X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=a093d45ff8cf78891ed4d78a741229270481d21d;hb=62254fe022c4c69988c2a71dabf93f90d93e0014;hp=b80463fe80cd7222507b081f56990be97a21e32e;hpb=24d1a2d1200afd8b6c88cb22a3c9b76248e994b1;p=samtools.git

diff --git a/padding.c b/padding.c
index b80463f..a093d45 100644
--- a/padding.c
+++ b/padding.c
@@ -136,7 +136,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
 					pre_op = bam_cigar_op(cigar2[i-2]);
 					post_op = bam_cigar_op(cigar2[i]);
 					/* Note don't need to check for X/= as code above will use M only */
-					if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
+					if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
 						/* This is a redundant P operator */
 						cigar2[i-1] = 0; // i.e. 0M
 						/* If had same operator either side, combine them in post_op */