// BamToolsIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 8 October 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the BamTools index format (".bti")
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/internal/BamException_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamToolsIndex_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAlignment.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamToolsIndex_p.h"
+#include "api/internal/BgzfStream_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
// ctor
BamToolsIndex::BamToolsIndex(Internal::BamReaderPrivate* reader)
: BamIndex(reader)
- , m_cacheMode(BamIndex::LimitedIndexCaching)
, m_blockSize(BamToolsIndex::DEFAULT_BLOCK_LENGTH)
, m_inputVersion(0)
, m_outputVersion(BTI_2_0) // latest version - used for writing new index files
throw BamException("BamToolsIndex::Seek", "could not seek in BAI file");
}
-// change the index caching behavior
-void BamToolsIndex::SetCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_cacheMode = mode;
- // do nothing else here ? cache mode will be ignored from now on, most likely
-}
-
void BamToolsIndex::SkipBlocks(const int& numBlocks) {
Seek( numBlocks*BamToolsIndex::SIZEOF_BLOCK, SEEK_CUR );
}