barcodesExtraction.h

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#ifndef __LREZ_BARCODES_EXTRACTION__
#define __LREZ_BARCODES_EXTRACTION__
 
#include "utils.h"
#include "robin_hood.h"
 
robin_hood::unordered_set<barcode> extractBarcodesBitsFromRegion_BamReader(BamReader& reader, string region);
 
robin_hood::unordered_set<string> extractBarcodesSeqsFromRegion_BamReader(BamReader& reader, string region);
 
robin_hood::unordered_set<barcode> extractBarcodesBitsFromRegion(string bamFile, string region);
 
 
robin_hood::unordered_set<string> extractBarcodesSeqsFromRegion(string bamFile, string region);
 
robin_hood::unordered_set<barcode> extractBarcodesBitsFromBAM(string bamFile, unsigned nbThreads = 1);
 
robin_hood::unordered_set<string> extractBarcodesSeqsFromBAM(string bamFile, unsigned nbThreads = 1);
 
vector<barcode> extractBarcodesBitsFromRegionWithDuplicates_BamReader(BamReader& reader, string region);
 
vector<string> extractBarcodesSeqsFromRegionWithDuplicates_BamReader(BamReader& reader, string region);
 
vector<barcode> extractBarcodesBitsFromRegionWithDuplicates(string bamFile, string region);
 
 
vector<string> extractBarcodesSeqsFromRegionWithDuplicates(string bamFile, string region);
 
vector<barcode> extractBarcodesBitsFromBAMWithDuplicates(string bamFile, unsigned nbThreads = 1);
 
vector<string> extractBarcodesSeqsFromBAMWithDuplicates(string bamFile, unsigned nbThreads = 1);
 
#endif