X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamReader_p.cpp;h=dc6792fe8c210b685557809f06f9a993d8f41ebc;hb=8b4c010999a8d0c482d84bbf17c98dc4bbae02b7;hp=5d154a1ec7f9f549b23d66c3421a5d0128630a02;hpb=8a90b7aefffaf186053ef4da96c8663bf528274a;p=bamtools.git

diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index 5d154a1..dc6792f 100644
--- a/src/api/internal/BamReader_p.cpp
+++ b/src/api/internal/BamReader_p.cpp
@@ -2,22 +2,21 @@
 // BamReader_p.cpp (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for reading BAM files
 // ***************************************************************************
 
-#include <api/BamConstants.h>
-#include <api/BamReader.h>
-#include <api/IBamIODevice.h>
-#include <api/internal/BamDeviceFactory_p.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamStandardIndex_p.h>
-#include <api/internal/BamToolsIndex_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamConstants.h"
+#include "api/BamReader.h"
+#include "api/IBamIODevice.h"
+#include "api/internal/BamDeviceFactory_p.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/BamToolsIndex_p.h"
 using namespace BamTools;
 using namespace BamTools::Internal;
 
@@ -367,7 +366,7 @@ bool BamReaderPrivate::Open(const string& filename) {
         Close();
 
         // open BgzfStream
-        m_stream.Open(filename, "rb");
+        m_stream.Open(filename, IBamIODevice::ReadOnly);
         assert(m_stream);
 
         // load BAM metadata
@@ -448,11 +447,6 @@ void BamReaderPrivate::SetIndex(BamIndex* index) {
     m_randomAccessController.SetIndex(index);
 }
 
-// change the index caching behavior
-void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
-    m_randomAccessController.SetIndexCacheMode(mode);
-}
-
 // sets current region & attempts to jump to it
 // returns success/failure
 bool BamReaderPrivate::SetRegion(const BamRegion& region) {