entire query sequence is aligned; *gtle keeps the position on the
	 * target where *gscore is achieved. Returning *gscore and *gtle helps the
	 * caller to decide whether an end-to-end hit or a partial hit is preferred.
	 *
	 * The first 9 parameters are identical to those in ksw_global()
	 *
	 * @param h0      alignment score of upstream sequences
	 * @param _qle    (out) length of the query in the alignment
	 * @param _tle    (out) length of the target in the alignment
	 * @param _gtle   (out) length of the target if query is fully aligned
	 * @param _gscore (out) score of the best end-to-end alignment; negative if not found
	 *
	 * @return        best semi-local alignment score
	 */
	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int zdrop, int h0, int *qle, int *tle, int *gtle, int *gscore, int *max_off);

#ifdef __cplusplus
}
#endif

#endif
bwa-0.7.3a/kvec.h000644 000767 000024 00000005476 12120745361 013404 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/*
  An example:

#include "kvec.h"
int main() {
	kvec_t(int) array;
	kv_init(array);
	kv_push(int, array, 10); // append
	kv_a(int, array, 20) = 5; // dynamic
	kv_A(array, 20) = 4; // static
	kv_destroy(array);
	return 0;
}
*/

/*
  2008-09-22 (0.1.0):

	* The initial version.

*/

#ifndef AC_KVEC_H
#define AC_KVEC_H

#include <stdlib.h>

#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))

#define kvec_t(type) struct { size_t n, m; type *a; }
#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
#define kv_destroy(v) free((v).a)
#define kv_A(v, i) ((v).a[(i)])
#define kv_pop(v) ((v).a[--(v).n])
#define kv_size(v) ((v).n)
#define kv_max(v) ((v).m)

#define kv_resize(type, v, s)  ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))

#define kv_copy(type, v1, v0) do {							\
		if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n);	\
		(v1).n = (v0).n;									\
		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n);		\
	} while (0)												\

#define kv_push(type, v, x) do {									\
		if ((v).n == (v).m) {										\
			(v).m = (v).m? (v).m<<1 : 2;							\
			(v).a = (type*)realloc((v).a, sizeof(type) * (v).m);	\
		}															\
		(v).a[(v).n++] = (x);										\
	} while (0)

#define kv_pushp(type, v) ((((v).n == (v).m)?							\
						   ((v).m = ((v).m? (v).m<<1 : 2),				\
							(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0)	\
						   : 0), &(v).a[(v).n++])

#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
						  ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
						   (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
						  : (v).n <= (size_t)(i)? (v).n = (i) + 1 \
						  : 0), (v).a[(i)])

#endif
bwa-0.7.3a/main.c000644 000767 000024 00000007371 12120745361 013367 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <string.h>
#include "utils.h"

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3a-r367"
#endif

int bwa_fa2pac(int argc, char *argv[]);
int bwa_pac2bwt(int argc, char *argv[]);
int bwa_bwtupdate(int argc, char *argv[]);
int bwa_bwt2sa(int argc, char *argv[]);
int bwa_index(int argc, char *argv[]);
int bwt_bwtgen_main(int argc, char *argv[]);

int bwa_aln(int argc, char *argv[]);
int bwa_sai2sam_se(int argc, char *argv[]);
int bwa_sai2sam_pe(int argc, char *argv[]);

int bwa_bwtsw2(int argc, char *argv[]);

int main_fastmap(int argc, char *argv[]);
int main_mem(int argc, char *argv[]);

int main_pemerge(int argc, char *argv[]);

static int usage()
{
	fprintf(stderr, "\n");
	fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
	fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
	fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
	fprintf(stderr, "Usage:   bwa <command> [options]\n\n");
	fprintf(stderr, "Command: index         index sequences in the FASTA format\n");
	fprintf(stderr, "         mem           BWA-MEM algorithm\n");
	fprintf(stderr, "         fastmap       identify super-maximal exact matches\n");
	fprintf(stderr, "         pemerge       merge overlapping paired ends (EXPERIMENTAL)\n");
	fprintf(stderr, "         aln           gapped/ungapped alignment\n");
	fprintf(stderr, "         samse         generate alignment (single ended)\n");
	fprintf(stderr, "         sampe         generate alignment (paired ended)\n");
	fprintf(stderr, "         bwasw         BWA-SW for long queries\n");
	fprintf(stderr, "\n");
	fprintf(stderr, "         fa2pac        convert FASTA to PAC format\n");
	fprintf(stderr, "         pac2bwt       generate BWT from PAC\n");
	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
	fprintf(stderr, "\n");
	return 1;
}

void bwa_print_sam_PG()
{
	printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
}

int main(int argc, char *argv[])
{
	int i, ret;
	double t_real;
	t_real = realtime();
	if (argc < 2) return usage();
	if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
	else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
	else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
	else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
	else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
	else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
	else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
	else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
	else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
	else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
	else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
	else if (strcmp(argv[1], "mem") == 0) ret = main_mem(argc-1, argv+1);
	else if (strcmp(argv[1], "pemerge") == 0) ret = main_pemerge(argc-1, argv+1);
	else {
		fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
		return 1;
	}
	err_fflush(stdout);
	err_fclose(stdout);
	if (ret == 0) {
		fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
		fprintf(stderr, "[%s] CMD:", __func__);
		for (i = 0; i < argc; ++i)
			fprintf(stderr, " %s", argv[i]);
		fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
	}
	return 0;
}
bwa-0.7.3a/Makefile000644 000767 000024 00000002426 12120745361 013733 0ustar00lh3staff000000 000000 CC=			gcc
CFLAGS=		-g -Wall -O2
AR=			ar
DFLAGS=		-DHAVE_PTHREAD
LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
			is.o bwtindex.o bwape.o kopen.o pemerge.o \
			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
PROG=		bwa bwamem-lite
INCLUDES=	
LIBS=		-lm -lz -lpthread
SUBDIRS=	.

.SUFFIXES:.c .o .cc

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all:$(PROG)

bwa:libbwa.a $(AOBJS) main.o
		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)

bwamem-lite:libbwa.a example.o
		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)

libbwa.a:$(LOBJS)
		$(AR) -csru $@ $(LOBJS)

ksw.o:ksw.h
kstring.o:kstring.h
utils.o:utils.h ksort.h kseq.h
bntseq.o:bntseq.h
bwt.o:bwt.h utils.h
bwa.o:bwa.h bwt.h bntseq.h
bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h
bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h

QSufSort.o:QSufSort.h
bwt_gen.o:QSufSort.h

fastmap.o:bwt.h bwamem.h

bwtaln.o:bwt.h bwtaln.h kseq.h
bwtgap.o:bwtgap.h bwtaln.h bwt.h

bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h
bwtsw2_main.o:bwtsw2.h

clean:
		rm -f gmon.out *.o a.out $(PROG) *~ *.a
bwa-0.7.3a/NEWS000644 000767 000024 00000060356 12120745361 013000 0ustar00lh3staff000000 000000 Release 0.7.3a (15 March, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
in another corner case.

(0.7.3a: 15 March 2013, r367)



Release 0.7.3 (15 March, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Changes to BWA-MEM:

 * Bugfix: pairing score is inaccurate when option -A does not take the default
   value. This is a very minor issue even if it happens.

 * Bugfix: occasionally wrong CIGAR. This happens when in the alignment there
   is a 1bp deletion and a 1bp insertion which are close to the end of the
   reads, and there are no other substitutions or indels. BWA-MEM would not do
   a gapped alignment due to the bug.

 * New feature: output other non-overlapping alignments in the XP tag such that
   we can see the entire picture of alignment from one SAM line. XP gives the
   position, CIGAR, NM and mapQ of each aligned subsequence of the query.

BWA-MEM has been used to align ~300Gbp 100-700bp SE/PE reads. SNP/indel calling
has also been evaluated on part of these data. BWA-MEM generally gives better
pre-filtered SNP calls than BWA. No significant issues have been observed since
0.7.2, though minor improvements or bugs (e.g. the bug fixed in this release)
are still possible. If you find potential issues, please send bug reports to
<bio-bwa-help@lists.sourceforge.net> (free registration required).

In addition, more detailed description of the BWA-MEM algorithm can be found at
<https://github.com/lh3/mem-paper>.

(0.7.3: 15 March 2013, r366)



Release 0.7.2 (9 March, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Emergent bug fix: 0.7.0 and 0.7.1 give a wrong sign to TLEN. In addition,
flagging `properly paired' also gets improved a little.

(0.7.2: 9 March 2013, r351)



Release 0.7.1 (8 March, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Changes to BWA-MEM:

 * Bugfix: rare segmentation fault caused by a partial hit to the end of the
   last sequence.

 * Bugfix: occasional mis-pairing given an interleaved fastq.

 * Bugfix: wrong mate information when the mate is unmapped. SAM generated by
   BWA-MEM can now be validated with Picard.

 * Improved the performance and accuracy for ultra-long query sequences.
   Short-read alignment is not affected.

Changes to other components:

 * In BWA-backtrack and BWA-SW, replaced the code for global alignment,
   Smith-Waterman and SW extension. The performance and accuracy of the two
   algorithms stay the same.

 * Added an experimental subcommand to merge overlapping paired ends. The
   algorithm is very conservative: it may miss true overlaps but rarely makes
   mistakes.

An important note is that like BWA-SW, BWA-MEM may output multiple primary
alignments for a read, which may cause problems to some tools. For aligning
sequence reads, it is advised to use `-M' to flag extra hits as secondary. This
option is not the default because multiple primary alignments are theoretically
possible in sequence alignment.

(0.7.1: 8 March 2013, r347)



Beta Release 0.7.0 (28 Feburary, 2013)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release comes with a new alignment algorithm, BWA-MEM, for 70bp-1Mbp query
sequences. BWA-MEM essentially seeds alignments with a variant of the fastmap
algorithm and extends seeds with banded affine-gap-penalty dynamic programming
(i.e. the Smith-Waterman-Gotoh algorithm). For typical Illumina 100bp reads or
longer low-divergence query sequences, BWA-MEM is about twice as fast as BWA
and BWA-SW and is more accurate. It also supports split alignments like BWA-SW
and may optionally output multiple hits like BWA. BWA-MEM does not guarantee
to find hits within a certain edit distance, but BWA is not efficient for such
task given longer reads anyway, and the edit-distance criterion is arguably
not as important in long-read alignment.

In addition to the algorithmic improvements, BWA-MEM also implements a few
handy features in practical aspects:

 1. BWA-MEM automatically switches between local and glocal (global wrt reads;
    local wrt reference) alignment. It reports the end-to-end glocal alignment
    if the glocal alignment is not much worse than the optimal local alignment.
    Glocal alignment reduces reference bias.

 2. BWA-MEM automatically infers pair orientation from a batch of single-end
    alignments. It allows more than one orientations if there are sufficient
    supporting reads. This feature has not been tested on reads from Illumina
    jumping library yet. (EXPERIMENTAL)

 3. BWA-MEM optionally takes one interleaved fastq for paired-end mapping. It
    is possible to convert a name-sorted BAM to an interleaved fastq on the fly
    and feed the data stream to BWA-MEM for mapping.

 4. BWA-MEM optionally copies FASTA/Q comments to the final SAM output, which
    helps to transfer individual read annotations to the output.

 5. BWA-MEM supports more advanced piping. Users can now run:
    (bwa mem ref.fa '<bzcat r1.fq.bz2' '<bzcat r2.fq.bz2') to map bzip'd read
    files without replying on bash features.

 6. BWA-MEM provides a few basic APIs for single-end mapping. The `example.c'
    program in the source code directory implements a full single-end mapper in
    50 lines of code.

The BWA-MEM algorithm is in the beta phase. It is not advised to use BWA-MEM
for production use yet. However, when the implementation becomes stable after a
few release cycles, existing BWA users are recommended to migrate to BWA-MEM
for 76bp or longer Illumina reads and long query sequences. The original BWA
short-read algorithm will not deliver satisfactory results for 150bp+ Illumina
reads. Change of mappers will be necessary sooner or later.

(0.7.0 beta: 28 Feburary 2013, r313)



Release 0.6.2 (19 June, 2012)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is largely a bug-fix release. Notable changes in BWA-short and BWA-SW:

 * Bugfix: BWA-SW may give bad alignments due to incorrect band width.

 * Bugfix: A segmentation fault due to an out-of-boundary error. The fix is a
   temporary solution. The real cause has not been identified.

 * Attempt to read index from prefix.64.bwt, such that the 32-bit and 64-bit
   index can coexist.

 * Added options '-I' and '-S' to control BWA-SW pairing.

(0.6.2: 19 June 2012, r126)



Release 0.6.1 (28 November, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes to BWA-short:

 * Bugfix: duplicated alternative hits in the XA tag.

 * Bugfix: when trimming enabled, bwa-aln trims 1bp less.

 * Disabled the color-space alignment. 0.6.x is not working with SOLiD reads at
   present.

Notable changes to BWA-SW:

 * Bugfix: segfault due to excessive ambiguous bases.

 * Bugfix: incorrect mate position in the SE mode.

 * Bugfix: rare segfault in the PE mode

 * When macro _NO_SSE2 is in use, fall back to the standard Smith-Waterman
   instead of SSE2-SW.

 * Optionally mark split hits with lower alignment scores as secondary.

Changes to fastmap:

 * Bugfix: infinite loop caused by ambiguous bases.

 * Optionally output the query sequence.

(0.6.1: 28 November 2011, r104)



Release 0.5.10 and 0.6.0 (12 November, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The 0.6.0 release comes with two major changes. Firstly, the index data
structure has been changed to support genomes longer than 4GB. The forward and
reverse backward genome is now integrated in one index. This change speeds up
BWA-short by about 20% and BWA-SW by 90% with the mapping acccuracy largely
unchanged. A tradeoff is BWA requires more memory, but this is the price almost
all mappers that index the genome have to pay.

Secondly, BWA-SW in 0.6.0 now works with paired-end data. It is more accurate
for highly unique reads and more robust to long indels and structural
variations. However, BWA-short still has edges for reads with many suboptimal
hits. It is yet to know which algorithm is the best for variant calling.

0.5.10 is a bugfix release only and is likely to be the last release in the 0.5
branch unless I find critical bugs in future.

Other notable changes:

 * Added the `fastmap' command that finds super-maximal exact matches. It does
   not give the final alignment, but runs much faster. It can be a building
   block for other alignment algorithms. [0.6.0 only]

 * Output the timing information before BWA exits. This also tells users that
   the task has been finished instead of being killed or aborted. [0.6.0 only]

 * Sped up multi-threading when using many (>20) CPU cores.

 * Check I/O error.

 * Increased the maximum barcode length to 63bp.

 * Automatically choose the indexing algorithm.

 * Bugfix: very rare segfault due to an uninitialized variable. The bug also
   affects the placement of suboptimal alignments. The effect is very minor.

This release involves quite a lot of tricky changes. Although it has been
tested on a few data sets, subtle bugs may be still hidden. It is *NOT*
recommended to use this release in a production pipeline. In future, however,
BWA-SW may be better when reads continue to go longer. I would encourage users
to try the 0.6 release. I would also like to hear the users' experience. Thank
you.

(0.6.0: 12 November 2011, r85)



Beta Release 0.5.9 (24 January, 2011)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Feature: barcode support via the `-B' option.

 * Feature: Illumina 1.3+ read format support via the `-I' option.

 * Bugfix: RG tags are not attached to unmapped reads.

 * Bugfix: very rare bwasw mismappings

 * Recommend options for PacBio reads in bwasw help message.


Also, since January 13, the BWA master repository has been moved to github:

  https://github.com/lh3/bwa

The revision number has been reset. All recent changes will be first
committed to this repository.

(0.5.9: 24 January 2011, r16)



Beta Release Candidate 0.5.9rc1 (10 December, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in bwasw:

 * Output unmapped reads.

 * For a repetitive read, choose a random hit instead of a fixed
   one. This is not well tested.

Notable changes in bwa-short:

 * Fixed a bug in the SW scoring system, which may lead to unexpected
   gaps towards the end of a read.

 * Fixed a bug which invalidates the randomness of repetitive reads.

 * Fixed a rare memory leak.

 * Allowed to specify the read group at the command line.

 * Take name-grouped BAM files as input.

Changes to this release are usually safe in that they do not interfere
with the key functionality. However, the release has only been tested on
small samples instead of on large-scale real data. If anything weird
happens, please report the bugs to the bio-bwa-help mailing list.

(0.5.9rc1: 10 December 2010, r1561)



Beta Release 0.5.8 (8 June, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in bwasw:

 * Fixed an issue of missing alignments. This should happen rarely and
   only when the contig/read alignment is multi-part. Very rarely, bwasw
   may still miss a segment in a multi-part alignment. This is difficult
   to fix, although possible.

Notable changes in bwa-short:

 * Discard the SW alignment when the best single-end alignment is much
   better. Such a SW alignment may caused by structural variations and
   forcing it to be aligned leads to false alignment. This fix has not
   been tested thoroughly. It would be great to receive more users
   feedbacks on this issue.

 * Fixed a typo/bug in sampe which leads to unnecessarily large memory
   usage in some cases.

 * Further reduced the chance of reporting `weird pairing'.

(0.5.8: 8 June 2010, r1442)



Beta Release 0.5.7 (1 March, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release only has an effect on paired-end data with fat insert-size
distribution. Users are still recommended to update as the new release
improves the robustness to poor data.

 * The fix for `weird pairing' was not working in version 0.5.6, pointed
   out by Carol Scott. It should work now.

 * Optionally output to a normal file rather than to stdout (by Tim
   Fennel).

(0.5.7: 1 March 2010, r1310)



Beta Release 0.5.6 (10 Feburary, 2010)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in bwa-short:

 * Report multiple hits in the SAM format at a new tag XA encoded as:
   (chr,pos,CIGAR,NM;)*. By default, if a paired or single-end read has
   4 or fewer hits, they will all be reported; if a read in a anomalous
   pair has 11 or fewer hits, all of them will be reported.

 * Perform Smith-Waterman alignment also for anomalous read pairs when
   both ends have quality higher than 17. This reduces false positives
   for some SV discovery algorithms.

 * Do not report "weird pairing" when the insert size distribution is
   too fat or has a mean close to zero.

 * If a read is bridging two adjacent chromsomes, flag it as unmapped.

 * Fixed a small but long existing memory leak in paired-end mapping.

 * Multiple bug fixes in SOLiD mapping: a) quality "-1" can be correctly
   parsed by solid2fastq.pl; b) truncated quality string is resolved; c)
   SOLiD read mapped to the reverse strand is complemented.

 * Bwa now calculates skewness and kurtosis of the insert size
   distribution.

 * Deploy a Bayesian method to estimate the maximum distance for a read
   pair considered to be paired properly. The method is proposed by
   Gerton Lunter, but bwa only implements a simplified version.

 * Export more functions for Java bindings, by Matt Hanna (See:
   http://www.broadinstitute.org/gsa/wiki/index.php/Sting_BWA/C_bindings)

 * Abstract bwa CIGAR for further extension, by Rodrigo Goya.

(0.5.6: 10 Feburary 2010, r1303)



Beta Release 0.5.5 (10 November, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is a bug fix release:

 * Fixed a serious bug/typo in aln which does not occur given short
   reads, but will lead to segfault for >500bp reads. Of course, the aln
   command is not recommended for reads longer than 200bp, but this is a
   bug anyway.

 * Fixed a minor bug/typo which leads to incorrect single-end mapping
   quality when one end is moved to meet the mate-pair requirement.

 * Fixed a bug in samse for mapping in the color space. This bug is
   caused by quality filtration added since 0.5.1.

(0.5.5: 10 November 2009, r1273)



Beta Release 0.5.4 (9 October, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Since this version, the default seed length used in the "aln" command is
changed to 32.

Notable changes in bwa-short:

 * Added a new tag "XC:i" which gives the length of clipped reads.

 * In sampe, skip alignments in case of a bug in the Smith-Waterman
   alignment module.

 * In sampe, fixed a bug in pairing when the read sequence is identical
   to its reverse complement.

 * In sampe, optionally preload the entire FM-index into memory to
   reduce disk operations.

Notable changes in dBWT-SW/BWA-SW:

 * Changed name dBWT-SW to BWA-SW.

 * Optionally use "hard clipping" in the SAM output.

(0.5.4: 9 October 2009, r1245)



Beta Release 0.5.3 (15 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Fixed a critical bug in bwa-short: reads mapped to the reverse strand
are not complemented.

(0.5.3: 15 September 2009, r1225)



Beta Release 0.5.2 (13 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in bwa-short:

 * Optionally trim reads before alignment. See the manual page on `aln
   -q' for detailed description.

 * Fixed a bug in calculating the NM tag for a gapped alignment.

 * Fixed a bug given a mixture of reads with some longer than the seed
   length and some shorter.

 * Print SAM header.

Notable changes in dBWT-SW:

 * Changed the default value of -T to 30. As a result, the accuracy is a
   little higher for short reads at the cost of speed.

(0.5.2: 13 September 2009, r1223)



Beta Release 0.5.1 (2 September, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes in the short read alignment component:

 * Fixed a bug in samse: do not write mate coordinates.

Notable changes in dBWT-SW:

 * Randomly choose one alignment if the read is a repetitive.

 * Fixed a flaw when a read is mapped across two adjacent reference
   sequences. However, wrong alignment reports may still occur rarely in
   this case.

 * Changed the default band width to 50. The speed is slower due to this
   change.

 * Improved the mapping quality a little given long query sequences.

(0.5.1: 2 September 2009, r1209)



Beta Release 0.5.0 (20 August, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release implements a novel algorithm, dBWT-SW, specifically
designed for long reads. It is 10-50 times faster than SSAHA2, depending
on the characteristics of the input data, and achieves comparable
alignment accuracy while allowing chimera detection. In comparison to
BLAT, dBWT-SW is several times faster and much more accurate especially
when the error rate is high. Please read the manual page for more
information.

The dBWT-SW algorithm is kind of developed for future sequencing
technologies which produce much longer reads with a little higher error
rate. It is still at its early development stage. Some features are
missing and it may be buggy although I have evaluated on several
simulated and real data sets. But following the "release early"
paradigm, I would like the users to try it first.

Other notable changes in BWA are:

 * Fixed a rare bug in the Smith-Waterman alignment module.

 * Fixed a rare bug about the wrong alignment coordinate when a read is
   poorly aligned.

 * Fixed a bug in generating the "mate-unmap" SAM tag when both ends in
   a pair are unmapped.

(0.5.0: 20 August 2009, r1200)



Beta Release 0.4.9 (19 May, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Interestingly, the integer overflow bug claimed to be fixed in 0.4.7 has
not in fact. Now I have fixed the bug. Sorry for this and thank Quan
Long for pointing out the bug (again).

(0.4.9: 19 May 2009, r1075)



Beta Release 0.4.8 (18 May, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

One change to "aln -R". Now by default, if there are no more than `-R'
equally best hits, bwa will search for suboptimal hits. This change
affects the ability in finding SNPs in segmental duplications.

I have not tested this option thoroughly, but this simple change is less
likely to cause new bugs. Hope I am right.

(0.4.8: 18 May 2009, r1073)



Beta Release 0.4.7 (12 May, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Output SM (single-end mapping quality) and AM (smaller mapping
   quality among the two ends) tag from sam output.

 * Improved the functionality of stdsw.

 * Made the XN tag more accurate.

 * Fixed a very rare segfault caused by integer overflow.

 * Improve the insert size estimation.

 * Fixed compiling errors for some Linux systems.

(0.4.7: 12 May 2009, r1066)



Beta Release 0.4.6 (9 March, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This release improves the SOLiD support. First, a script for converting
SOLiD raw data is provided. This script is adapted from solid2fastq.pl
in the MAQ package. Second, a nucleotide reference file can be directly
used with `bwa index'. Third, SOLiD paired-end support is
completed. Fourth, color-space reads will be converted to nucleotides
when SAM output is generated. Color errors are corrected in this
process. Please note that like MAQ, BWA cannot make use of the primer
base and the first color.

In addition, the calculation of mapping quality is also improved a
little bit, although end-users may barely observe the difference.

(0.4.6: 9 March 2009, r915)



Beta Release 0.4.5 (18 Feburary, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Not much happened, but I think it would be good to let the users use the
latest version.

Notable changes (Thank Bob Handsaker for catching the two bugs):

 * Improved bounary check. Previous version may still give incorrect
   alignment coordinates in rare cases.

 * Fixed a bug in SW alignment when no residue matches. This only
   affects the `sampe' command.

 * Robustly estimate insert size without setting the maximum on the
   command line. Since this release `sampe -a' only has an effect if
   there are not enough good pairs to infer the insert size
   distribution.

 * Reduced false PE alignments a little bit by using the inferred insert
   size distribution. This fix may be more important for long insert
   size libraries.

(0.4.5: 18 Feburary 2009, r829)



Beta Release 0.4.4 (15 Feburary, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is mainly a bug fix release. Notable changes are:

 * Imposed boundary check for extracting subsequence from the
   genome. Previously this causes memory problem in rare cases.

 * Fixed a bug in failing to find whether an alignment overlapping with
   N on the genome.

 * Changed MD tag to meet the latest SAM specification.

(0.4.4: 15 Feburary 2009, r815)



Beta Release 0.4.3 (22 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Notable changes:

 * Treat an ambiguous base N as a mismatch. Previous versions will not
   map reads containing any N.

 * Automatically choose the maximum allowed number of differences. This
   is important when reads of different lengths are mixed together.

 * Print mate coordinate if only one end is unmapped.

 * Generate MD tag. This tag encodes the mismatching positions and the
   reference bases at these positions. Deletions from the reference will
   also be printed.

 * Optionally dump multiple hits from samse, in another concise format
   rather than SAM.

 * Optionally disable iterative search. This is VERY SLOOOOW, though.

 * Fixed a bug in generate SAM.

(0.4.3: 22 January 2009, r787)



Beta Release 0.4.2 (9 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Aaron Quinlan found a bug in the indexer: the bwa indexer segfaults if
there are no comment texts in the FASTA header. This is a critical
bug. Nothing else was changed.

(0.4.2: 9 January 2009, r769)



Beta Release 0.4.1 (7 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I am sorry for the quick updates these days. I like to set a milestone
for BWA and this release seems to be. For paired end reads, BWA also
does Smith-Waterman alignment for an unmapped read whose mate can be
mapped confidently. With this strategy BWA achieves similar accuracy to
maq. Benchmark is also updated accordingly.

(0.4.1: 7 January 2009, r760)



Beta Release 0.4.0 (6 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In comparison to the release two days ago, this release is mainly tuned
for performance with some tricks I learnt from Bowtie. However, as the
indexing format has also been changed, I have to increase the version
number to 0.4.0 to emphasize that *DATABASE MUST BE RE-INDEXED* with
`bwa index'.

 * Improved the speed by about 20%.

 * Added multi-threading to `bwa aln'.

(0.4.0: 6 January 2009, r756)



Beta Release 0.3.0 (4 January, 2009)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Added paired-end support by separating SA calculation and alignment
   output.

 * Added SAM output.

 * Added evaluation to the documentation.

(0.3.0: 4 January 2009, r741)



Beta Release 0.2.0 (15 Augusst, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Take the subsequence at the 5'-end as seed. Seeding strategy greatly
   improves the speed for long reads, at the cost of missing a few true
   hits that contain many differences in the seed. Seeding also increase
   the memory by 800MB.

 * Fixed a bug which may miss some gapped alignments. Fixing the bug
   also slows the speed a little.

(0.2.0: 15 August 2008, r428)



Beta Release 0.1.6 (08 Augusst, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Give accurate CIGAR string.

 * Add a simple interface to SW/NW alignment

(0.1.6: 08 August 2008, r414)



Beta Release 0.1.5 (27 July, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Improve the speed. This version is expected to give the same results.

(0.1.5: 27 July 2008, r400)



Beta Release 0.1.4 (22 July, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 * Fixed a bug which may cause missing gapped alignments.

 * More clearly define what alignments can be found by BWA (See
   manual). Now BWA runs a little slower because it will visit more
   potential gapped alignments.

 * A bit code clean up.

(0.1.4: 22 July 2008, r387)



Beta Release 0.1.3 (21 July, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Improve the speed with some tricks on retrieving occurences. The results
should be exactly the same as that of 0.1.2.

(0.1.3: 21 July 2008, r382)



Beta Release 0.1.2 (17 July, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Support gapped alignment. Codes for ungapped alignment has been removed.

(0.1.2: 17 July 2008, r371)



Beta Release 0.1.1 (03 June, 2008)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This is the first release of BWA, Burrows-Wheeler Alignment tool. Please
read man page for more information about this software.

(0.1.1: 03 June 2008, r349)



bwa-0.7.3a/pemerge.c000644 000767 000024 00000020065 12120745361 014062 0ustar00lh3staff000000 000000 #include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <string.h>
#include <zlib.h>
#include <pthread.h>
#include "ksw.h"
#include "kseq.h"
#include "kstring.h"
#include "bwa.h"
KSEQ_DECLARE(gzFile)

#define MAX_SCORE_RATIO 0.9f
#define MAX_ERR 8

static const char *err_msg[MAX_ERR+1] = {
	"successful merges",
	"low-scoring pairs",
	"pairs where the best SW alignment is not an overlap (long left end)",
	"pairs where the best SW alignment is not an overlap (long right end)",
	"pairs with large 2nd best SW score",
	"pairs with gapped overlap",
	"pairs where the end-to-end alignment is inconsistent with SW",
	"pairs potentially with tandem overlaps",
	"pairs with high sum of errors"
};

typedef struct {
	int a, b, q, r, w;
	int q_def, q_thres;
	int T;
	int chunk_size;
	int n_threads;
	int flag; // bit 1: print merged; 2: print unmerged
	int8_t mat[25];
} pem_opt_t;

pem_opt_t *pem_opt_init()
{
	pem_opt_t *opt;
	opt = calloc(1, sizeof(pem_opt_t));
	opt->a = 5; opt->b = 4; opt->q = 2, opt->r = 17; opt->w = 20;
	opt->T = opt->a * 10;
	opt->q_def = 20;
	opt->q_thres = 70;
	opt->chunk_size = 10000000;
	opt->n_threads = 1;
	opt->flag = 3;
	bwa_fill_scmat(opt->a, opt->b, opt->mat);
	return opt;
}

int bwa_pemerge(const pem_opt_t *opt, bseq1_t x[2])
{
	uint8_t *s[2], *q[2], *seq, *qual;
	int i, xtra, l, l_seq, sum_q, ret = 0;
	kswr_t r;

	s[0] = malloc(x[0].l_seq); q[0] = malloc(x[0].l_seq);
	s[1] = malloc(x[1].l_seq); q[1] = malloc(x[1].l_seq);
	for (i = 0; i < x[0].l_seq; ++i) {
		int c = x[0].seq[i];
		s[0][i] = c < 0 || c > 127? 4 : c <= 4? c : nst_nt4_table[c];
		q[0][i] = x[0].qual? x[0].qual[i] - 33 : opt->q_def;
	}
	for (i = 0; i < x[1].l_seq; ++i) {
		int c = x[1].seq[x[1].l_seq - 1 - i];
		c = c < 0 || c > 127? 4 : c < 4? c : nst_nt4_table[c];
		s[1][i] = c < 4? 3 - c : 4;
		q[1][i] = x[1].qual? x[1].qual[x[1].l_seq - 1 - i] - 33 : opt->q_def;
	}

	xtra = KSW_XSTART | KSW_XSUBO;
	r = ksw_align(x[1].l_seq, s[1], x[0].l_seq, s[0], 5, opt->mat, opt->q, opt->r, xtra, 0);
	++r.qe; ++r.te; // change to the half-close-half-open coordinates

	if (r.score < opt->T) { ret = -1; goto pem_ret; } // poor alignment
	if (r.tb < r.qb) { ret = -2; goto pem_ret; } // no enough space for the left end
	if (x[0].l_seq - r.te > x[1].l_seq - r.qe) { ret = -3; goto pem_ret; } // no enough space for the right end
	if ((double)r.score2 / r.score >= MAX_SCORE_RATIO) { ret = -4; goto pem_ret; } // the second best score is too large
	if (r.qe - r.qb != r.te - r.tb) { ret = -5; goto pem_ret; } // we do not allow gaps

	{ // test tandem match; O(n^2)
		int max_m, max_m2, min_l, max_l, max_l2;
		max_m = max_m2 = 0; max_l = max_l2 = 0;
		min_l = x[0].l_seq < x[1].l_seq? x[0].l_seq : x[1].l_seq;
		for (l = 1; l < min_l; ++l) {
			int m = 0, o = x[0].l_seq - l;
			uint8_t *s0o = &s[0][o], *s1 = s[1];
			for (i = 0; i < l; ++i) // TODO: in principle, this can be done with SSE2. It is the bottleneck!
				m += opt->mat[(s1[i]<<2) + s1[i] + s0o[i]]; // equivalent to s[1][i]*5 + s[0][o+i]
			if (m > max_m) max_m2 = max_m, max_m = m, max_l2 = max_l, max_l = l;
			else if (m > max_m2) max_m2 = m, max_l2 = l;
		}
		if (max_m < opt->T || max_l != x[0].l_seq - (r.tb - r.qb)) { ret = -6; goto pem_ret; }
		if (max_l2 < max_l && max_m2 >= opt->T && (double)(max_m2 + (max_l - max_l2) * opt->a) / max_m >= MAX_SCORE_RATIO) {
			ret = -7; goto pem_ret;
		}
		if (max_l2 > max_l && (double)max_m2 / max_m >= MAX_SCORE_RATIO) { ret = -7; goto pem_ret; }
	}

	l = x[0].l_seq - (r.tb - r.qb); // length to merge
	l_seq = x[0].l_seq + x[1].l_seq - l;
	seq = malloc(l_seq + 1);
	qual = malloc(l_seq + 1);
	memcpy(seq,  s[0], x[0].l_seq); memcpy(seq  + x[0].l_seq, &s[1][l], x[1].l_seq - l);
	memcpy(qual, q[0], x[0].l_seq); memcpy(qual + x[0].l_seq, &q[1][l], x[1].l_seq - l);
	for (i = 0, sum_q = 0; i < l; ++i) {
		int k = x[0].l_seq - l + i;
		if (s[0][k] == 4) { // ambiguous
			seq[k]  = s[1][i];
			qual[k] = q[1][i];
		} else if (s[1][i] == 4) { // do nothing
		} else if (s[0][k] == s[1][i]) {
			qual[k] = qual[k] > q[1][i]? qual[k] : q[1][i];
		} else { // s[0][k] != s[1][i] and neither is N
			int qq = q[0][k] < q[1][i]? q[0][k] : q[1][i];
			sum_q += qq >= 3? qq<<1 : 1;
			seq[k]  = q[0][k] > q[1][i]? s[0][k] : s[1][i];
			qual[k] = abs((int)q[0][k] - (int)q[1][i]);
		}
	}
	if (sum_q>>1 > opt->q_thres) { // too many mismatches
		free(seq); free(qual);
		ret = -8; goto pem_ret;
	}

	for (i = 0; i < l_seq; ++i) seq[i] = "ACGTN"[(int)seq[i]], qual[i] += 33;
	seq[l_seq] = qual[l_seq] = 0;

	free(x[1].name); free(x[1].seq); free(x[1].qual); free(x[1].comment);
	memset(&x[1], 0, sizeof(bseq1_t));
	free(x[0].seq); free(x[0].qual);
	x[0].l_seq = l_seq; x[0].seq = (char*)seq; x[0].qual = (char*)qual;

pem_ret:
	free(s[0]); free(s[1]); free(q[0]); free(q[1]);
	return ret;
}

static inline void print_bseq(const bseq1_t *s, int rn)
{
	putchar(s->qual? '@' : '>');
	fputs(s->name, stdout);
	if (rn == 1 || rn == 2) {
		putchar('/'); putchar('0' + rn); putchar('\n');
	} else puts(" merged");
	puts(s->seq);
	if (s->qual) {
		puts("+"); puts(s->qual);
	}
}

typedef struct {
	int n, start;
	bseq1_t *seqs;
	int64_t cnt[MAX_ERR+1];
	const pem_opt_t *opt;
} worker_t;

void *worker(void *data)
{
	worker_t *w = (worker_t*)data;
	int i;
	for (i = w->start; i < w->n>>1; i += w->opt->n_threads)
		++w->cnt[-bwa_pemerge(w->opt, &w->seqs[i<<1])];
	return 0;
}

static void process_seqs(const pem_opt_t *opt, int n_, bseq1_t *seqs, int64_t cnt[MAX_ERR+1])
{
	int i, j, n = n_>>1<<1;
	worker_t *w;

	w = calloc(opt->n_threads, sizeof(worker_t));
	for (i = 0; i < opt->n_threads; ++i) {
		worker_t *p = &w[i];
		p->start = i; p->n = n;
		p->opt = opt;
		p->seqs = seqs;
	}
	if (opt->n_threads == 1) {
		worker(w);
	} else {
		pthread_t *tid;
		tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
		for (i = 0; i < opt->n_threads; ++i) pthread_create(&tid[i], 0, worker, &w[i]);
		for (i = 0; i < opt->n_threads; ++i) pthread_join(tid[i], 0);
		free(tid);
	}
	for (i = 0; i < opt->n_threads; ++i) {
		worker_t *p = &w[i];
		for (j = 0; j <= MAX_ERR; ++j) cnt[j] += p->cnt[j];
	}
	free(w);
	for (i = 0; i < n>>1; ++i) {
		if (seqs[i<<1|1].l_seq != 0) {
			if (opt->flag&2) {
				print_bseq(&seqs[i<<1|0], 1);
				print_bseq(&seqs[i<<1|1], 2);
			}
		} else if (opt->flag&1)
			print_bseq(&seqs[i<<1|0], 0);
	}
	for (i = 0; i < n; ++i) {
		bseq1_t *s = &seqs[i];
		free(s->name); free(s->seq); free(s->qual); free(s->comment);
	}
}

int main_pemerge(int argc, char *argv[])
{
	int c, flag = 0, i, n, min_ovlp = 10;
	int64_t cnt[MAX_ERR+1];
	bseq1_t *bseq;
	gzFile fp, fp2 = 0;
	kseq_t *ks, *ks2 = 0;
	pem_opt_t *opt;

	opt = pem_opt_init();
	while ((c = getopt(argc, argv, "muQ:t:T:")) >= 0) {
		if (c == 'm') flag |= 1;
		else if (c == 'u') flag |= 2;
		else if (c == 'Q') opt->q_thres = atoi(optarg);
		else if (c == 't') opt->n_threads = atoi(optarg);
		else if (c == 'T') min_ovlp = atoi(optarg);
	}
	if (flag == 0) flag = 3;
	opt->flag = flag;
	opt->T = opt->a * min_ovlp;

	if (optind == argc) {
		fprintf(stderr, "\n");
		fprintf(stderr, "Usage:   bwa pemerge [-mu] <read1.fq> [read2.fq]\n\n");
		fprintf(stderr, "Options: -m       output merged reads only\n");
		fprintf(stderr, "         -u       output unmerged reads only\n");
		fprintf(stderr, "         -t INT   number of threads [%d]\n", opt->n_threads);
		fprintf(stderr, "         -T INT   minimum end overlap [%d]\n", min_ovlp);
		fprintf(stderr, "         -Q INT   max sum of errors [%d]\n", opt->q_thres);
		fprintf(stderr, "\n");
		free(opt);
		return 1;
	}

	fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
	ks = kseq_init(fp);
	if (optind + 1 < argc) {
		fp2 = strcmp(argv[optind+1], "-")? gzopen(argv[optind+1], "r") : gzdopen(fileno(stdin), "r");
		ks2 = kseq_init(fp2);
	}

	memset(cnt, 0, 8 * (MAX_ERR+1));
	while ((bseq = bseq_read(opt->n_threads * opt->chunk_size, &n, ks, ks2)) != 0) {
		process_seqs(opt, n, bseq, cnt);
		free(bseq);
	}

	fprintf(stderr, "%12ld %s\n", (long)cnt[0], err_msg[0]);
	for (i = 1; i <= MAX_ERR; ++i)
		fprintf(stderr, "%12ld %s\n", (long)cnt[i], err_msg[i]);
	kseq_destroy(ks);
	gzclose(fp);
	if (ks2) {
		kseq_destroy(ks2);
		gzclose(fp2);
	}
	free(opt);
	return 0;
}
bwa-0.7.3a/QSufSort.c000644 000767 000024 00000030536 12120745361 014170 0ustar00lh3staff000000 000000 /* QSufSort.c

   Original source from qsufsort.c

   Copyright 1999, N. Jesper Larsson, all rights reserved.

   This file contains an implementation of the algorithm presented in "Faster
   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
   Sadakane (sada@is.s.u-tokyo.ac.jp).

   This software may be used freely for any purpose. However, when distributed,
   the original source must be clearly stated, and, when the source code is
   distributed, the copyright notice must be retained and any alterations in
   the code must be clearly marked. No warranty is given regarding the quality
   of this software.

   Modified by Wong Chi-Kwong, 2004

   Changes summary:	- Used long variable and function names
					- Removed global variables
					- Replace pointer references with array references
					- Used insertion sort in place of selection sort and increased insertion sort threshold
					- Reconstructing suffix array from inverse becomes an option
					- Add handling where end-of-text symbol is not necessary < all characters
					- Removed codes for supporting alphabet size > number of characters
  
  No warrenty is given regarding the quality of the modifications.

*/


#include <stdio.h>
#include <stdlib.h>
#include <limits.h>
#include "QSufSort.h"

#define min(value1, value2)						( ((value1) < (value2)) ? (value1) : (value2) )
#define med3(a, b, c)							( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
#define swap(a, b, t);							t = a; a = b; b = t;

// Static functions
static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
							  const qsint_t highestPos, const qsint_t numSortedChar);
static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
							   const qsint_t highestPos, const qsint_t numSortedChar);
static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
									const qsint_t highestPos, const qsint_t numSortedChar);
static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize);
static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
							 const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated);

/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
   n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
   contents of x[n] is disregarded, the n-th symbol being regarded as
   end-of-string smaller than all other symbols.*/
void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
						const qsint_t smallestInputSymbol, const int skipTransform)
{
	qsint_t i, j;
	qsint_t s, negatedSortedGroupLength;
	qsint_t numSymbolAggregated;
	qsint_t numSortedPos = 1;
	qsint_t newAlphabetSize;
   
	if (!skipTransform) {
		/* bucketing possible*/
		newAlphabetSize = QSufSortTransform(V, I, numChar, largestInputSymbol, smallestInputSymbol, 
											numChar, &numSymbolAggregated);
		QSufSortBucketSort(V, I, numChar, newAlphabetSize);
		I[0] = -1;
		V[numChar] = 0;
		numSortedPos = numSymbolAggregated;
	}

	while ((qsint_t)(I[0]) >= -(qsint_t)numChar) {
		i = 0;
		negatedSortedGroupLength = 0;
		do {
			s = I[i];
			if (s < 0) {
				i -= s;						/* skip over sorted group.*/
				negatedSortedGroupLength += s;
			} else {
				if (negatedSortedGroupLength) {
					I[i+negatedSortedGroupLength] = negatedSortedGroupLength;	/* combine preceding sorted groups */
					negatedSortedGroupLength = 0;
				}
				j = V[s] + 1;
				QSufSortSortSplit(V, I, i, j - 1, numSortedPos);
				i = j;
			}
		} while (i <= numChar);
		if (negatedSortedGroupLength) {
			/* array ends with a sorted group.*/
			I[i+negatedSortedGroupLength] = negatedSortedGroupLength;	/* combine sorted groups at end of I.*/
		}
		numSortedPos *= 2;	/* double sorted-depth.*/
	}
}

void QSufSortGenerateSaFromInverse(const qsint_t* V, qsint_t* __restrict I, const qsint_t numChar)
{
	qsint_t i;
	for (i=0; i<=numChar; i++)
		I[V[i]] = i + 1;
}

/* Sorting routine called for each unsorted group. Sorts the array of integers
   (suffix numbers) of length n starting at p. The algorithm is a ternary-split
   quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
   Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
   function is based on Program 7.*/
static void QSufSortSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
							  const qsint_t highestPos, const qsint_t numSortedChar) {

	qsint_t a, b, c, d;
	qsint_t l, m;
	qsint_t f, v, s, t;
	qsint_t tmp;
	qsint_t numItem;

	numItem = highestPos - lowestPos + 1;

	if (numItem <= INSERT_SORT_NUM_ITEM) {
		QSufSortInsertSortSplit(V, I, lowestPos, highestPos, numSortedChar);
		return;
	}

	v = QSufSortChoosePivot(V, I, lowestPos, highestPos, numSortedChar);

	a = b = lowestPos;
	c = d = highestPos;

	while (1) {
		while (c >= b && (f = KEY(V, I, b, numSortedChar)) <= v) {
			if (f == v) {
				swap(I[a], I[b], tmp);
				a++;
			}
			b++;
		}
		while (c >= b && (f = KEY(V, I, c, numSortedChar)) >= v) {
			if (f == v) {
				swap(I[c], I[d], tmp);
				d--;
			}
			c--;
		}
		if (b > c)
			break;
		swap(I[b], I[c], tmp);
		b++;
		c--;
	}

	s = a - lowestPos;
	t = b - a;
	s = min(s, t);
	for (l = lowestPos, m = b - s; m < b; l++, m++) {
		swap(I[l], I[m], tmp);
	}

	s = d - c;
	t = highestPos - d;
	s = min(s, t);
	for (l = b, m = highestPos - s + 1; m <= highestPos; l++, m++) {
		swap(I[l], I[m], tmp);
	}

	s = b - a;
	t = d - c;
	if (s > 0)
		QSufSortSortSplit(V, I, lowestPos, lowestPos + s - 1, numSortedChar);

	// Update group number for equal portion
	a = lowestPos + s;
	b = highestPos - t;
	if (a == b) {
		// Sorted group
		V[I[a]] = a;
		I[a] = -1;
	} else {
		// Unsorted group
		for (c=a; c<=b; c++)
			V[I[c]] = b;
	}

	if (t > 0)
		QSufSortSortSplit(V, I, highestPos - t + 1, highestPos, numSortedChar);

}

/* Algorithm by Bentley & McIlroy.*/
static qsint_t QSufSortChoosePivot(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
							   const qsint_t highestPos, const qsint_t numSortedChar) {

	qsint_t m;
	qsint_t keyl, keym, keyn;
	qsint_t key1, key2, key3;
	qsint_t s;
	qsint_t numItem;

	numItem = highestPos - lowestPos + 1;

	m = lowestPos + numItem / 2;

	s = numItem / 8;
	key1 = KEY(V, I, lowestPos, numSortedChar);
	key2 = KEY(V, I, lowestPos+s, numSortedChar);
	key3 = KEY(V, I, lowestPos+2*s, numSortedChar);
	keyl = med3(key1, key2, key3);
	key1 = KEY(V, I, m-s, numSortedChar);
	key2 = KEY(V, I, m, numSortedChar);
	key3 = KEY(V, I, m+s, numSortedChar);
	keym = med3(key1, key2, key3);
	key1 = KEY(V, I, highestPos-2*s, numSortedChar);
	key2 = KEY(V, I, highestPos-s, numSortedChar);
	key3 = KEY(V, I, highestPos, numSortedChar);
	keyn = med3(key1, key2, key3);

	return med3(keyl, keym, keyn);


}

/* Quadratic sorting method to use for small subarrays. */
static void QSufSortInsertSortSplit(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t lowestPos, 
									const qsint_t highestPos, const qsint_t numSortedChar)
{
	qsint_t i, j;
	qsint_t tmpKey, tmpPos;
	qsint_t numItem;
	qsint_t key[INSERT_SORT_NUM_ITEM], pos[INSERT_SORT_NUM_ITEM];
	qsint_t negativeSortedLength;
	qsint_t groupNum;

	numItem = highestPos - lowestPos + 1;

	for (i=0; i<numItem; i++) {
		pos[i] = I[lowestPos + i];
		key[i] = V[pos[i] + numSortedChar];
	}

	for (i=1; i<numItem; i++) {
		tmpKey = key[i];
		tmpPos = pos[i];
		for (j=i; j>0 && key[j-1] > tmpKey; j--) {
			key[j] = key[j-1];
			pos[j] = pos[j-1];
		}
		key[j] = tmpKey;
		pos[j] = tmpPos;
	}

	negativeSortedLength = -1;

	i = numItem - 1;
	groupNum = highestPos;
	while (i > 0) {
		I[i+lowestPos] = pos[i];
		V[I[i+lowestPos]] = groupNum;
		if (key[i-1] == key[i]) {
			negativeSortedLength = 0;
		} else {
			if (negativeSortedLength < 0)
				I[i+lowestPos] = negativeSortedLength;
			groupNum = i + lowestPos - 1;
			negativeSortedLength--;
		}
		i--;
	}

	I[lowestPos] = pos[0];
	V[I[lowestPos]] = groupNum;
	if (negativeSortedLength < 0)
		I[lowestPos] = negativeSortedLength;
}

/* Bucketsort for first iteration.

   Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
   at least once. x[n] is 0. (This is the corresponding output of transform.) k
   must be at most n+1. p is array of size n+1 whose contents are disregarded.

   Output: x is V and p is I after the initial sorting stage of the refined
   suffix sorting algorithm.*/
      
static void QSufSortBucketSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t alphabetSize)
{
	qsint_t i, c;
	qsint_t d;
	qsint_t groupNum;
	qsint_t currentIndex;

	// mark linked list empty
	for (i=0; i<alphabetSize; i++)
		I[i] = -1;

	// insert to linked list
	for (i=0; i<=numChar; i++) {
		c = V[i];
		V[i] = (qsint_t)(I[c]);
		I[c] = i;
	}

	currentIndex = numChar;
	for (i=alphabetSize; i>0; i--) {
		c = I[i-1];
		d = (qsint_t)(V[c]);
		groupNum = currentIndex;
		V[c] = groupNum;
		if (d >= 0) {
			I[currentIndex] = c;
			while (d >= 0) {
				c = d;
				d = V[c];
				V[c] = groupNum;
				currentIndex--;
				I[currentIndex] = c;
			}
		} else {
			// sorted group
			I[currentIndex] = -1;
		}
		currentIndex--;
	}
}

/* Transforms the alphabet of x by attempting to aggregate several symbols into
   one, while preserving the suffix order of x. The alphabet may also be
   compacted, so that x on output comprises all integers of the new alphabet
   with no skipped numbers.

   Input: x is an array of size n+1 whose first n elements are positive
   integers in the range l...k-1. p is array of size n+1, used for temporary
   storage. q controls aggregation and compaction by defining the maximum intue
   for any symbol during transformation: q must be at least k-l; if q<=n,
   compaction is guaranteed; if k-l>n, compaction is never done; if q is
   INT_MAX, the maximum number of symbols are aggregated into one.
   
   Output: Returns an integer j in the range 1...q representing the size of the
   new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
   set to the number of old symbols grouped into one. Only x[n] is 0.*/
static qsint_t QSufSortTransform(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
							 const qsint_t smallestInputSymbol, const qsint_t maxNewAlphabetSize, qsint_t *numSymbolAggregated)
{
	qsint_t c, i, j;
	qsint_t a;	// numSymbolAggregated
	qsint_t mask;
	qsint_t minSymbolInChunk = 0, maxSymbolInChunk = 0;
	qsint_t newAlphabetSize;
	qsint_t maxNumInputSymbol, maxNumBit, maxSymbol;

	maxNumInputSymbol = largestInputSymbol - smallestInputSymbol + 1;

	for (maxNumBit = 0, i = maxNumInputSymbol; i; i >>= 1) ++maxNumBit;
	maxSymbol = QSINT_MAX >> maxNumBit;

	c = maxNumInputSymbol;
	for (a = 0; a < numChar && maxSymbolInChunk <= maxSymbol && c <= maxNewAlphabetSize; a++) {
		minSymbolInChunk = (minSymbolInChunk << maxNumBit) | (V[a] - smallestInputSymbol + 1);
		maxSymbolInChunk = c;
		c = (maxSymbolInChunk << maxNumBit) | maxNumInputSymbol;
	}

	mask = (1 << (a-1) * maxNumBit) - 1;	/* mask masks off top old symbol from chunk.*/
	V[numChar] = smallestInputSymbol - 1;	/* emulate zero terminator.*/

	/* bucketing possible, compact alphabet.*/
	for (i=0; i<=maxSymbolInChunk; i++)
		I[i] = 0;	/* zero transformation table.*/
	c = minSymbolInChunk;
	for (i=a; i<=numChar; i++) {
		I[c] = 1;			/* mark used chunk symbol.*/
		c = ((c & mask) << maxNumBit) | (V[i] - smallestInputSymbol + 1);	/* shift in next old symbol in chunk.*/
	}
	for (i=1; i<a; i++) {	/* handle last r-1 positions.*/
		I[c] = 1;			/* mark used chunk symbol.*/
		c = (c & mask) << maxNumBit;	/* shift in next old symbol in chunk.*/
	}
	newAlphabetSize = 1;
	for (i=0; i<=maxSymbolInChunk; i++) {
		if (I[i]) {
			I[i] = newAlphabetSize;
			newAlphabetSize++;
		}
	}
	c = minSymbolInChunk;
	for (i=0, j=a; j<=numChar; i++, j++) {
		V[i] = I[c];						/* transform to new alphabet.*/
		c = ((c & mask) << maxNumBit) | (V[j] - smallestInputSymbol + 1);	/* shift in next old symbol in chunk.*/
	}
	for (; i<numChar; i++) {	/* handle last a-1 positions.*/
		V[i] = I[c];			/* transform to new alphabet.*/
		c = (c & mask) << maxNumBit;	/* shift right-end zero in chunk.*/
	}

	V[numChar] = 0;		/* end-of-string symbol is zero.*/

    *numSymbolAggregated = a;
	return newAlphabetSize;
}
bwa-0.7.3a/QSufSort.h000644 000767 000024 00000003156 12120745361 014173 0ustar00lh3staff000000 000000 /* QSufSort.h

   Header file for QSufSort.c

   This file contains an implementation of the algorithm presented in "Faster
   Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko
   Sadakane (sada@is.s.u-tokyo.ac.jp).

   This software may be used freely for any purpose. However, when distributed,
   the original source must be clearly stated, and, when the source code is
   distributed, the copyright notice must be retained and any alterations in
   the code must be clearly marked. No warranty is given regarding the quality
   of this software.

   Modified by Wong Chi-Kwong, 2004

   Changes summary:	- Used long variable and function names
					- Removed global variables
					- Replace pointer references with array references
					- Used insertion sort in place of selection sort and increased insertion sort threshold
					- Reconstructing suffix array from inverse becomes an option
					- Add handling where end-of-text symbol is not necessary < all characters
					- Removed codes for supporting alphabet size > number of characters
  
  No warrenty is given regarding the quality of the modifications.

*/

#ifndef __QSUFSORT_H__
#define __QSUFSORT_H__

#include <stdint.h>

#define KEY(V, I, p, h)					( V[ I[p] + h ] )
#define INSERT_SORT_NUM_ITEM	16

typedef int64_t qsint_t;
#define QSINT_MAX INT64_MAX

void QSufSortSuffixSort(qsint_t* __restrict V, qsint_t* __restrict I, const qsint_t numChar, const qsint_t largestInputSymbol, 
						const qsint_t smallestInputSymbol, const int skipTransform);
void QSufSortGenerateSaFromInverse(const qsint_t *V, qsint_t* __restrict I, const qsint_t numChar);


#endif
bwa-0.7.3a/qualfa2fq.pl000755 000767 000024 00000001150 12120745361 014506 0ustar00lh3staff000000 000000 #!/usr/bin/perl -w

use strict;
use warnings;

die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);

my ($fhs, $fhq, $q);
open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;

$/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
while (<$fhs>) {
  $q = <$fhq>;
  print "\@$_";
  $/ = ">";
  $_ = <$fhs>; $q = <$fhq>;
  chomp; chomp($q);
  $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
  print $_, "+\n";
  for (my $i = 0; $i < length($q); $i += 60) {
	print substr($q, $i, 60), "\n";
  }
  $/ = "\n";
}

close($fhs); close($fhq);
bwa-0.7.3a/README000644 000767 000024 00000001456 12120745361 013155 0ustar00lh3staff000000 000000 Released packages can be downloaded from SourceForge.net:

  http://sourceforge.net/projects/bio-bwa/files/

Introduction and FAQ are available at:

  http://bio-bwa.sourceforge.net

Manual page at:

  http://bio-bwa.sourceforge.net/bwa.shtml

Mailing list:

  bio-bwa-help@lists.sourceforge.net

To sign up:

  http://sourceforge.net/mail/?group_id=276243

Publications (Open Access):

  http://www.ncbi.nlm.nih.gov/pubmed/20080505
  http://www.ncbi.nlm.nih.gov/pubmed/19451168

Incomplete list of citations (via HubMed.org):

  http://www.hubmed.org/references.cgi?uids=20080505
  http://www.hubmed.org/references.cgi?uids=19451168

Related projects:

  http://pbwa.sourceforge.net/
  http://www.many-core.group.cam.ac.uk/projects/lam.shtml
  http://biodoop-seal.sourceforge.net/
  http://gitorious.org/bwa-cuda
bwa-0.7.3a/utils.c000644 000767 000024 00000010235 12120745361 013574 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#include <stdio.h>
#include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <errno.h>
#include <sys/resource.h>
#include <sys/time.h>
#include "utils.h"

#include "ksort.h"
#define pair64_lt(a, b) ((a).x < (b).x || ((a).x == (b).x && (a).y < (b).y))
KSORT_INIT(128, pair64_t, pair64_lt)
KSORT_INIT(64,  uint64_t, ks_lt_generic)

#include "kseq.h"
KSEQ_INIT2(, gzFile, gzread)

/********************
 * System utilities *
 ********************/

FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
{
	FILE *fp = 0;
	if (strcmp(fn, "-") == 0)
		return (strstr(mode, "r"))? stdin : stdout;
	if ((fp = fopen(fn, mode)) == 0) {
		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
		abort();
	}
	return fp;
}

FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp)
{
	if (freopen(fn, mode, fp) == 0) {
		fprintf(stderr, "[%s] fail to open file '%s': ", func, fn);
		perror(NULL);
		fprintf(stderr, "Abort!\n");
		abort();
	}
	return fp;
}

gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
{
	gzFile fp;
	if (strcmp(fn, "-") == 0)
		return gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
	if ((fp = gzopen(fn, mode)) == 0) {
		fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
		abort();
	}
	return fp;
}

void err_fatal(const char *header, const char *fmt, ...)
{
	va_list args;
	va_start(args, fmt);
	fprintf(stderr, "[%s] ", header);
	vfprintf(stderr, fmt, args);
	fprintf(stderr, " Abort!\n");
	va_end(args);
	abort();
}

void err_fatal_simple_core(const char *func, const char *msg)
{
	fprintf(stderr, "[%s] %s Abort!\n", func, msg);
	abort();
}

size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
{
	size_t ret = fwrite(ptr, size, nmemb, stream);
	if (ret != nmemb) 
		err_fatal_simple_core("fwrite", strerror(errno));
	return ret;
}

int err_printf(const char *format, ...) 
{
	va_list arg;
	int done;
	va_start(arg, format);
	done = vfprintf(stdout, format, arg);
	int saveErrno = errno;
	va_end(arg);
	if (done < 0) err_fatal_simple_core("vfprintf(stdout)", strerror(saveErrno));
	return done;
}

int err_fprintf(FILE *stream, const char *format, ...) 
{
	va_list arg;
	int done;
	va_start(arg, format);
	done = vfprintf(stream, format, arg);
	int saveErrno = errno;
	va_end(arg);
	if (done < 0) err_fatal_simple_core("vfprintf", strerror(saveErrno));
	return done;
}

int err_fflush(FILE *stream) 
{
	int ret = fflush(stream);
	if (ret != 0) err_fatal_simple_core("fflush", strerror(errno));
	return ret;
}

int err_fclose(FILE *stream) 
{
	int ret = fclose(stream);
	if (ret != 0) err_fatal_simple_core("fclose", strerror(errno));
	return ret;
}

/*********
 * Timer *
 *********/

double cputime()
{
	struct rusage r;
	getrusage(RUSAGE_SELF, &r);
	return r.ru_utime.tv_sec + r.ru_stime.tv_sec + 1e-6 * (r.ru_utime.tv_usec + r.ru_stime.tv_usec);
}

double realtime()
{
	struct timeval tp;
	struct timezone tzp;
	gettimeofday(&tp, &tzp);
	return tp.tv_sec + tp.tv_usec * 1e-6;
}
bwa-0.7.3a/utils.h000644 000767 000024 00000006000 12120745361 013574 0ustar00lh3staff000000 000000 /* The MIT License

   Copyright (c) 2008 Genome Research Ltd (GRL).

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <lh3@sanger.ac.uk> */

#ifndef LH3_UTILS_H
#define LH3_UTILS_H

#include <stdint.h>
#include <stdio.h>
#include <zlib.h>

#ifdef __GNUC__
// Tell GCC to validate printf format string and args
#define ATTRIBUTE(list) __attribute__ (list)
#else
#define ATTRIBUTE(list)
#endif

#define err_fatal_simple(msg) err_fatal_simple_core(__func__, msg)
#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
#define xreopen(fn, mode, fp) err_xreopen_core(__func__, fn, mode, fp)
#define xzopen(fn, mode) err_xzopen_core(__func__, fn, mode)
#define xassert(cond, msg) if ((cond) == 0) err_fatal_simple_core(__func__, msg)

typedef struct {
	uint64_t x, y;
} pair64_t;

typedef struct { size_t n, m; uint64_t *a; } uint64_v;
typedef struct { size_t n, m; pair64_t *a; } pair64_v;

#ifdef __cplusplus
extern "C" {
#endif

	void err_fatal(const char *header, const char *fmt, ...);
	void err_fatal_simple_core(const char *func, const char *msg);
	FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
	FILE *err_xreopen_core(const char *func, const char *fn, const char *mode, FILE *fp);
	gzFile err_xzopen_core(const char *func, const char *fn, const char *mode);
    size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
	int err_fprintf(FILE *stream, const char *format, ...)
        ATTRIBUTE((format(printf, 2, 3)));
	int err_printf(const char *format, ...)
        ATTRIBUTE((format(printf, 1, 2)));
	int err_fflush(FILE *stream);
	int err_fclose(FILE *stream);

	double cputime();
	double realtime();

	void ks_introsort_64 (size_t n, uint64_t *a);
	void ks_introsort_128(size_t n, pair64_t *a);

#ifdef __cplusplus
}
#endif

static inline uint64_t hash_64(uint64_t key)
{
	key += ~(key << 32);
	key ^= (key >> 22);
	key += ~(key << 13);
	key ^= (key >> 8);
	key += (key << 3);
	key ^= (key >> 15);
	key += ~(key << 27);
	key ^= (key >> 31);
	return key;
}

#endif
bwa-0.7.3a/xa2multi.pl000755 000767 000024 00000001332 12120745361 014373 0ustar00lh3staff000000 000000 #!/usr/bin/perl -w

use strict;
use warnings;

while (<>) {
	if (/\tXA:Z:(\S+)/) {
		my $l = $1;
		print;
		my @t = split("\t");
		while ($l =~ /([^,;]+),([-+]\d+),([^,]+),(\d+);/g) {
			my $mchr = ($t[6] eq $1)? '=' : $t[6]; # FIXME: TLEN/ISIZE is not calculated!
			my $seq = $t[9];
			my $phred = $t[10];
			# if alternative alignment has other orientation than primary, 
			# then print the reverse (complement) of sequence and phred string
			if ((($t[1]&0x10)>0) xor ($2<0)) {
				$seq = reverse $seq;
				$seq =~ tr/ACGTacgt/TGCAtgca/;
				$phred = reverse $phred;
			}
			print(join("\t", $t[0], 0x100|($t[1]&0x6e9)|($2<0?0x10:0), $1, abs($2), 0, $3, @t[6..7], 0, $seq, $phred, "NM:i:$4"), "\n");
		}
	} else { print; }
}