alignmentsRetrieval.h

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#ifndef __LREZ_ALIGNMENTS_RETRIEVAL__
#define __LREZ_ALIGNMENTS_RETRIEVAL__
 
#include "utils.h"
#include "indexManagementBam.h"
 
 
vector<BamAlignment> retrieveAlignmentsWithBarcodeBits_BamReader(BamReader& reader, BarcodesOffsetsIndex& BarcodesOffsetsIndex, barcode b);
 
 
vector<BamAlignment> retrieveAlignmentsWithBarcode_BamReader(BamReader& reader, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string bc);
 
vector<BamAlignment> retrieveAlignmentsWithBarcode(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string bc);
 
vector<BamAlignment> retrieveAlignmentsWithBarcodeBits(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, barcode bc);
 
vector<BamAlignment> retrieveAlignmentsWithBarcodes_BamReader(BamReader& reader, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string barcodesList);
 
vector<BamAlignment> retrieveAlignmentsWithBarcodes(string bamFile, BarcodesOffsetsIndex& BarcodesOffsetsIndex, string barcodesList, unsigned nbThreads = 1);
 
#endif