From: peterjc <p.j.a.cock@googlemail.com>
Date: Thu, 22 Mar 2012 17:48:47 +0000 (+0000)
Subject: Helpful error message on bad CIGAR in unpad_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=83a75621d9b3d0dcdef7848e9170a0c5e0aac242;p=samtools.git

Helpful error message on bad CIGAR in unpad_seq
---

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);
 		}
 	}
 }