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to test the new sam writer...

This commit is contained in:
Heng Li 2013-03-11 21:55:52 -04:00
parent 47952b6f3f
commit c7edaa8e84
1 changed files with 33 additions and 1 deletions
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34
bwamem.c
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@ -742,7 +742,7 @@ void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const m
// print up to CIGAR // print up to CIGAR
kputs(s->name, str); kputc('\t', str); // QNAME kputs(s->name, str); kputc('\t', str); // QNAME
kputw(p->flag, str); kputc('\t', str); // FLAG kputw((p->flag&0xffff) | (p->flag&0x10000? 0x100 : 0), str); kputc('\t', str); // FLAG
if (p->rid >= 0) { // with coordinate if (p->rid >= 0) { // with coordinate
kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
kputl(p->pos + 1, str); kputc('\t', str); // POS kputl(p->pos + 1, str); kputc('\t', str); // POS
@ -874,6 +874,38 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
s->sam = str.s; s->sam = str.s;
} }
void mem_aln2sam_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;
kv_init(aa);
for (k = 0; k < a->n; ++k) {
mem_alnreg_t *p = &a->a[k];
mem_aln_t *q;
if (p->score < opt->T) continue;
if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
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;
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 {
mem_aln_t t;
t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, 0);
mem_aln2sam(bns, &str, s, 1, &t, 0, m);
}
s->sam = str.s;
}
mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq) mem_alnreg_v mem_align1_core(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bns, const uint8_t *pac, int l_seq, char *seq)
{ {
int i; int i;