// ***************************************************************************
// BamIndexFactory_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides interface for generating BamIndex implementations
// ***************************************************************************
-#include <api/BamAux.h>
-#include <api/internal/BamIndexFactory_p.h>
-#include <api/internal/BamStandardIndex_p.h>
-#include <api/internal/BamToolsIndex_p.h>
+#include "api/BamAux.h"
+#include "api/internal/BamIndexFactory_p.h"
+#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/BamToolsIndex_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
-
-#include <cstdio>
using namespace std;
// generates index filename from BAM filename (depending on requested type)
const BamIndex::IndexType& type)
{
switch ( type ) {
- case ( BamIndex::STANDARD ) : return ( bamFilename + BAI_EXTENSION );
- case ( BamIndex::BAMTOOLS ) : return ( bamFilename + BTI_EXTENSION );
+ case ( BamIndex::STANDARD ) : return ( bamFilename + BamStandardIndex::Extension() );
+ case ( BamIndex::BAMTOOLS ) : return ( bamFilename + BamToolsIndex::Extension() );
default :
- fprintf(stderr, "BamIndexFactory ERROR: unknown index type %u\n", type);
return string();
}
}
// creates a new BamIndex object, depending on extension of @indexFilename
-BamIndex* BamIndexFactory::CreateIndexFromFilename(const string& indexFilename) {
+BamIndex* BamIndexFactory::CreateIndexFromFilename(const string& indexFilename, BamReaderPrivate* reader) {
// if file doesn't exist, return null index
if ( !BamTools::FileExists(indexFilename) )
return 0;
// create index based on extension
- if ( extension == BAI_EXTENSION ) return new BamStandardIndex;
- else if ( extension == BTI_EXTENSION ) return new BamToolsIndex;
- else return 0;
+ if ( extension == BamStandardIndex::Extension() ) return new BamStandardIndex(reader);
+ else if ( extension == BamToolsIndex::Extension() ) return new BamToolsIndex(reader);
+ else
+ return 0;
}
// creates a new BamIndex, object of requested @type
-BamIndex* BamIndexFactory::CreateIndexOfType(const BamIndex::IndexType& type) {
+BamIndex* BamIndexFactory::CreateIndexOfType(const BamIndex::IndexType& type,
+ BamReaderPrivate* reader)
+{
switch ( type ) {
- case ( BamIndex::STANDARD ) : return new BamStandardIndex;
- case ( BamIndex::BAMTOOLS ) : return new BamToolsIndex;
+ case ( BamIndex::STANDARD ) : return new BamStandardIndex(reader);
+ case ( BamIndex::BAMTOOLS ) : return new BamToolsIndex(reader);
default :
- fprintf(stderr, "BamIndexFactory ERROR: unknown index type %u\n", type);
return 0;
}
}
return string();
// look for last dot in filename
- size_t lastDotPosition = filename.find_last_of('.');
+ const size_t lastDotPosition = filename.find_last_of('.');
// if none found, return empty string
if ( lastDotPosition == string::npos )
const string BamIndexFactory::FindIndexFilename(const string& bamFilename,
const BamIndex::IndexType& preferredType)
{
+ // skip if BAM filename provided is empty
+ if ( bamFilename.empty() )
+ return string();
+
// try to find index of preferred type first
// return index filename if found
string indexFilename = CreateIndexFilename(bamFilename, preferredType);