From 83a75621d9b3d0dcdef7848e9170a0c5e0aac242 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Thu, 22 Mar 2012 17:48:47 +0000
Subject: [PATCH] Helpful error message on bad CIGAR in unpad_seq
---
padding.c | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/padding.c b/padding.c
index fb3bc13..17da758 100644
--- a/padding.c
+++ b/padding.c
@@ -37,14 +37,16 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
int op, ol;
op = bam_cigar_op(cigar[k]);
ol = bam_cigar_oplen(cigar[k]);
- assert(op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CSOFT_CLIP);
if (op == BAM_CMATCH) {
for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
++j;
} else if (op == BAM_CSOFT_CLIP) {
j += ol;
- } else {
+ } else if (op == BAM_CDEL) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+ } else {
+ fprintf(stderr, "[unpad_seq] Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ assert(-1);
}
}
}
--
2.39.2