indexManagementBam.h

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#ifndef __LREZ_INDEX_MANAGEMENT_BAM__
#define __LREZ_INDEX_MANAGEMENT_BAM__
 
#include <vector>
#include "robin_hood.h"
#include "api/BamAux.h"
#include "utils.h"
 
using namespace std;
using namespace BamTools;
 
typedef robin_hood::unordered_map<barcode, vector<int64_t>> BarcodesOffsetsIndex;
 
typedef robin_hood::unordered_map<barcode, vector<pair<int32_t, int32_t>>> BarcodesPositionsIndex;
 
 
BarcodesPositionsIndex indexBarcodesPositionsFromBam(string bamFile, bool primary, unsigned quality, unsigned nbThreads = 1);
 
void saveBarcodesPositionsIndex(BarcodesPositionsIndex& index, string file);
 
BarcodesPositionsIndex loadBarcodesPositionsIndex(string file);
 
 
BarcodesOffsetsIndex indexBarcodesOffsetsFromBam(string bamFile, bool primary, unsigned quality, unsigned nbThreads = 1);
 
void saveBarcodesOffsetsIndex(BarcodesOffsetsIndex& index, string file);
 
BarcodesOffsetsIndex loadBarcodesOffsetsIndex(string file);
 
#endif