From 0043e2dd10151e457731e477b2efc8c3c24e27c8 Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Wed, 8 Sep 2010 16:17:20 -0400 Subject: [PATCH] prefer bamtools index in BamMultiReader --- src/api/BamMultiReader.h | 2 +- src/toolkit/bamtools_convert.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index cc30326..e2c1dad 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -61,7 +61,7 @@ class BamMultiReader { // also useful for merging // @preferStandardIndex - look for standard BAM index ".bai" first. If false, // will look for BamTools index ".bti". - bool Open(const vector filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = true); + bool Open(const vector filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = false); // returns whether underlying BAM readers ALL have an index loaded // this is useful to indicate whether Jump() or SetRegion() are possible diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp index 1c5ba48..edfc83c 100644 --- 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 -- 2.39.2