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#include <string.h>
#include <stdio.h>
#include <zlib.h>
#include <assert.h>
#include "bntseq.h"
#include "bwa.h"
#include "ksw.h"
#include "utils.h"
#include "kstring.h"
#include "kvec.h"
#ifdef USE_MALLOC_WRAPPERS
# include "malloc_wrap.h"
#endif
int bwa_verbose = 3;
char bwa_rg_id[256];
char *bwa_pg;
/************************
* 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]);
seqs[n].id = n;
size += seqs[n++].l_seq;
if (ks2) {
trim_readno(&ks2->name);
kseq2bseq1(ks2, &seqs[n]);
seqs[n].id = 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;
}
void bseq_classify(int n, bseq1_t *seqs, int m[2], bseq1_t *sep[2])
{
int i, has_last;
kvec_t(bseq1_t) a[2] = {{0,0,0}, {0,0,0}};
for (i = 1, has_last = 1; i < n; ++i) {
if (has_last) {
if (strcmp(seqs[i].name, seqs[i-1].name) == 0) {
kv_push(bseq1_t, a[1], seqs[i-1]);
kv_push(bseq1_t, a[1], seqs[i]);
has_last = 0;
} else kv_push(bseq1_t, a[0], seqs[i-1]);
} else has_last = 1;
}
if (has_last) kv_push(bseq1_t, a[0], seqs[i-1]);
sep[0] = a[0].a, m[0] = a[0].n;
sep[1] = a[1].a, m[1] = a[1].n;
}
/*****************
* 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_cigar2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, 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;
kstring_t str;
const char *int2base;
if (n_cigar) *n_cigar = 0;
if (NM) *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
// UPDATE: we come to this block now... FIXME: due to an issue in mem_reg2aln(), we never come to this block. This does not affect accuracy, but it hurts performance.
if (n_cigar) {
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, max_ins, max_del, min_w;
// set the band-width
max_ins = (int)((double)(((l_query+1)>>1) * mat[0] - o_ins) / e_ins + 1.);
max_del = (int)((double)(((l_query+1)>>1) * mat[0] - o_del) / e_del + 1.);
max_gap = max_ins > max_del? max_ins : max_del;
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
if (bwa_verbose >= 4) {
printf("* Global bandwidth: %d\n", w);
printf("* Global ref: "); for (i = 0; i < rlen; ++i) putchar("ACGTN"[(int)rseq[i]]); putchar('\n');
printf("* Global query: "); for (i = 0; i < l_query; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
}
*score = ksw_global2(l_query, query, rlen, rseq, 5, mat, o_del, e_del, o_ins, e_ins, w, n_cigar, &cigar);
}
if (NM && n_cigar) {// compute NM and MD
int k, x, y, u, n_mm = 0, n_gap = 0;
str.l = str.m = *n_cigar * 4; str.s = (char*)cigar; // append MD to CIGAR
int2base = rb < l_pac? "ACGTN" : "TGCAN";
for (k = 0, x = y = u = 0; k < *n_cigar; ++k) {
int op, len;
cigar = (uint32_t*)str.s;
op = cigar[k]&0xf, len = cigar[k]>>4;
if (op == 0) { // match
for (i = 0; i < len; ++i) {
if (query[x + i] != rseq[y + i]) {
kputw(u, &str);
kputc(int2base[rseq[y+i]], &str);
++n_mm; u = 0;
} else ++u;
}
x += len; y += len;
} else if (op == 2) { // deletion
if (k > 0 && k < *n_cigar - 1) { // don't do the following if D is the first or the last CIGAR
kputw(u, &str); kputc('^', &str);
for (i = 0; i < len; ++i)
kputc(int2base[rseq[y+i]], &str);
u = 0; n_gap += len;
}
y += len;
} else if (op == 1) x += len, n_gap += len; // insertion
}
kputw(u, &str); kputc(0, &str);
*NM = n_mm + n_gap;
cigar = (uint32_t*)str.s;
}
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;
}
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)
{
return bwa_gen_cigar2(mat, q, r, q, r, w_, l_pac, pac, l_query, query, rb, re, score, n_cigar, NM);
}
/*********************
* 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_from_disk(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) {
int i, c;
idx->bns = bns_restore(prefix);
for (i = c = 0; i < idx->bns->n_seqs; ++i)
if (idx->bns->anns[i].is_alt) ++c;
if (bwa_verbose >= 3)
fprintf(stderr, "[M::%s] read %d ALT contigs\n", __func__, c);
if (which & BWA_IDX_PAC) {
idx->pac = calloc(idx->bns->l_pac/4+1, 1);
err_fread_noeof(idx->pac, 1, idx->bns->l_pac/4+1, idx->bns->fp_pac); // concatenated 2-bit encoded sequence
err_fclose(idx->bns->fp_pac);
idx->bns->fp_pac = 0;
}
}
free(prefix);
return idx;
}
bwaidx_t *bwa_idx_load(const char *hint, int which)
{
return bwa_idx_load_from_disk(hint, which);
}
void bwa_idx_destroy(bwaidx_t *idx)
{
if (idx == 0) return;
if (idx->mem == 0) {
if (idx->bwt) bwt_destroy(idx->bwt);
if (idx->bns) bns_destroy(idx->bns);
if (idx->pac) free(idx->pac);
} else {
free(idx->bwt); free(idx->bns->anns); free(idx->bns);
if (!idx->is_shm) free(idx->mem);
}
free(idx);
}
int bwa_mem2idx(int64_t l_mem, uint8_t *mem, bwaidx_t *idx)
{
int64_t k = 0, x;
int i;
// generate idx->bwt
x = sizeof(bwt_t); idx->bwt = malloc(x); memcpy(idx->bwt, mem + k, x); k += x;
x = idx->bwt->bwt_size * 4; idx->bwt->bwt = (uint32_t*)(mem + k); k += x;
x = idx->bwt->n_sa * sizeof(bwtint_t); idx->bwt->sa = (bwtint_t*)(mem + k); k += x;
// generate idx->bns and idx->pac
x = sizeof(bntseq_t); idx->bns = malloc(x); memcpy(idx->bns, mem + k, x); k += x;
x = idx->bns->n_holes * sizeof(bntamb1_t); idx->bns->ambs = (bntamb1_t*)(mem + k); k += x;
x = idx->bns->n_seqs * sizeof(bntann1_t); idx->bns->anns = malloc(x); memcpy(idx->bns->anns, mem + k, x); k += x;
for (i = 0; i < idx->bns->n_seqs; ++i) {
idx->bns->anns[i].name = (char*)(mem + k); k += strlen(idx->bns->anns[i].name) + 1;
idx->bns->anns[i].anno = (char*)(mem + k); k += strlen(idx->bns->anns[i].anno) + 1;
}
idx->pac = (uint8_t*)(mem + k); k += idx->bns->l_pac/4+1;
assert(k == l_mem);
idx->l_mem = k; idx->mem = mem;
return 0;
}
int bwa_idx2mem(bwaidx_t *idx)
{
int i;
int64_t k, x, tmp;
uint8_t *mem;
// copy idx->bwt
x = idx->bwt->bwt_size * 4;
mem = realloc(idx->bwt->bwt, sizeof(bwt_t) + x); idx->bwt->bwt = 0;
memmove(mem + sizeof(bwt_t), mem, x);
memcpy(mem, idx->bwt, sizeof(bwt_t)); k = sizeof(bwt_t) + x;
x = idx->bwt->n_sa * sizeof(bwtint_t); mem = realloc(mem, k + x); memcpy(mem + k, idx->bwt->sa, x); k += x;
free(idx->bwt->sa);
free(idx->bwt); idx->bwt = 0;
// copy idx->bns
tmp = idx->bns->n_seqs * sizeof(bntann1_t) + idx->bns->n_holes * sizeof(bntamb1_t);
for (i = 0; i < idx->bns->n_seqs; ++i) // compute the size of heap-allocated memory
tmp += strlen(idx->bns->anns[i].name) + strlen(idx->bns->anns[i].anno) + 2;
mem = realloc(mem, k + sizeof(bntseq_t) + tmp);
x = sizeof(bntseq_t); memcpy(mem + k, idx->bns, x); k += x;
x = idx->bns->n_holes * sizeof(bntamb1_t); memcpy(mem + k, idx->bns->ambs, x); k += x;
free(idx->bns->ambs);
x = idx->bns->n_seqs * sizeof(bntann1_t); memcpy(mem + k, idx->bns->anns, x); k += x;
for (i = 0; i < idx->bns->n_seqs; ++i) {
x = strlen(idx->bns->anns[i].name) + 1; memcpy(mem + k, idx->bns->anns[i].name, x); k += x;
x = strlen(idx->bns->anns[i].anno) + 1; memcpy(mem + k, idx->bns->anns[i].anno, x); k += x;
free(idx->bns->anns[i].name); free(idx->bns->anns[i].anno);
}
free(idx->bns->anns);
// copy idx->pac
x = idx->bns->l_pac/4+1;
mem = realloc(mem, k + x);
memcpy(mem + k, idx->pac, x); k += x;
free(idx->bns); idx->bns = 0;
free(idx->pac); idx->pac = 0;
return bwa_mem2idx(k, mem, idx);
}
/***********************
* SAM header routines *
***********************/
void bwa_print_sam_hdr(const bntseq_t *bns, const char *hdr_line)
{
int i, n_SQ = 0;
extern char *bwa_pg;
if (hdr_line) {
const char *p = hdr_line;
while ((p = strstr(p, "@SQ\t")) != 0) {
if (p == hdr_line || *(p-1) == '\n') ++n_SQ;
p += 4;
}
}
if (n_SQ == 0) {
for (i = 0; i < bns->n_seqs; ++i)
err_printf("@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
} else if (n_SQ != bns->n_seqs && bwa_verbose >= 2)
fprintf(stderr, "[W::%s] %d @SQ lines provided with -H; %d sequences in the index. Continue anyway.\n", __func__, n_SQ, bns->n_seqs);
if (hdr_line) err_printf("%s\n", hdr_line);
if (bwa_pg) err_printf("%s\n", bwa_pg);
}
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;
}
char *bwa_insert_header(const char *s, char *hdr)
{
int len = 0;
if (s == 0 || s[0] != '@') return hdr;
if (hdr) {
len = strlen(hdr);
hdr = realloc(hdr, len + strlen(s) + 2);
hdr[len++] = '\n';
strcpy(hdr + len, s);
} else hdr = strdup(s);
bwa_escape(hdr + len);
return hdr;
}
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