From 2594fb7e8055fefc08b37a14ad437aa9bafbe837 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Mon, 26 Mar 2012 15:22:15 +0100
Subject: [PATCH 1/1] Tolerate CIGAR H operators in 'samtools depad'
---
padding.c | 2 ++
1 file changed, 2 insertions(+)
diff --git a/padding.c b/padding.c
index e2afefb..a3008fc 100644
--- 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 {
--
2.39.2