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 730a061e62a407cc42b2834c2206179c458e4d30..1a01cffdafcb3e198bab8cb017340e543cd17be0 100644 (file)
--- 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();