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family.h
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#ifndef FAMILY_h
#define FAMILY_h
#include <array>
#include <set>
#include <cmath>
#include "api/BamWriter.h"
#include "api/algorithms/Sort.h"
#include "ds.h"
#include "defines.h"
extern int MinBaseQual;
extern int MinMapQual;
extern int ConsensusUniqueCount;
extern int MinConSize;
extern bool CallMutations;
extern bool UseSingletonReads;
extern std::string UMIT;
extern std::string OUMI;
extern std::set<Site> germlineSet;
extern std::string refStr;
extern std::vector<std::string> intervalVector;
// extern std::vector<BamTools::BamAlignment> nonConsensusAlignmentVector;
extern std::vector<BamTools::BamAlignment> consensusAlignmentVector;
extern std::array<std::array<int,MAX_INTERVAL_LEN>,5> pileup;
extern std::array<std::array<int,MAX_INTERVAL_LEN>,5> pileupSS;
extern std::array<std::array<int,MAX_INTERVAL_LEN>,5> pileupSingleton;
extern std::array<std::vector<int>,MAX_INTERVAL_LEN> pileupCluster;
extern std::array<std::vector<int>,MAX_INTERVAL_LEN> pileupSSCluster;
extern std::array<std::vector<int>,MAX_INTERVAL_LEN> pileupSingletonCluster;
std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems);
std::vector<std::string> split(const std::string &s, char delim);
class PairedRead {
private:
void baseSeqToArray(std::string seq, int orient, int order, std::vector<BamTools::CigarOp> &cigarData, std::string qual, uint16_t mapq, std::string leftRefSeq, std::string rightRefSeq);
public:
bool paired;
bool marked;
bool leftPair;
bool rightPair;
int firstOrient, secondOrient;
uint16_t firstMapq, secondMapq;
std::string readID;
std::string firstBaseQual;
std::string secondBaseQual;
std::array<std::array<int,MAX_READ_LEN>,4> firstSeq;
std::array<std::array<int,MAX_READ_LEN>,4> secondSeq;
BamTools::BamAlignment firstAlignment;
BamTools::BamAlignment secondAlignment;
PairedRead *nextPair;
PairedRead(bool pair, int orient, int order, std::string ID, std::string seq, std::vector<BamTools::CigarOp> &cigarData, std::string qual, uint16_t mapq, std::string leftRefSeq, std::string rightRefSeq, BamTools::BamAlignment al);
PairedRead(const PairedRead &rp, int order);
void addRead(int orient, int order, std::string seq, std::vector<BamTools::CigarOp> cigarData, std::string qual, uint16_t mapq, std::string leftRefSeq, std::string rightRefSeq, BamTools::BamAlignment al);
void dumpTags(BamTools::BamAlignment &al, std::string barcode, int edit, int pair, std::string key, int ct);
};
class ReadFamily {
private:
bool leftReads;
bool rightReads;
bool report;
int count;
int leftCount;
int rightCount;
int leftRef;
int leftPos;
int rightRef;
int rightPos;
int insertSize;
int readLen;
int leftEdit;
int rightEdit;
std::string key;
std::string leftRefSeq;
std::string rightRefSeq;
public:
std::string leftSeq;
std::string rightSeq;
std::string leftMatch;
std::string rightMatch;
PairedRead *readPair, *lastPair;
ReadFamily() {}
ReadFamily(std::string key, PairedRead &rp, int lref, int lpos, int rref, int rpos, int order, int insertSize, std::string leftRefSeq, std::string rightRefSeq, int rl);
std::string getKey();
void getContig(int *ref, int *pos);
bool checkReadPair(std::string ID);
int missingReadPair();
void addReadToPair(std::string ID, std::string seq, int orient, int order, std::vector<BamTools::CigarOp> cigarData, std::string qual, uint16_t mapq, BamTools::BamAlignment);
void addNewReadPair(PairedRead &RP, int order);
void callConsensus(int startPosition, int endPosition);
bool checkBarcodeCollision();
void matchConsensus(ReadFamily family);
void addPileup(int, int);
void addSingleStrandedPileup(int, int);
void addSingletonPileup(int startPosition, int endPosition);
void clearFamily();
void printFamily();
void getSingleStrandedCoverage(int leftPosition, int rightPosition);
int getFamilySize() {return count;}
int getFirstPairCount() {return leftCount;}
int getSecondPairCount() {return rightCount;}
//int dumpNonConsensusBAM();
int dumpConsensusBAM();
};
void addPileupCounts(int pileupPos, char ls, char lrs, double E, int leftPos, int rightPos, int A, int C, int G, int T, int ind);
void addLOD(PairedRead *rpit, int pileupPos, char leftSeq, char leftRefSeq, int sit, int ind);
#endif