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r188: renamed bseq* to mm_bseq*

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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
This commit is contained in:
Heng Li
2017-07-19 09:26:46 -04:00
parent b9b0b6f49c
commit 71c988f6ab
10 changed files with 65 additions and 57 deletions
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format.c
+2 -2
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@@ -62,7 +62,7 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
}
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
{
s->l = 0;
mm_sprintf_lite(s, "%s\t%d\t%d\t%d\t%c\t", t->name, t->l_seq, r->qs, r->qe, "+-"[r->rev]);
@@ -105,7 +105,7 @@ static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
} else str_copy(s, seq, seq + l);
}
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r)
{
int flag = 0;
s->l = 0;