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Merge branch 'master' into master_fixes

This commit is contained in:
Rob Davies 2013-03-19 12:11:51 +00:00
parent c862a1a396 8437cd4edd
commit c89756e2b0
3 changed files with 32 additions and 24 deletions
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2
bwa.c
View File

@ -144,7 +144,7 @@ int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns,
{
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
if (*rb < bns->l_pac && *re > bns->l_pac) { // cross the for-rev boundary; actually with BWA-MEM, we should never come to here
*qb = *qe = *rb = *re = -1;
return -1; // unable to fix
} else {

26
bwamem.c
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@ -759,11 +759,11 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
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;
int k;
kv_init(aa);
str.l = str.m = 0; str.s = 0;
for (k = 0; k < a->n; ++k) {
mem_alnreg_t *p = &a->a[k];
mem_aln_t *q;
@ -772,20 +772,25 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
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);
if (q->rid < 0) { // unfixable cross-reference alignment
--aa.n;
continue;
}
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 {
if (aa.n == 0) { // no alignments good enough; then write an unaligned record
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);
} else {
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);
}
s->sam = str.s;
}
@ -848,7 +853,10 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
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);
if (bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) { // unfixable cross-reference alignment
a.rid = -1; a.pos = -1; a.flag |= 0x4;
return a;
}
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);

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.3a-r367"
#define PACKAGE_VERSION "0.7.3-r369-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);