Helpful error message on bad CIGAR in unpad_seq

diff --git a/padding.c b/padding.c
index fb3bc13eb65b9b127bd7d8f82b95b6bbe27aab27..17da7582fdc3efd3775c9a16c7fa548c86809e40 100644 (file)
--- 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);
                }
        }
 }