From 4782d394d544d459fe7badd5f803490f0a48f8c3 Mon Sep 17 00:00:00 2001
From: derek <derekwbarnett@gmail.com>
Date: Fri, 3 Dec 2010 15:45:20 -0500
Subject: [PATCH] Fixed: bug in the BamReader::Jump() codepath, specifically
 the BRP::AdjustRegion() logic

---
 src/api/internal/BamReader_p.cpp | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index bffbfba..f7ab548 100644
--- a/src/api/internal/BamReader_p.cpp
+++ b/src/api/internal/BamReader_p.cpp
@@ -52,7 +52,9 @@ void BamReaderPrivate::AdjustRegion(BamRegion& region) {
     // see if any references in region have alignments
     HasAlignmentsInRegion = false;
     int currentId = region.LeftRefID;
-    while ( currentId <= region.RightRefID ) {
+
+    const int rightBoundRefId = ( region.isRightBoundSpecified() ? region.RightRefID : References.size() - 1 );
+    while ( currentId <= rightBoundRefId ) {
 	HasAlignmentsInRegion = Index->HasAlignments(currentId);
 	if ( HasAlignmentsInRegion ) break;
 	++currentId;
-- 
2.39.5