prefer bamtools index in BamMultiReader

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index cc30326b59f0773750739dda999df6e89bb153f0..e2c1dad87fd054aae6299d8480afa01c80e87c68 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -61,7 +61,7 @@ class BamMultiReader {
         // also useful for merging\r
         // @preferStandardIndex - look for standard BAM index ".bai" first.  If false, \r
         // will look for BamTools index ".bti".  \r
-        bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = true);\r
+        bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = false);\r
 \r
         // returns whether underlying BAM readers ALL have an index loaded\r
         // this is useful to indicate whether Jump() or SetRegion() are possible\r

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index 1c5ba4884ac73412f9e45a38575d9fba6de4dc88..edfc83c6761823430531bc672b355ab1a28e2a71 100644 (file)
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -186,7 +186,7 @@ bool ConvertTool::ConvertToolPrivate::Run(void) {
     
     // open input files
     BamMultiReader reader;
-    reader.Open(m_settings->InputFiles, false);
+    reader.Open(m_settings->InputFiles);
     m_references = reader.GetReferenceData();
 
     // set region if specified