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#pragma once
#include "stdafx.h"
#include "GenomeNTdata.h"
#include "AlignmentsQ.h"
/*
* This class is a base class for CReadsMapping, which collects the counters for statistics of mapping reads.
*/
class CReadsMappingStats
{
public:
CReadsMappingStats(void);
virtual ~CReadsMappingStats(void);
CAlignmentsQ alignmentsQ[2]; // Queue the founded alignments (Two Queues for paired end reads)
protected:
static const unsigned int SNP_TYPE_NUM = 4; // Complement, Transition, Transvertion and Mixed
int iReadsFileCount;
/* Basic mapping statistics counter */
void initializeStatsCounter(void);
// return true if print the alignments
void bookKeepMapping(CAlignmentsQ& que);
// return to a bool value indicating the alignment should be printed or not
bool printAlignmentOrNot(CAlignmentsQ& que, bool bExcludeAmbiguous, bool ambiguousOnly) const;
// Print the counter in an order of Runs,Chr0,Chr1,Chr2,Total Hits,Sub0,Sub1,Sub2,Total Kmers
int printMappingStats(ostream& out, const char* readSetName, unsigned int uiSubThreshold) const;
void printCommand(ostream& out, string command);
unsigned int iMapCount;
unsigned int iMapDiffCount[MAXTOLERATSUBMIS + 1];
unsigned int iReadCounter;
unsigned int iBadReadCounter;
unsigned int iMissReadCounter;
// # of reads that has multiple place mapping(repeats or ambiguous read)
unsigned int iMultiMappedReads;
unsigned int iReadsMapped2tooManyLocations;
unsigned int iMultiMappedLocationThreshold;
private:
void initialization(void);
};
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