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r158: optionally ignore base quality

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Heng Li
2017-07-05 18:23:50 -04:00
parent d1f518e3ca
commit 9823317e8f
4 changed files with 11 additions and 4 deletions
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map.c
+2 -1
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@@ -305,9 +305,10 @@ static void *worker_pipeline(void *shared, int step, void *in)
int i, j;
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
step_t *s;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = bseq_read(p->fp, p->mini_batch_size, !!(p->opt->flag & MM_F_OUT_SAM), &s->n_seq);
s->seq = bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
if (s->seq) {
s->p = p;
for (i = 0; i < s->n_seq; ++i)