From: Heng Li <lh3@live.co.uk>
Date: Thu, 21 May 2009 11:53:14 +0000 (+0000)
Subject:  * samtools-0.1.3-24 (r296)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=187343102a19bfb8f83669b53d6b34039f613bc6;p=samtools.git

 * samtools-0.1.3-24 (r296)
 * another similar bug in the indel caller
---

diff --git a/bam_maqcns.c b/bam_maqcns.c
index 230f891..c6c9af7 100644
--- a/bam_maqcns.c
+++ b/bam_maqcns.c
@@ -408,7 +408,7 @@ bam_maqindel_ret_t *bam_maqindel(int n, int pos, const bam_maqindel_opt_t *mi, c
 				if (types[i] != 0) { // then try the other way to calculate the score
 					for (ps = s = 0, l = seg.qbeg; c->pos + l + types[i] < right && l < seg.qend; ++l) {
 						int cq = bam1_seqi(bam1_seq(p->b), l), ct;
-						ct = c->pos + l + types[i] >= left? ref2[c->pos + l + types[i] - left] : 15;
+						ct = c->pos + l - seg.qbeg + types[i] >= left? ref2[c->pos + l - seg.qbeg + types[i] - left] : 15;
 						if (cq < 15 && ct < 15) {
 							s += cq == ct? 1 : -mi->mm_penalty;
 							if (cq != ct) ps += bam1_qual(p->b)[l];
diff --git a/bamtk.c b/bamtk.c
index 5280c1f..b38b0d4 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-23 (r295)"
+#define PACKAGE_VERSION "0.1.3-24 (r296)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);