computeStats.h

Go to the documentation of this file.

#ifndef __LREZ_COMPUTE_STATS__
#define __LREZ_COMPUTE_STATS__
 
#include "utils.h"
#include <map>
 
struct Stats {
    unsigned nbBarcodes;
    unsigned nbMappedReads;
    vector<unsigned> readsPerBarcode;
};
 
 
vector<unsigned> extractBarcodesCountsPerRegion(BamReader& reader, vector<string> regionsList, unsigned numberOfRegions);
 
vector<unsigned> extractCommonBarcodesCounts(BamReader& reader, vector<string> regionsList, unsigned numberOfRegions);
 
pair<vector<unsigned>, vector<unsigned>> extractBarcodesAndCommonBarcodesCounts(string bamFile, vector<string> regionsList, unsigned numberOfRegions, unsigned nbThreads = 1);
 
Stats extractGlobalStats(string bamFile, unsigned nbThreads = 1);
 
#endif