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#pragma once
#include "ReadsMapping.h"
#include "MappingResult.h"
#include "LongReadsSet.h"
class CBestPairedMapping
{
public:
CBestPairedMapping(void);
~CBestPairedMapping(void);
CMappingResult bm1, bm2;
int bestMappingNo;
int validMappingNo;
unsigned int minDiff;
inline void update(CMappingResult &m1, CMappingResult &m2, bool excludeAmbigousRead);
};
class CPairedReadsMapping : public CReadsMapping
{
public:
CPairedReadsMapping(void);
CPairedReadsMapping(const MappingOpts P);
~CPairedReadsMapping(void);
//int mapPairedReadsInASingleFile(CPairedReadsSet& readSet, CGenome_Index_TableQ& table);
int mapPairedReadsInPairedFiles(CReadInBitsSet& readSet1, CReadInBitsSet& readSet2,
CGenome_Index_TableQ& table);
int mapPairedReads(CReadInBitsSet& readSet1, CReadInBitsSet& readSet2,
CGenome_Index_TableQ& table);
int mapPairedLongReadsInBases(CLongReadsSet& longReadSet1, CLongReadsSet& longReadSet2, const CGenome_Index_TableQ& table);
int dealMappedSingleRead(const CGenome_Index_TableQ& table, CAlignmentsQ & Que, CMappingResult &m, bool bFirstEnd);
int dealMappedPairedReads(CGenome_Index_TableQ& table);
int dealMappedLongPairedRead(CAlignmentsQ& q1, CAlignmentsQ& q2, CMappingResult& m1, CMappingResult& m2, const CGenome_Index_TableQ& table);
// F3read and R3read are index in AlignmentsQ
void dealNoMapping(const CGenome_Index_TableQ& table, CMappingResult& m1, CMappingResult& m2);
int dealBestMapping(const CGenome_Index_TableQ& table, CBestPairedMapping& bestMP, CMappingResult& m1, CMappingResult& m2);
int printValidMappedPair(const CGenome_Index_TableQ& table, CMappingResult& m1, CMappingResult& m2, int validMappedPairNo);
int printBestMappedPair(const CGenome_Index_TableQ& table, CMappingResult& m1, CMappingResult& m2, int minMismatchNo, int bestMappedPairNo);
inline void getPairedRInfo(const CGenome_Index_TableQ& table, CMappingResult &m1, CMappingResult &m2, bool samFormat);
void printAMappedPair(const CGenome_Index_TableQ& table, CMappingResult &m1, CMappingResult &m2, int noPairedLoc);
void printMappedPairStats(ostream& out, CReadInBitsSet& readSet, unsigned int uiSubThreshold);
protected:
void initialization(void);
inline void bookNoMappedKeepPairs(bool sepMore, bool sepLess, bool pairedOnExpStrand);
inline void bookKeepMappedPairs(CBestPairedMapping& bestMP);
unsigned int getPairedReadSetSize
(CReadInBitsSet& setA1, CReadInBitsSet& setA2, CReadInBitsSet& setB1, CReadInBitsSet& setB2);
int noOfPairsInRange;
int noOfPairsSepMore;
int noOfPairsSepLess;
int noOfPairsSepMoreAndLess;
int noOfSingle1stEndMapped;
int noOfSingle2ndEndMapped;
int noOfAmbiguousPairs;
int noOfExpMappedPairedStrand;
};
inline void CPairedReadsMapping::bookNoMappedKeepPairs(bool sepMore, bool sepLess, bool pairedOnExpStrand)
{
if (sepMore && sepLess) {
noOfPairsSepMoreAndLess++;
} else if (sepMore) {
noOfPairsSepMore++;
} else if (sepLess) {
noOfPairsSepLess++;
}
if (pairedOnExpStrand) {
this->noOfExpMappedPairedStrand++;
}
}
inline void CPairedReadsMapping::bookKeepMappedPairs(CBestPairedMapping& bestMP)
{
this->noOfPairsInRange++;
this->iMapCount++;
this->iMapDiffCount[bestMP.minDiff]++;
bool stricklyExcludeAmbiguous = opt.bExcludeAmbiguousPaired && opt.bGetAllAlignments; // -A -e
bool bAmbiguous = (stricklyExcludeAmbiguous && bestMP.validMappingNo > 1) || bestMP.bestMappingNo > 1;
if (bAmbiguous) {
this->iMultiMappedReads++;
}
}
inline void getSingleMappingInfo(CMappingResult &m, CAlignmentsQ &q, int mappingIndex);
// Map mated paired reads parallelly
int parallelMappingPairedReads(vector<string>& readSetsList1, vector<string>& readSetsList2,
CGenome_Index_TableQ& indexTable, MappingOpts P);
// For the paired read set in a file with 5'-3' concatenated with 3'-5'.
int parallelMappingPairedReads(vector<string>& readSetsList,
CGenome_Index_TableQ& indexTable, MappingOpts P);
int parallelMappingPairedLongReads(vector<string>& readSetsList1, vector<string>& readSetsList2,\
CGenome_Index_TableQ& indexTable, MappingOpts P);
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