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r533: added --no-pairing

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to prevent the use of any pairing information for paired-end reads.
This commit is contained in:
Heng Li
2017-10-23 14:09:32 -04:00
parent 5acd709524
commit d4b5dfc297
3 changed files with 10 additions and 2 deletions
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map.c
+6 -1
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@@ -414,7 +414,12 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
qseqs[j] = s->seq[off + j].seq;
quals[j] = is_sr? s->seq[off + j].qual : 0;
}
mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, quals, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
if (s->p->opt->flag & MM_F_INDEPEND_SEG) {
for (j = 0; j < s->n_seg[i]; ++j)
mm_map_frag(s->p->mi, 1, &qlens[j], &qseqs[j], &quals[j], &s->n_reg[off+j], &s->reg[off+j], b, s->p->opt, s->seq[off+j].name);
} else {
mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, quals, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
}
for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
int k, t;