From cbb6d034f4e2cc1548f69cd86b9badab9a3402f8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@live.co.uk>
Date: Wed, 18 Feb 2009 22:23:27 +0000
Subject: [PATCH]  * samtools-0.1.2-9  * fixed a bug in bam_fetch, caused by
 completely contained adjacent chunks

---
 bam_index.c | 10 +++++++---
 bamtk.c     |  2 +-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/bam_index.c b/bam_index.c
index 8c25552..59deca0 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -410,16 +410,20 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
 	free(bins);
 	{
 		bam1_t *b;
-		int ret, n_seeks;
+		int l, ret, n_seeks;
 		uint64_t curr_off;
 		b = (bam1_t*)calloc(1, sizeof(bam1_t));
 		ks_introsort(off, n_off, off);
-		// resolve overlaps between adjecent blocks; this may happen due to the merge in indexing
+		// resolve completely contained adjacent blocks
+		for (i = 1, l = 0; i < n_off; ++i)
+			if (off[l].v < off[i].v)
+				off[++l] = off[i];
+		n_off = l + 1;
+		// resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
 		for (i = 1; i < n_off; ++i)
 			if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
 		{ // merge adjacent blocks
 #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16)
-			int l;
 			for (i = 1, l = 0; i < n_off; ++i) {
 #ifdef BAM_TRUE_OFFSET
 				if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v;
diff --git a/bamtk.c b/bamtk.c
index f9df678..950eae0 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-8"
+#define PACKAGE_VERSION "0.1.2-9"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-- 
2.39.2