zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

bugfix: incorrect bandwidth

This commit is contained in:
Heng Li 2012-04-02 11:39:40 -04:00
parent d3169804f6
commit 36f2fd6238
1 changed files with 20 additions and 24 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

44
bwtsw2_aux.c
View File

@ -1,7 +1,6 @@
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <assert.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@ -46,8 +45,6 @@ unsigned char nt_comp_table[256] = {
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);
static int64_t g_l_pac = 0;
bsw2opt_t *bsw2_init_opt()
{
bsw2opt_t *o = (bsw2opt_t*)calloc(1, sizeof(bsw2opt_t));
@ -191,7 +188,6 @@ static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8
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;
assert(p->k + p->len <= g_l_pac);
for (k = p->k; k < p->k + p->len; ++k) // in principle, no out-of-boundary here
target[k - p->k] = pac[k>>2] >> (~k&3)*2 & 0x3;
score = aln_global_core(target, p->len, query, end - beg, &par, path, &path_len);
@ -201,14 +197,8 @@ static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], const uint8
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) = (%d, %d, %d, %d)\n", __func__, name, score, p->G, lq, end - beg, p->len, glen);
if (p->G - score > 100) {
char *t;
t = malloc((p->len > end - beg? p->len : end - beg) + 2);
for (j = 0; j < p->len; ++j) t[j] = "ACGTN"[target[j]]; t[j++] = '\n'; t[j] = 0; fputs(t, stderr);
for (j = 0; j < end - beg; ++j) t[j] = "ACGTN"[query[j]]; t[j++] = '\n'; t[j] = 0; fputs(t, stderr);
free(t);
}
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);
}
if (beg != 0 || end < lq) { // write soft clipping
q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2));
@ -572,12 +562,27 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
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;
dst->t = src->t;
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 = *_opt;
bsw2opt_t opt;
bsw2global_t *pool = bsw2_global_init();
bwtsw2_t **buf;
buf = calloc(_seq->n, sizeof(void*));
@ -587,21 +592,12 @@ static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t
int i, l, k;
bwtsw2_t *b[2];
l = p->l;
// set opt->t
opt.t = _opt->t;
if (opt.t < log(l) * opt.coef) opt.t = (int)(log(l) * opt.coef + .499);
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 opt->bw
opt.bw = _opt->bw;
k = (l * opt.a - 2 * opt.q) / (2 * opt.r + opt.a);
i = (l * opt.a - opt.a - opt.t) / opt.r;
if (k > i) k = i;
if (k < 1) k = 1; // I do not know if k==0 causes troubles
opt.bw = _opt->bw < k? _opt->bw : k;
// set seq[2] and rseq[2]
seq[0] = calloc(l * 4, 1);
seq[1] = seq[0] + l;
@ -655,6 +651,7 @@ static void bsw2_aln_core(bsw2seq_t *_seq, const bsw2opt_t *_opt, const bntseq_t
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]);
}
@ -766,7 +763,6 @@ void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, c
uint8_t *pac;
bsw2seq_t *_seq;
g_l_pac = bns->l_pac;
pac = calloc(bns->l_pac/4+1, 1);
if (pac == 0) {
fprintf(stderr, "[bsw2_aln] insufficient memory!\n");