From: derek <derekwbarnett@gmail.com>
Date: Mon, 6 Dec 2010 17:02:18 +0000 (-0500)
Subject: Fixed: core mode setting for BamMultiReader::Open() in FilterTool
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8749b649779b660c20226581328c078b99c4d37f;p=bamtools.git

Fixed: core mode setting for BamMultiReader::Open() in FilterTool

  * Was opening with coreMode=true, which caused errors filtering the
first alignment's char data
---

diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
index d2de3b4..b57cf05 100644
--- a/src/toolkit/bamtools_filter.cpp
+++ b/src/toolkit/bamtools_filter.cpp
@@ -740,7 +740,7 @@ bool FilterTool::FilterToolPrivate::Run(void) {
 
     // open reader without index
     BamMultiReader reader;
-    if ( !reader.Open(m_settings->InputFiles, false, true) ) {
+    if ( !reader.Open(m_settings->InputFiles, false, false) ) {
         cerr << "Could not open input files for reading." << endl;
         return false;
     }
@@ -774,7 +774,7 @@ bool FilterTool::FilterToolPrivate::Run(void) {
 
             // attempt to re-open reader with index files
             reader.Close();
-            bool openedOK = reader.Open(m_settings->InputFiles, true, true );
+	    bool openedOK = reader.Open(m_settings->InputFiles, true, false );
             
             // if error
             if ( !openedOK ) {