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r474: replaced -S and --cs-no-equal with --cs

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This commit is contained in:
Heng Li
2017-10-05 15:03:03 -04:00
parent 3ff6eda3a4
commit f4a5d3a692
3 changed files with 27 additions and 11 deletions
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format.c
+2 -2
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@@ -223,7 +223,7 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, "MIDN"[r->p->cigar[k]&0xf]);
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r, opt_flag&MM_F_CS_NO_EQUAL);
write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
}
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
@@ -391,7 +391,7 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
}
}
if (r->p && (opt_flag & MM_F_OUT_CS))
write_cs(km, s, mi, t, r, MM_F_CS_NO_EQUAL);
write_cs(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG));
}
s->s[s->l] = 0; // we always have room for an extra byte (see str_enlarge)