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r752: option to copy comments to output (#136)

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This commit is contained in:
Heng Li
2018-03-23 10:04:33 -04:00
parent 8766d286df
commit 08bd2123b6
8 changed files with 37 additions and 12 deletions
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5
format.c
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@@ -274,6 +274,8 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
}
if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_MD)))
write_cs_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD);
if ((opt_flag & MM_F_COPY_COMMENT) && t->comment)
mm_sprintf_lite(s, "\t%s", t->comment);
}
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
@@ -475,6 +477,9 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
write_sam_cigar(s, flag, 1, t->l_seq, r, opt_flag);
}
if ((opt_flag & MM_F_COPY_COMMENT) && t->comment)
mm_sprintf_lite(s, "\t%s", t->comment);
s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)
}