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#pragma once
#include "Genome_Index_Table.h"
#include "AlignmentsQ.h"
#include "ColorSpaceRead.h"
#include "ShortReadUtil.h"
/*
* This class has base class CGenome_Index_Table and add query function
*/
class CGenome_Index_TableQ : public CGenome_Index_Table
{
public:
CGenome_Index_TableQ(void);
~CGenome_Index_TableQ(void);
bool getSeqFromFasta(const char* genomeListfileName, string refFormat = "");
bool getSeqFromDS(CGenomeNTdata* pgenomeNT);
bool getSeqFromIndex(char* indexFile);
inline unsigned int extendAlignment(CAlignmentsQ& aQue, CReadInBits readInBases) const;
// check the number of Diff between long read and ref
inline unsigned int checkAlignment(unsigned int genomeStartIndex, CReadInBits& half1, CReadInBits& half2, bool oddReadLength) const;
inline unsigned int checkColorAlignment(unsigned int alignStartGenomeIndex, CReadInBits& half1, CReadInBits& half2, bool oddReadLength) const;
// Query a long read in bases (illumina) for hit and check uiDiff and put the result into the given Queue
unsigned int queryLongReadBases(CReadInBits r1, CReadInBits r2, bool bOddReadLength, CAlignmentsQ& aQue, int queryRead, bool bClearQ, bool bForward) const;
// Query a read in bases (illumina) for hit and check uiDiff and put the result into the given Queue
unsigned int queryReadBases(CReadInBits readInBases, CAlignmentsQ& aQue, bool bClearQ, bool bForward) const;
// Query a long read in colors (ABI) for hit and check uiDiff and put the result into the given Queue
unsigned int queryLongReadColors(CReadInBits r1, CReadInBits r2, bool oddReadLength, CAlignmentsQ& aQue, int queryHalf, bool bClearQ, bool bForward) const;
// Query a read in colors (SOLiD) for hit and check uiDiff and put the result into the given Queue
// unsigned int queryReadColors(CReadInBits readInColors, CAlignmentsQ& aQue, bool bClearQ, bool bForward) const;
unsigned int queryReadColors(CReadInBits readInColors, CAlignmentsQ& aQue, bool bClearQ, bool bForward, bool bDEBUG = false) const;
// Given alignments in alignmentsQ, check reads can be also will aligned in the extended position
bool bExcludeAmbiguous; // If ambiguous reads are exclude, queries can be accelerated.
protected:
// Query a read for hit and return the hit index range as pair.
// (Input is pure base or pure color read's substring)
pair<CIndex_Type*, CIndex_Type*> queryKmer(CReadInBits window, unsigned int shift) const;
private:
int initialization(void);
unsigned int getSeedKeyUpperBound(CReadInBits window, unsigned int shift) const;
};
// Special functor used for lower_bound()
class CcompareFunctor4LowerBound
{
public:
const CGenome_Index_Table* pGenomeIndexTable;
CcompareFunctor4LowerBound(const CGenome_Index_Table* pGenomeIndexTable) {
this->pGenomeIndexTable = pGenomeIndexTable;
}
bool operator()(CIndex_Type I1, unsigned int uiQuerySeedKey) {
unsigned int uiSeedKey;
if (pGenomeIndexTable->bMapReadInColors) {
CReadInBits ref = pGenomeIndexTable->pgenomeNTInBits->getSubstringInBits(I1 , pGenomeIndexTable->uiSeedLength + 1);
CReadInBits refInColors = bases2PureColors(ref);
uiSeedKey = this->pGenomeIndexTable->getSeedKey(refInColors);
} else {
CReadInBits ref = pGenomeIndexTable->pgenomeNTInBits->getSubstringInBits(I1 , pGenomeIndexTable->uiSeedLength);
uiSeedKey = this->pGenomeIndexTable->getSeedKey(ref);
}
return(uiSeedKey < uiQuerySeedKey);
}
};
// Special functor used for upper_bound()
class CcompareFunctor4UpperBound
{
public:
const CGenome_Index_Table* pGenomeIndexTable;
CcompareFunctor4UpperBound(const CGenome_Index_Table* pGenomeIndexTable) {
this->pGenomeIndexTable = pGenomeIndexTable;
}
bool operator()(unsigned int uiQuerySeedKey, CIndex_Type I2) {
unsigned int uiSeedKey;
if (pGenomeIndexTable->bMapReadInColors) {
CReadInBits ref = pGenomeIndexTable->pgenomeNTInBits->getSubstringInBits(I2 , pGenomeIndexTable->uiSeedLength + 1);
CReadInBits refInColors = bases2PureColors(ref);
uiSeedKey = this->pGenomeIndexTable->getSeedKey(refInColors);
} else {
CReadInBits ref = pGenomeIndexTable->pgenomeNTInBits->getSubstringInBits(I2, pGenomeIndexTable->uiSeedLength);
uiSeedKey = this->pGenomeIndexTable->getSeedKey(ref);
}
return(uiQuerySeedKey < uiSeedKey);
}
};
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