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#include "Genome_Index_TableQ.h"
CGenome_Index_TableQ::CGenome_Index_TableQ(void)
{
initialization();
}
CGenome_Index_TableQ::~CGenome_Index_TableQ(void)
{
// this->pgenomeNTInBits and this->pgenome will be deleted in parent class;
}
int CGenome_Index_TableQ::initialization(void)
{
this->bExcludeAmbiguous = true;
return(0);
}
bool CGenome_Index_TableQ::getSeqFromFasta(const char* genomeListfileName, string refFormat)
{
getBasename(genomeListfileName, this->caRefName);
if (fileExist(genomeListfileName)) {
this->getGenomeNTdata(genomeListfileName, refFormat);
TIME_INFO(this->pgenomeNTInBits = new CGenomeInBits(this->pgenomeNT), "Build genome in bits ");
this->pgenomeNT->freeChromosomeSpace();
return(true);
} else {
cout << "File " << genomeListfileName << " not found!" << endl;
return(false);
}
}
bool CGenome_Index_TableQ::getSeqFromDS(CGenomeNTdata* pgenomeNT)
{
this->pgenomeNT = pgenomeNT;
myStrCpy(this->caRefName, pgenomeNT->refName, FILENAME_MAX);
TIME_INFO(this->pgenomeNTInBits = new CGenomeInBits(this->pgenomeNT), "Build genome in bits ");
this->pgenomeNT->freeChromosomeSpace();
return(true);
}
// (1) Query each seed pattern for hit. (2) Check each hit for valid alignment and put in the palignmentsQ
// (3) Return the minDiff for alignment
pair<CIndex_Type*, CIndex_Type*> CGenome_Index_TableQ::queryKmer\
(CReadInBits window, unsigned int shift) const
{
unsigned int BIN_SIZE_CHECK_THRESHOLD = 1; // If there are only this number in bin, check
window = window.getSuffixStr(shift);
unsigned int uiHashValue = this->getHashValue(window);
unsigned int uiSeedKeyL = this->getSeedKey(window);
unsigned int uiSeedKeyU;
if (bEXTEND_SEED) {
uiSeedKeyU = this->getSeedKeyUpperBound(window, shift);
} else {
uiSeedKeyU = uiSeedKeyL;
}
// cout << uiHashValue << ',' << uiSeedKey << endl;
unsigned int bucketStart = this->pHashIndexTable->aiIndexTable[uiHashValue];
unsigned int nextBucketStart = this->pHashIndexTable->aiIndexTable[uiHashValue + 1];
if (bucketStart > nextBucketStart) ERR; // Error Case
if (bucketStart >= nextBucketStart) { // empty bucket
CIndex_Type* tmp = NULL;
return(pair<CIndex_Type*, CIndex_Type*>(tmp, tmp)); //No hit
}
CIndex_Type* hitStart = &this->pIndexTable[bucketStart];
CIndex_Type* hitEndPlus1 = &this->pIndexTable[nextBucketStart];
// If the bin is large enough, use binary search to find the correct hituiSeedKey
if (bucketStart + BIN_SIZE_CHECK_THRESHOLD < nextBucketStart) {
hitStart = lower_bound(hitStart, hitEndPlus1, uiSeedKeyL, CcompareFunctor4LowerBound(this));
// TODO fill the suffix digit for the uiSeedKey
hitEndPlus1 = upper_bound(hitStart, hitEndPlus1, uiSeedKeyU, CcompareFunctor4UpperBound(this));
} // else assume everything in the bucket is a hit without equal_range check
return(pair<CIndex_Type*, CIndex_Type*>(hitStart, hitEndPlus1));
}
unsigned int CGenome_Index_TableQ::getSeedKeyUpperBound(CReadInBits window, unsigned int shift) const
{
//WORD_SIZE padding = 0xffffffffffffffff;
WORD_SIZE padding = -1;
if (this->bMapReadInColors) {
padding <<= (this->uiRead_Length - 1 - shift);
} else {
padding <<= (this->uiRead_Length - shift);
}
window.UpperBits |= padding;
window.LowerBits |= padding;
return(this->getSeedKey(window));
}
// Query a read in bases (Illumina) for hit and check uiDiff and put the result into the given Queue
unsigned int CGenome_Index_TableQ::queryReadBases(CReadInBits readInBases, CAlignmentsQ& aQue, bool bClearQ, bool bForward) const
{
if (bClearQ) {
aQue.clearHits();
}
if (!bForward) { //Query reverse complement read for alignment
readInBases = reverseCompliment(this->uiRead_Length, readInBases);
}
bool bUseShortCut = this->bExcludeAmbiguous && !(aQue.qAllInThreshold());
bool qAllHits = aQue.qAllInThreshold();
for (unsigned int shift = 0; shift <= this->uiNoOfShift; shift++) {
// If the best match is exact matched, no need to go to the next shift
// for all exact matches must be found previously.
if ((aQue.MinDiff == 0) && (shift > 0) && (aQue.load > 0) && !qAllHits) {
break;
}
pair<CIndex_Type*, CIndex_Type*> hits = queryKmer(readInBases, shift);
if (hits.first != NULL) {
for (CIndex_Type* it = hits.first; it < hits.second; it++) {
if (*it >= shift) {
unsigned int alignStart = *it - shift;
if (isMasked(alignStart)) {
continue;
} else {
CReadInBits ref = this->pgenomeNTInBits->getSubstringInBits(alignStart);
unsigned int uiDiff = bitsStrNCompare(ref, readInBases, this->uiRead_Length);
// The flag in alignmentsQ decide whether all alignments within uiDiff or
// only the alignments with minimum Diff are queue.
if (uiDiff <= this->uiSubDiffThreshold) {
aQue.saveHits(alignStart, (unsigned short)uiDiff);
}
if (bUseShortCut) { // short cut to exclude ambiguous reads
bool bMap2Repeat = this->pbaRepeatRepresentativeFlag->b(alignStart);
if (bMap2Repeat) {
aQue.AmbiguousFlag = true;
}
if (aQue.MinDiff == 0 && (aQue.load >= 2 || bMap2Repeat)) {
aQue.setForwardLoad(bForward);
return(0);
}
}
}
}
}
if (aQue.MinDiff == 0) {
// short cut. Output no more than iMaxCapacity exaxt alignment
/* if (aQue.load >= aQue.iMaxCapacity - 1) {
aQue.setForwardLoad(bForward);
return(0);
}*/
// short cut. All exact matches will be found after first shift
if (bUseShortCut && aQue.load >= 2) {
aQue.setForwardLoad(bForward);
return(1);
}
}
}
}
/* DEBUG
if(palignmentsQ.MinDiff <= this->uiSubDiffThreshold) {
CReadInBits ref = this->pgenomeNTInBits->getSubstringInBits(aQue.aiHitIndex[0]);
printBitsStrCompare(ref, readInBases, "Good Alignments!!");
}*/
// The records before are for the forward direction if this is a forward query
aQue.setForwardLoad(bForward);
return(aQue.MinDiff);
}
// Query a read in bases (Illumina) for hit and check uiDiff and put the result into the given Queue
unsigned int CGenome_Index_TableQ::queryLongReadBases(CReadInBits r1, CReadInBits r2, bool oddReadLength, CAlignmentsQ& aQue, int queryHalf, bool bClearQ, bool bForward) const
{
const unsigned int firstPartLength = this->uiRead_Length;
const unsigned int secondPartLength = oddReadLength ? this->uiRead_Length - 1 : this->uiRead_Length;
if (bClearQ) {
aQue.clearHits();
}
if (!bForward) { //Query reverse complement read for alignment
CReadInBits tmp = r2;
r2 = reverseCompliment(firstPartLength, r1);
r1 = reverseCompliment(firstPartLength, tmp);
}
CReadInBits readInBases = (queryHalf == 1) ? r1 : r2;
bool bUseShortCut = this->bExcludeAmbiguous && !(aQue.qAllInThreshold());
bool qAllHits = aQue.qAllInThreshold();
for (unsigned int shift = 0; shift <= this->uiNoOfShift; shift++) {
// If the best match is exact matched, no need to go to the next shift
// for all exact matches must be found previously.
if ((aQue.MinDiff == 0) && (shift > 0) && (aQue.load > 0) && !qAllHits) {
break;
}
pair<CIndex_Type*, CIndex_Type*> hits = queryKmer(readInBases, shift);
if (hits.first != NULL) {
for (CIndex_Type* it = hits.first; it < hits.second; it++) {
if (*it >= shift) {
unsigned int alignStart = *it - shift;
if (queryHalf == 2 ) {
if ( alignStart >= secondPartLength) {
alignStart -= secondPartLength;
} else {
continue;
}
}
if (isMasked(alignStart) || isMasked(alignStart + secondPartLength)) {
continue; // if the two windows contain N or is in references' border
} else {
unsigned int uiDiff = checkAlignment(alignStart, r1, r2, oddReadLength);
// The flag in alignmentsQ decide whether all alignments within uiDiff or
// only the alignments with minimum Diff are queue.
if (uiDiff <= this->uiSubDiffThreshold) {
aQue.saveHits(alignStart, (unsigned short)uiDiff);
}
if (bUseShortCut) { // short cut to exclude ambiguous reads
bool bMap2Repeat = this->pbaRepeatRepresentativeFlag->b(alignStart);
if (bMap2Repeat) {
aQue.AmbiguousFlag = true;
}
if (aQue.MinDiff == 0 && (aQue.load >= 2 || bMap2Repeat)) {
aQue.setForwardLoad(bForward);
return(0);
}
}
}
}
}
if (aQue.MinDiff == 0) {
// short cut. Output no more than iMaxCapacity exaxt alignment
/* if (aQue.load >= aQue.iMaxCapacity - 1) {
aQue.setForwardLoad(bForward);
return(0);
}*/
// short cut. All exact matches will be found after first shift
if (bUseShortCut && aQue.load >= 2) {
aQue.setForwardLoad(bForward);
return(1);
}
}
}
}
// The records before are for the forward direction if this is a forward query
aQue.setForwardLoad(bForward);
return(aQue.MinDiff);
}
// TODO Complete the function
// Query a read in bases (Illumina) for hit and check uiDiff and put the result into the given Queue
unsigned int CGenome_Index_TableQ::queryLongReadColors(CReadInBits r1, CReadInBits r2, bool oddReadLength, CAlignmentsQ& aQue, int queryHalf, bool bClearQ, bool bForward) const
{
// const unsigned int firstPartLength = this->uiRead_Length;
const unsigned int secondPartLength = oddReadLength ? this->uiRead_Length - 1 : this->uiRead_Length;
if (bClearQ) {
aQue.clearHits();
}
if (!bForward) { // Query reverse complement read for alignment
reverseLongColorRead(r1, r2, oddReadLength);
}
CReadInBits readInBases = (queryHalf == 1) ? r1 : r2;
bool bUseShortCut = this->bExcludeAmbiguous && !(aQue.qAllInThreshold());
bool qAllHits = aQue.qAllInThreshold();
for (unsigned int shift = 0; shift <= this->uiNoOfShift; shift++) {
// If the best match is exact matched, no need to go to the next shift
// for all exact matches must be found previously.
if ((aQue.MinDiff == 0) && (shift > 0) && (aQue.load > 0) && !qAllHits) {
break;
}
pair<CIndex_Type*, CIndex_Type*> hits = queryKmer(readInBases, shift);
if (hits.first != NULL) {
for (CIndex_Type* it = hits.first; it < hits.second; it++) {
if (*it >= shift) {
unsigned int alignStart = *it - shift;
if (queryHalf == 2 ) {
if ( alignStart >= secondPartLength) {
alignStart -= secondPartLength;
} else {
continue;
}
}
if (isMasked(alignStart) || isMasked(alignStart + secondPartLength)) {
continue; // if the two windows contain N or is in references' border
} else {
// TODO implement the checkColor
unsigned int uiDiff = checkColorAlignment(alignStart, r1, r2, oddReadLength);
// The flag in alignmentsQ decide whether all alignments within uiDiff or
// only the alignments with minimum Diff are queue.
if (uiDiff <= this->uiSubDiffThreshold) {
aQue.saveHits(alignStart, (unsigned short)uiDiff);
}
if (bUseShortCut) { // short cut to exclude ambiguous reads
bool bMap2Repeat = this->pbaRepeatRepresentativeFlag->b(alignStart);
if (bMap2Repeat) {
aQue.AmbiguousFlag = true;
}
if (aQue.MinDiff == 0 && (aQue.load >= 2 || bMap2Repeat)) {
aQue.setForwardLoad(bForward);
return(0);
}
}
}
}
}
if (aQue.MinDiff == 0) {
// short cut. All exact matches will be found after first shift
if (bUseShortCut && aQue.load >= 2) {
aQue.setForwardLoad(bForward);
return(1);
}
}
}
}
// The records before are for the forward direction if this is a forward query
aQue.setForwardLoad(bForward);
return(aQue.MinDiff);
}
// check match for long read
unsigned int CGenome_Index_TableQ::checkAlignment(unsigned int alignStartGenomeIndex, CReadInBits& half1, CReadInBits& half2, bool oddReadLength) const
{
unsigned int uiDiff = 0;
CReadInBits ref1, ref2;
ref1 = this->pgenomeNTInBits->getSubstringInBits(alignStartGenomeIndex);
uiDiff += bitsStrNCompare(ref1, half1, this->uiRead_Length);
int secondPartStart;
if (oddReadLength) {
secondPartStart = alignStartGenomeIndex + this->uiRead_Length - 1;
ref2 = this->pgenomeNTInBits->getSubstringInBits(secondPartStart);
uiDiff += bitsStrMNCompare(ref2, half2, 1, this->uiRead_Length - 1); // skip the 1st (middle) base
} else {
secondPartStart = alignStartGenomeIndex + this->uiRead_Length;
ref2 = this->pgenomeNTInBits->getSubstringInBits(secondPartStart);
uiDiff += bitsStrNCompare(ref2, half2, this->uiRead_Length);
}
return(uiDiff);
}
// TODO complete the function for color alignment
unsigned int CGenome_Index_TableQ::checkColorAlignment(unsigned int alignStartGenomeIndex, CReadInBits& half1, CReadInBits& half2, bool oddReadLength) const
{
unsigned int uiDiff = 0;
CReadInBits ref1 = this->pgenomeNTInBits->getSubstringInBits(alignStartGenomeIndex);
CReadInBits ref1InColors = bases2Colors(ref1);
uiDiff += bitsStrNCompare(ref1InColors, half1, this->uiRead_Length);
int secondPartStart = alignStartGenomeIndex + this->uiRead_Length - 1;
if (oddReadLength) {
CReadInBits ref2 = this->pgenomeNTInBits->getSubstringInBits(secondPartStart - 1);
CReadInBits ref2InColor = bases2PureColors(ref2);
uiDiff += bitsStrMNCompare(ref2, half2, 1, this->uiRead_Length - 1);
// TODO Check the middle and last color signal.
// Watch out the boundary
} else {
CReadInBits ref2 = this->pgenomeNTInBits->getSubstringInBits(secondPartStart - 1);
CReadInBits ref2InColor = bases2PureColors(ref2);
// Warning! The last base info is missing due to bases2PureColors
uiDiff += bitsStrNCompare(ref2, half2, this->uiRead_Length - 1);
}
return(uiDiff);
}
// Given alignments in alignmentsQ, check reads can be also aligned in the extended position
unsigned int CGenome_Index_TableQ::extendAlignment\
(CAlignmentsQ& alignmentsQ, CReadInBits extendedReadHalf) const
{
unsigned int i;
int minDiff = this->uiRead_Length;
bool extendForward = true;
for (i = 0; i < alignmentsQ.ForwardAlignmentLoad; i++) {
unsigned int alignStart = alignmentsQ.aiHitIndex[i] + this->uiRead_Length;
if (alignStart + this->uiRead_Length >= this->pgenomeNT->iGenomeSize || this->isMasked(alignStart)) {
alignmentsQ.asdiff[i] += (unsigned short)this->uiRead_Length; // no space to align
} else {
CReadInBits ref = this->pgenomeNTInBits->getSubstringInBits(alignStart, this->uiRead_Length);
alignmentsQ.asdiff[i] += (unsigned short)bitsStrNCompare(ref, extendedReadHalf, this->uiRead_Length);
if (alignmentsQ.asdiff[i] < minDiff)
minDiff = alignmentsQ.asdiff[i];
}
}
extendForward = false;
CReadInBits reverseComplimentRead = reverseCompliment(this->uiRead_Length, extendedReadHalf);
for (; i < alignmentsQ.load; i++) { // reverse read
if ( alignmentsQ.aiHitIndex[i] < this->uiRead_Length) {
alignmentsQ.asdiff[i] += (unsigned short)this->uiRead_Length; // no space to align
} else {
unsigned int alignStart = alignmentsQ.aiHitIndex[i] - this->uiRead_Length;
if ( this->isMasked(alignStart) ) {
alignmentsQ.asdiff[i] += (unsigned short)this->uiRead_Length; // no space to align
} else {
CReadInBits ref = this->pgenomeNTInBits->getSubstringInBits(alignStart, this->uiRead_Length);
alignmentsQ.asdiff[i] += (unsigned short)bitsStrNCompare(ref, reverseComplimentRead, this->uiRead_Length);
alignmentsQ.aiHitIndex[i] = alignStart;
if (alignmentsQ.asdiff[i] < minDiff) {
minDiff = alignmentsQ.asdiff[i];
}
}
}
}
alignmentsQ.MinDiff = minDiff;
// The alignments may exceed the threshold so it should be checked outside the function.
return(alignmentsQ.MinDiff);
}
// Query a read in colors (SOLiD) for hit and check uiDiff and put the result into the given Queue
unsigned int CGenome_Index_TableQ::queryReadColors(CReadInBits readInColors, CAlignmentsQ& alignmentsQ, bool bClearQ, bool bForward, bool bDEBUG) const
{
if (bClearQ) {
alignmentsQ.clearHits();
}
CReadInBits pureColors = readInColors.getSuffixStr(1); // query colors
if (!bForward) { // Query alignment with reversed color. (Reverse complement reads has color in reversed direction)
pureColors = reversePureColors(pureColors, this->uiRead_Length - 1);
}
bool bUseShortCut = this->bExcludeAmbiguous && !(alignmentsQ.qAllInThreshold());
bool qAllHits = alignmentsQ.qAllInThreshold();
for (unsigned int shift = 0; shift <= this->uiNoOfShift; shift++) {
// If the best alignment is exact matched, no need to go to the next shift, for all exact matches must be found previously.
if ((alignmentsQ.MinDiff == 0) && (shift > 0) && (alignmentsQ.load > 0) && !qAllHits) {
break;
}
/*
if(bDEBUG) {
cout << shift << "-Shift" << endl;
if(shift == 7) {
cout << "Got you" << endl;
}
}*/
// printBitsStr(pureColors.getSuffixStr(shift), this->uiSeedLength);// DEBUG
pair<CIndex_Type*, CIndex_Type*> hits = queryKmer(pureColors, shift);
if (hits.first != NULL) { // for each hit, check if it is a good alignment.
for (CIndex_Type* it = hits.first; it < hits.second; it++) {
if (*it >= shift) {
unsigned int alignStart = *it - shift;
if (isMasked(alignStart)) {
continue;
} else {
CReadInBits ref = this->pgenomeNTInBits->getSubstringInBits(alignStart, this->uiRead_Length);
unsigned int uiDiff;
if (bForward) {
CReadInBits refInColors = bases2Colors(ref);
uiDiff = bitsStrNCompare(refInColors, readInColors, this->uiRead_Length);
} else { //reverse complement the reference to compare in the read
CReadInBits rcRefInColors = bases2Colors(reverseCompliment(this->uiRead_Length, ref));
uiDiff = bitsStrNCompare(rcRefInColors, readInColors, this->uiRead_Length);
}
// To queue all alignment within uiDiff or the alignments with min difference are set in flag of alignmentsQ
if (uiDiff <= this->uiSubDiffThreshold) {
alignmentsQ.saveHits(alignStart, (unsigned short)uiDiff);
}
if (bUseShortCut) { // short cut to exclude ambiguous reads
bool bMap2Repeat = this->pbaRepeatRepresentativeFlag->b(alignStart);
if (bMap2Repeat) {
alignmentsQ.AmbiguousFlag = true;
}
if (alignmentsQ.MinDiff == 0 && (alignmentsQ.load >= 2 || bMap2Repeat)) {
alignmentsQ.setForwardLoad(bForward);
return(0);
}
}
}
}
}
if (alignmentsQ.MinDiff == 0) {
/*
// short cut to exclude reads that has too many ambiguous mapping
if (alignmentsQ.load >= MAX_Q_CAPACITY) {
alignmentsQ.setForwardLoad(bForward);
return(alignmentsQ.MinDiff);
}
*/
// short cut for ambiguous reads
if (bUseShortCut && alignmentsQ.load >= 2) {
alignmentsQ.setForwardLoad(bForward);
return(1);
}
}
}
}
alignmentsQ.setForwardLoad(bForward);
return(alignmentsQ.MinDiff);
}
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