From: Derek Barnett <derekwbarnett@gmail.com>
Date: Tue, 27 Sep 2011 04:10:59 +0000 (-0700)
Subject: Merge pull request #16 from gabeiscoding/patch-2
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=08215752fee2e55fc6e0114030f1f8836d38aee0;hp=72f5b82ad353b4cc9d6f8153f1ad19cc387b9597;p=bamtools.git

Merge pull request #16 from gabeiscoding/patch-2

Fixed: Crash in BamStandardIndex::GetOffset for small BAM files
---

diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp
index b92c47b..11f570a 100644
--- a/src/api/internal/BamStandardIndex_p.cpp
+++ b/src/api/internal/BamStandardIndex_p.cpp
@@ -434,6 +434,12 @@ bool BamStandardIndex::GetOffset(const BamRegion& region, int64_t& offset, bool*
         return false;
     }
 
+    // if not candidate offsets are present in the indexed (most likely sparce coverage)
+    // then silently bail
+    if( offsets.size() == 0 ) {
+        return false;
+    }
+    
     // ensure that offsets are sorted before processing
     sort( offsets.begin(), offsets.end() );