// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 13 July 2010 (DB)
+// Last modified: 17 August 2010 (DB)
// ---------------------------------------------------------------------------
// Provides index functionality - both for the default (standardized) BAM
// index format (.bai) as well as a BamTools-specific (nonstandard) index
#include <cstdio>
#include <cstdlib>
#include <algorithm>
-#include <iostream>
+// #include <iostream>
#include <map>
#include "BamIndex.h"
#include "BamReader.h"
namespace BamTools {
+// --------------------------------------------------
+// BamDefaultIndex data structures & typedefs
struct Chunk {
// data members
{ }
};
-typedef vector<ReferenceIndex> BamDefaultIndexData;
+typedef vector<ReferenceIndex> BamDefaultIndexData;
} // namespace BamTools
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 13 July 2010 (DB)
+// Last modified: 17 August 2010 (DB)
// ---------------------------------------------------------------------------
// Provides index functionality - both for the default (standardized) BAM
// index format (.bai) as well as a BamTools-specific (nonstandard) index
class BamReader;
class BgzfData;
+// --------------------------------------------------
// BamIndex base class
class BamIndex {
bool m_isBigEndian;
};
+// --------------------------------------------------
// BamDefaultIndex class
//
// implements default (per SAM/BAM spec) index file ops
BamDefaultIndexPrivate* d;
};
+// --------------------------------------------------
// BamToolsIndex class
//
// implements BamTools-specific index file ops