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r360: output alternative primary alignments in XA

This commit is contained in:
Heng Li 2013-03-11 23:43:58 -04:00
parent 6c665189ad
commit dab5b17c1a
2 changed files with 19 additions and 2 deletions
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19
bwamem.c
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@ -702,6 +702,22 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }
if (n > 1) { // output multiple primary hits
kputsn("\tXA:Z:", 6, str);
for (i = 0; i < n; ++i) {
const mem_aln_t *r = &list[i];
int k;
if (i == which) continue;
kputs(bns->anns[r->rid].name, str); kputc(',', str);
kputc("+-"[r->is_rev], str);
kputl(r->pos+1, str); kputc(',', str);
for (k = 0; k < r->n_cigar; ++k) {
kputw(r->cigar[k]>>4, str); kputc("MIDSH"[r->cigar[k]&0xf], str);
}
kputc(',', str);
kputw(r->NM, str); kputc(';', str);
}
}
if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
kputc('\n', str);
}
@ -742,7 +758,8 @@ 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);
q->flag |= extra_flag;
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;
}

2
main.c
View File

@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.2-r359-beta"
#define PACKAGE_VERSION "0.7.2-r360-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);