indexManagementFastq.h

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#ifndef __LREZ_INDEX_MANAGEMENT_FASTQ__
#define __LREZ_INDEX_MANAGEMENT_FASTQ__
 
#include <vector>
#include "robin_hood.h"
#include "utils.h"
 
using namespace std;
 
#define BUFSIZE 134217728
 
typedef robin_hood::unordered_map<barcode, vector<int64_t>> BarcodesIndex;
 
 
BarcodesIndex indexBarcodesFromFastq(string fastqFile, unsigned nbThreads = 1);
 
 
BarcodesIndex indexBarcodesFromFastqGz(string fastqFile, unsigned nbThreads = 1);
 
void saveBarcodesIndex(BarcodesIndex& index, string file);
 
BarcodesIndex loadBarcodesIndex(string file);
 
#endif