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r112: output z-drop

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This commit is contained in:
Heng Li
2017-06-29 22:08:46 -04:00
parent 3825feeeac
commit 11167f511b
5 changed files with 22 additions and 16 deletions
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format.c
+16 -10
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@@ -54,7 +54,16 @@ static void mm_sprintf_lite(kstring_t *s, const char *fmt, ...)
s->s[s->l] = 0;
}
void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
{
mm_sprintf_lite(s, "\tcm:i:%d", r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->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)
{
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]);
@@ -63,12 +72,11 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
mm_sprintf_lite(s, "\t%d\t%d\t%d", mi->seq[r->rid].len, r->rs, r->re);
if (r->p) mm_sprintf_lite(s, "\t%d\t%d", r->p->blen - r->p->n_ambi - r->p->n_diff, r->p->blen);
else mm_sprintf_lite(s, "\t%d\t%d", r->score, r->re - r->rs > r->qe - r->qs? r->re - r->rs : r->qe - r->qs);
mm_sprintf_lite(s, "\t%d\tcm:i:%d", r->mapq, r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
mm_sprintf_lite(s, "\t%d", r->mapq);
write_tags(s, r);
if (r->p) {
uint32_t k;
mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d\tcg:Z:", r->p->n_diff, r->p->score, r->p->n_ambi);
mm_sprintf_lite(s, "cg:Z:");
for (k = 0; k < r->p->n_cigar; ++k)
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MID"[r->p->cigar[k]&0xf]);
}
@@ -98,7 +106,7 @@ 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, bseq1_t *t, mm_reg1_t *r)
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_reg1_t *r)
{
int flag = 0;
s->l = 0;
@@ -115,8 +123,6 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, mm_reg1_t *r)
} else mm_sprintf_lite(s, "*");
mm_sprintf_lite(s, "\t*\t0\t0\t");
sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
mm_sprintf_lite(s, "\t*\tcm:i:%d", r->cnt);
if (r->p) mm_sprintf_lite(s, "\ts1:i:%d", r->score);
if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->score, r->p->n_ambi);
mm_sprintf_lite(s, "\t*");
write_tags(s, r);
}