From: Erik Garrison <erik.garrison@bc.edu>
Date: Wed, 29 Sep 2010 15:54:48 +0000 (-0400)
Subject: prior commit caused bug with convert
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=229a33c5e9e6b17a7d8c19d3c37382d6e5fc0605;p=bamtools.git

prior commit caused bug with convert

Fix: attempt to open indexes when we are not reading from stdin.
---

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index 730a061..1a01cff 100644
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -160,9 +160,16 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
     
     // open input files
     BamMultiReader reader;
-    if (!reader.Open(m_settings->InputFiles, false)) {
-        cerr << "Could not open input files" << endl;
-        return false;
+    if ( !m_settings->HasInput ) { // don't attempt to open index for stdin
+        if ( !reader.Open(m_settings->InputFiles, false) ) {
+            cerr << "Could not open input files" << endl;
+            return false;
+        }
+    } else {
+        if ( !reader.Open(m_settings->InputFiles, true) ) {
+            cerr << "Could not open input files" << endl;
+            return false;
+        }
     }
     m_references = reader.GetReferenceData();