From c2c1d8a5d8444b30b8af2a4bbb291ddab059be2d Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@bc.edu>
Date: Wed, 29 Sep 2010 16:23:56 -0400
Subject: [PATCH] convert: cleanup of prior fix, report if no index file found

---
 src/toolkit/bamtools_convert.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index 1a01cff..1d8bad4 100644
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -167,8 +167,12 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
         }
     } else {
         if ( !reader.Open(m_settings->InputFiles, true) ) {
-            cerr << "Could not open input files" << endl;
-            return false;
+            if ( !reader.Open(m_settings->InputFiles, false) ) {
+                cerr << "Could not open input files" << endl;
+                return false;
+            } else {
+                cerr << "Opened reader without index file, jumping is disabled." << endl;
+            }
         }
     }
     m_references = reader.GetReferenceData();
-- 
2.39.2