From 229a33c5e9e6b17a7d8c19d3c37382d6e5fc0605 Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Wed, 29 Sep 2010 11:54:48 -0400 Subject: [PATCH] prior commit caused bug with convert Fix: attempt to open indexes when we are not reading from stdin. --- src/toolkit/bamtools_convert.cpp | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) 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(); -- 2.39.2