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fast-bwa/bwa.c

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/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2009-2018 Broad Institute, Inc.
2008-2009 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.
*/
#include <string.h>
#include <stdio.h>
#include <zlib.h>
#include <assert.h>
#include <unistd.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;
int bwa_dbg = 0;
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 char *dupkstring(const kstring_t *str, int dupempty)
{
char *s = (str->l > 0 || dupempty)? malloc(str->l + 1) : NULL;
if (!s) return NULL;
memcpy(s, str->s, str->l);
s[str->l] = '\0';
return s;
}
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 = dupkstring(&ks->name, 1);
s->comment = dupkstring(&ks->comment, 0);
s->seq = dupkstring(&ks->seq, 1);
s->qual = dupkstring(&ks->qual, 0);
s->l_seq = ks->seq.l;
}
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((int)rlen - l_query) + 1) >> 1;
w = w < w_? w : w_;
min_w = abs((int)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 + 10);
strcpy(prefix, hint);
//strcpy(prefix + l_hint, ".64.bwt");
strcpy(prefix + l_hint, ".ne.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;
}
fprintf(stderr, "zzh-1\n");
tmp = calloc(strlen(prefix) + 5, 1);
strcat(strcpy(tmp, prefix), ".bwt"); // FM-index
bwt = bwt_restore_bwt(tmp);
fprintf(stderr, "zzh-1\n");
strcat(strcpy(tmp, prefix), ".33.4.sa"); // partial suffix array (SA)
bwt_restore_sa(tmp, bwt);
fprintf(stderr, "zzh-after-sa\n");
free(tmp); free(prefix);
return bwt;
}
FMTIndex *bwa_idx_load_fmt(const char *hint)
{
char *fmt_idx_fn, *kmer_idx_fn, *sa_fn;
FMTIndex *fmt;
char suffix[32];
int l_hint = strlen(hint);
fmt_idx_fn = malloc(l_hint + 32);
kmer_idx_fn = malloc(l_hint + 32);
sa_fn = malloc(l_hint + 32);
sprintf(suffix, ".256.%d.fmt", FMT_MID_INTERVAL);
strcpy(fmt_idx_fn, hint);
strcpy(fmt_idx_fn + l_hint, suffix);
sprintf(suffix, ".%d.kmer", KMER_LEN);
strcpy(kmer_idx_fn, hint);
strcpy(kmer_idx_fn + l_hint, suffix);
if (access(fmt_idx_fn, F_OK) != 0 || access(kmer_idx_fn, F_OK) != 0)
{
if (bwa_verbose >= 1)
fprintf(stderr, "[E::%s] fail to locate the index files\n", __func__);
return 0;
}
fprintf(stderr, "zzh-fmt-1\n");
fmt = fmt_restore_fmt(fmt_idx_fn);
fprintf(stderr, "%s\n", kmer_idx_fn);
fmt->kmer_entry = fmt_restore_kmer_idx(kmer_idx_fn);
fprintf(stderr, "zzh-fmt-2\n");
strcpy(sa_fn, hint);
sprintf(suffix, ".33.%d.sa", SA_INTV);
strcpy(sa_fn + l_hint, suffix); // partial suffix array (SA)
// fmt_restore_sa(sa_fn, fmt);
free(fmt_idx_fn);
free(kmer_idx_fn);
free(sa_fn);
return fmt;
}
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_BWT) {
idx->fmt = bwa_idx_load_fmt(hint);
idx->fmt->sa = idx->bwt->sa;
idx->fmt->n_sa = idx->bwt->n_sa;
idx->fmt->sa_intv = idx->bwt->sa_intv;
}
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 = SA_BYTES(idx->bwt->n_sa); idx->bwt->sa = (uint8_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 = SA_BYTES(idx->bwt->n_sa); 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_HD = 0, n_SQ = 0;
extern char *bwa_pg;
if (hdr_line) {
// check for HD line
const char *p = hdr_line;
if ((p = strstr(p, "@HD")) != 0) {
++n_HD;
}
// check for SQ lines
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", bns->anns[i].name, bns->anns[i].len);
if (bns->anns[i].is_alt) err_printf("\tAH:*\n");
else err_fputc('\n', stdout);
}
} 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 (n_HD == 0) {
err_printf("@HD\tVN:1.5\tSO:unsorted\tGO:query\n");
}
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;
}
if (strstr(s, "\t") != NULL) {
if (bwa_verbose >= 1) fprintf(stderr, "[E::%s] the read group line contained literal <tab> characters -- replace with escaped tabs: \\t\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 within 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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