Tolerate CIGAR H operators in 'samtools depad'

diff --git a/padding.c b/padding.c
index e2afefb4840cd8acca35f07f200501b87990051a..a3008fc54a531093200dd1b61960bf040a48cee8 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -41,6 +41,8 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                        for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
                } else if (op == BAM_CSOFT_CLIP) {
                        j += ol;
+               } else if (op == BAM_CHARD_CLIP) {
+                       /* do nothing */
                } else if (op == BAM_CDEL || op == BAM_CPAD) {
                        for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
                 } else {