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bugfix: when no seed hits found

This commit is contained in:
Heng Li 2013-02-07 20:07:31 -05:00
parent cd6bd524d4
commit 45b0d3423a
1 changed files with 11 additions and 2 deletions
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13
bwamem.c
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@ -457,16 +457,24 @@ ret_gen_cigar:
void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a)
{
int k, m;
int i, k, m;
kstring_t str;
char *seq;
str.l = str.m = 0; str.s = 0;
m = mem_choose_alnreg_se(opt, a->n, a->a);
seq = malloc(s->l_seq);
if (m == 0) { // no seeds found
for (i = 0; i < s->l_seq; ++i) seq[i] = "ACGTN"[(int)s->seq[i]];
kputs(s->name, &str); kputs("\t8\t*\t0\t0\t*\t*\t0\t0\t", &str);
kputsn(seq, s->l_seq, &str);
if (s->qual) kputsn(s->qual, s->l_seq, &str);
else kputc('*', &str);
kputc('\n', &str);
}
for (k = 0; k < m; ++k) {
uint32_t *cigar = 0;
int score, is_rev, nn, rid, i, flag = 0, n_cigar = 0, mapq = 0;
int score, is_rev, nn, rid, flag = 0, n_cigar = 0, mapq = 0;
int64_t pos;
mem_alnreg_t *p = &a->a[k];
cigar = mem_gen_cigar(opt, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar);
@ -494,6 +502,7 @@ void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, b
else for (i = 0; i < s->l_seq; ++i) seq[i] = "ACGTN"[(int)s->seq[i]];
kputsn(seq, s->l_seq, &str); kputc('\t', &str);
if (s->qual) kputsn(s->qual, s->l_seq, &str);
else kputc('*', &str);
kputsn("\tAS:i:", 6, &str); kputw(p->score, &str);
kputsn("\tss:i:", 6, &str); kputw(p->sub, &str);
kputsn("\tnw:i:", 6, &str); kputw(score, &str);