Fetching contributors…
Cannot retrieve contributors at this time
447 lines (420 sloc) 13.5 KB
/* 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 <errno.h>
#include "bntseq.h"
#include "utils.h"
#include "kseq.h"
KSEQ_DECLARE(gzFile)
#include "khash.h"
KHASH_MAP_INIT_STR(str, int)
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
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");
err_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;
err_fprintf(fp, "%d %s", p->gi, p->name);
if (p->anno[0]) err_fprintf(fp, " %s\n", p->anno);
else err_fprintf(fp, "\n");
err_fprintf(fp, "%lld %d %d\n", (long long)p->offset, p->len, p->n_ambs);
}
err_fflush(fp);
err_fclose(fp);
}
{ // dump .amb
strcpy(str, prefix); strcat(str, ".amb");
fp = xopen(str, "w");
err_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;
err_fprintf(fp, "%lld %d %c\n", (long long)p->offset, p->len, p->amb);
}
err_fflush(fp);
err_fclose(fp);
}
}
bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename)
{
char str[8192];
FILE *fp;
const char *fname;
bntseq_t *bns;
long long xx;
int i;
int scanres;
bns = (bntseq_t*)calloc(1, sizeof(bntseq_t));
{ // read .ann
fp = xopen(fname = ann_filename, "r");
scanres = fscanf(fp, "%lld%d%u", &xx, &bns->n_seqs, &bns->seed);
if (scanres != 3) goto badread;
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
scanres = fscanf(fp, "%u%s", &p->gi, str);
if (scanres != 2) goto badread;
p->name = strdup(str);
// read fasta comments
while (q - str < sizeof(str) - 1 && (c = fgetc(fp)) != '\n' && c != EOF) *q++ = c;
while (c != '\n' && c != EOF) c = fgetc(fp);
if (c == EOF) {
scanres = EOF;
goto badread;
}
*q = 0;
if (q - str > 1 && strcmp(str, " (null)") != 0) p->anno = strdup(str + 1); // skip leading space
else p->anno = strdup("");
// read the rest
scanres = fscanf(fp, "%lld%d%d", &xx, &p->len, &p->n_ambs);
if (scanres != 3) goto badread;
p->offset = xx;
}
err_fclose(fp);
}
{ // read .amb
int64_t l_pac;
int32_t n_seqs;
fp = xopen(fname = amb_filename, "r");
scanres = fscanf(fp, "%lld%d%d", &xx, &n_seqs, &bns->n_holes);
if (scanres != 3) goto badread;
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;
scanres = fscanf(fp, "%lld%d%s", &xx, &p->len, str);
if (scanres != 3) goto badread;
p->offset = xx;
p->amb = str[0];
}
err_fclose(fp);
}
{ // open .pac
bns->fp_pac = xopen(pac_filename, "rb");
}
return bns;
badread:
if (EOF == scanres) {
err_fatal(__func__, "Error reading %s : %s\n", fname, ferror(fp) ? strerror(errno) : "Unexpected end of file");
}
err_fatal(__func__, "Parse error reading %s\n", fname);
}
bntseq_t *bns_restore(const char *prefix)
{
char ann_filename[1024], amb_filename[1024], pac_filename[1024], alt_filename[1024];
FILE *fp;
bntseq_t *bns;
strcat(strcpy(ann_filename, prefix), ".ann");
strcat(strcpy(amb_filename, prefix), ".amb");
strcat(strcpy(pac_filename, prefix), ".pac");
bns = bns_restore_core(ann_filename, amb_filename, pac_filename);
if (bns == 0) return 0;
if ((fp = fopen(strcat(strcpy(alt_filename, prefix), ".alt"), "r")) != 0) { // read .alt file if present
char str[1024];
khash_t(str) *h;
int c, i, absent;
khint_t k;
h = kh_init(str);
for (i = 0; i < bns->n_seqs; ++i) {
k = kh_put(str, h, bns->anns[i].name, &absent);
kh_val(h, k) = i;
}
i = 0;
while ((c = fgetc(fp)) != EOF) {
if (c == '\t' || c == '\n' || c == '\r') {
str[i] = 0;
if (str[0] != '@') {
k = kh_get(str, h, str);
if (k != kh_end(h))
bns->anns[kh_val(h, k)].is_alt = 1;
}
while (c != '\n' && c != EOF) c = fgetc(fp);
i = 0;
} else str[i++] = c; // FIXME: potential segfault here
}
kh_destroy(str, h);
fclose(fp);
}
return bns;
}
void bns_destroy(bntseq_t *bns)
{
if (bns == 0) return;
else {
int i;
if (bns->fp_pac) err_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.l > 0? 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;
err_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;
err_fwrite(&ct, 1, 1, fp);
}
ct = bns->l_pac % 4;
err_fwrite(&ct, 1, 1, fp);
// close .pac file
err_fflush(fp);
err_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);
err_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_intv2rid(const bntseq_t *bns, int64_t rb, int64_t re)
{
int is_rev, rid_b, rid_e;
if (rb < bns->l_pac && re > bns->l_pac) return -2;
assert(rb <= re);
rid_b = bns_pos2rid(bns, bns_depos(bns, rb, &is_rev));
rid_e = rb < re? bns_pos2rid(bns, bns_depos(bns, re - 1, &is_rev)) : rid_b;
return rid_b == rid_e? rid_b : -1;
}
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;
}
uint8_t *bns_fetch_seq(const bntseq_t *bns, const uint8_t *pac, int64_t *beg, int64_t mid, int64_t *end, int *rid)
{
int64_t far_beg, far_end, len;
int is_rev;
uint8_t *seq;
if (*end < *beg) *end ^= *beg, *beg ^= *end, *end ^= *beg; // if end is smaller, swap
assert(*beg <= mid && mid < *end);
*rid = bns_pos2rid(bns, bns_depos(bns, mid, &is_rev));
far_beg = bns->anns[*rid].offset;
far_end = far_beg + bns->anns[*rid].len;
if (is_rev) { // flip to the reverse strand
int64_t tmp = far_beg;
far_beg = (bns->l_pac<<1) - far_end;
far_end = (bns->l_pac<<1) - tmp;
}
*beg = *beg > far_beg? *beg : far_beg;
*end = *end < far_end? *end : far_end;
seq = bns_get_seq(bns->l_pac, pac, *beg, *end, &len);
if (seq == 0 || *end - *beg != len) {
fprintf(stderr, "[E::%s] begin=%ld, mid=%ld, end=%ld, len=%ld, seq=%p, rid=%d, far_beg=%ld, far_end=%ld\n",
__func__, (long)*beg, (long)mid, (long)*end, (long)len, seq, *rid, (long)far_beg, (long)far_end);
}
assert(seq && *end - *beg == len); // assertion failure should never happen
return seq;
}