readsRetrieval.h

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#ifndef __LREZ_READS_RETRIEVAL__
#define __LREZ_READS_RETRIEVAL__
 
#include "utils.h"
#include "indexManagementFastq.h"
#include "gzIndex.h"
 
vector<string> retrieveReadsWithBarcodeBits_Stream(ifstream& in, BarcodesIndex& BarcodesIndex, barcode bc);
 
vector<string> retrieveReadsWithBarcodeBits(string fastqFile, BarcodesIndex& BarcodesIndex, barcode bc);
 
vector<string> retrieveReadsWithBarcode_Stream(ifstream& reader, BarcodesIndex& BarcodesIndex, string bc);
 
vector<string> retrieveReadsWithBarcode(string fastqFile, BarcodesIndex& BarcodesIndex, string bc);
 
vector<string> retrieveReadsWithBarcodes_Stream(ifstream& in, BarcodesIndex& BarcodesIndex, string barcodesList);
 
vector<string> retrieveReadsWithBarcodes(string fastqFile, BarcodesIndex& BarcodesIndex, string barcodesList, unsigned nbThreads = 1);
 
 
vector<string> retrieveReadsWithBarcodeBits_Gzip_Stream_Index(FILE* in, struct access* gzIndex, BarcodesIndex& barcodexIndex, barcode bc);
 
vector<string> retrieveReadsWithBarcodeBits_Gzip(string fastqFile, BarcodesIndex& barcodexIndex, barcode bc);
 
 
vector<string> retrieveReadsWithBarcode_Gzip_Stream_Index(FILE* in, struct access* gzIndex, BarcodesIndex& BarcodesIndex, string barcode);
 
 
vector<string> retrieveReadsWithBarcode_Gzip(string fastqFile, BarcodesIndex& BarcodesIndex, string barcode);
 
vector<string> retrieveReadsWithBarcodes_Gzip_Stream_Index(FILE* in, struct access* gzIndex, BarcodesIndex& BarcodesIndex, string barcodesList);
 
vector<string> retrieveReadsWithBarcodes_Gzip(string fastqFile, BarcodesIndex& BarcodesIndex, string barcodesList, unsigned nbThreads = 1);
 
 
 
#endif