From 08771285f60f3434c796cd4126ea02c577632ddb Mon Sep 17 00:00:00 2001
From: walaj <jeremiah.wala@gmail.com>
Date: Sat, 1 Jun 2019 07:37:01 -0400
Subject: [PATCH] fixed issue 46

---
 SeqLib/BamRecord.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/SeqLib/BamRecord.h b/SeqLib/BamRecord.h
index 47907fe2d..3ad3b4e22 100644
--- a/SeqLib/BamRecord.h
+++ b/SeqLib/BamRecord.h
@@ -639,9 +639,9 @@ class BamRecord {
     uint32_t* c = bam_get_cigar(b);
     int32_t p = 0;
     for (size_t i = 0; i < b->core.n_cigar; ++i) {
-      if ( (bam_cigar_opchr(c[i]) == 'S') || (bam_cigar_opchr(c[i]) == 'H'))
+      if (bam_cigar_opchr(c[i]) == 'S')
 	p += bam_cigar_oplen(c[i]);
-      else // not a clip, so stop counting
+      else if (bam_cigar_opchr(c[i]) != 'H') 
 	break;
     }
     return p;