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BGS-HostAlgnmtAlgoSingle.cpp
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BGS-HostAlgnmtAlgoSingle.cpp
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/*
*
* BGS-HostAlgnmtAlgoSingle.c
* Soap3(gpu)
*
* Copyright (C) 2011, HKU
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
#include "BGS-HostAlgnmtAlgoSingle.h"
//====================MODELIZED BELOW======================
// BWTxxxModelxxx functions are fully generalised BWT search algorithm that searchs for reads contain any number of edit/mismatch
// However, calling these functions requires user to define themselves a 'searching model'.
// The searching model requires each BWT step to be defined. The search algorithm will then follow the defined model.
// BWTMismatchModelAnyDirection_CE matches steps with check and extend mechanism.
// It allows starting off CE in the middle of a step and recursive CE until SRACase completes.
unsigned long long BWTMismatchModelAnyDirection_CE3 ( SRAQueryInput * qInput, int i, int mismatchInserted,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges,
int occMismatch, uint8_t nbMismatch, char occQuality, SingleAlgnResult * algnResult )
{
// This function should not be invoked because the constant MAX_CE_THRESHOLD is set to 0
unsigned long long l = saRanges[0];
unsigned long long r = saRanges[1];
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
int OutputType = qSetting->OutputType;
HSP * hsp = aIndex->hsp;
BWT * ceBwt = aIndex->bwt;
int * leftMostAligned = alignmentCase->leftMostAligned;
int * occMismatches = rOutput->Shared_AccMismatch;
unsigned long long * saPositions = rOutput->Shared_ReadPositions;
char * occQualities = rOutput->Shared_AccQualities;
unsigned long long extensionSeq[MAX_CE_BUFFER_SIZE];
unsigned long long extensionSeq2[MAX_CE_BUFFER_SIZE];
SRAError errorsTmp[SRA_MAX_READ_LENGTH];
int occNBMismatch[MAX_CE_THRESHOLD];
unsigned int readPos;
int mismatch;
uint8_t mismatchCe;
uint8_t minMismatch;
uint8_t maxMismatch;
int step, len, start, end, pos, newPosCount, swap, left, right, posCount;
int bufferCount;
int k = 0;
unsigned long long saCount = 0;
step = alignmentCase->steps[stepInCase].step;
start = alignmentCase->steps[stepInCase].start;
pos = start + step * i;
int leftAlign = leftMostAligned[pos];
unsigned long long j;
int param_i = i;
int param_stepInCase = stepInCase;
int flag;
int errorsIdx;
for ( j = l; j <= r; j++ )
{
occMismatches[k] = occMismatch;
occNBMismatch[k] = nbMismatch;
occQualities[k] = occQuality;
saPositions[k] = ( *ceBwt->_bwtSaValue ) ( ceBwt, j ) - leftAlign;
k++;
}
posCount = k;
newPosCount = 0;
while ( alignmentCase->steps[stepInCase].type != SRA_STEP_TYPE_COMPLETE )
{
minMismatch = alignmentCase->steps[stepInCase].MinError;
maxMismatch = alignmentCase->steps[stepInCase].MaxError;
step = alignmentCase->steps[stepInCase].step;
len = alignmentCase->steps[stepInCase].len;
start = alignmentCase->steps[stepInCase].start;
end = alignmentCase->steps[stepInCase].end;
pos = start + step * i;
swap = ( pos - end ) & - ( pos < end );
left = end + swap;
right = pos - swap;
len = right - left + 1;
//bufferCount = GetPackedPatternLong(convertedKey,left,len,extensionSeq);
bufferCount = CEPackPattern ( convertedKey, left, len, extensionSeq );
//printf("> ");
//for (j=0;j<len;j++) {
// printf("%c",dnaChar[convertedKey[left+j]]);
// if ((j+1) % 4==0) {printf(" ");}
//}printf("\n");
for ( j = 0; j < posCount; j++ )
{
readPos = saPositions[j];
//mismatch = PackedDifferenceLong(extensionSeq,hsp,readPos+left,len);
//mismatch = CEPackedMismatchMatching(extensionSeq,len,0,hsp,readPos+left,len);
if ( readPos + left > ceBwt->textLength )
{
mismatchCe = MAX_NUM_OF_ERROR + 1;
}
else
{
mismatchCe = CEPackedMismatchMatchingWithQuality ( extensionSeq, len, 0, hsp, readPos + left, len, errorsTmp );
}
//int mismatch2 = CEPackedMismatchMatching(extensionSeq,len,0,hsp,readPos+left,len);
//if (mismatch != mismatch2) {
// printf("Return number of mismatch is different : %d %d\n",mismatch,mismatch2);
//}
mismatch = mismatchCe + mismatchInserted;
if ( mismatch >= minMismatch && mismatch <= ( maxMismatch + qSetting->MaxNBMismatch - occNBMismatch[j] ) )
{
occNBMismatch[newPosCount] = occNBMismatch[j] + ( ( mismatch - maxMismatch ) * ( mismatch > maxMismatch ) );
occQualities[newPosCount] = occQualities[j];
for ( errorsIdx = 0; errorsIdx < mismatchCe; errorsIdx++ )
{
occQualities[newPosCount] += keyQuality[errorsTmp[errorsIdx].position];
}
occMismatches[newPosCount] = occMismatches[j] + mismatch;
saPositions[newPosCount] = readPos;
newPosCount++;
}
}
posCount = newPosCount;
newPosCount = 0;
stepInCase++;
i = 0;
mismatchInserted = 0;
}
// collect the answers to occ_list
for ( j = 0; j < posCount; j++ )
{
addOccToAlgnResult ( algnResult, saPositions[j], qInfo->ReadStrand );
}
return posCount;
// return OCCReportTextPositions(qInput, posCount);
}
/*unsigned long long BWTMismatchModelAnyDirection_CE(SRAQueryInput * qInput, int i, int mismatchInserted,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges,
int occMismatch, uint8_t nbMismatch, char occQuality) {
unsigned long long l = saRanges[0];
unsigned long long r = saRanges[1];
unsigned char * convertedKey = qInfo->ReadCode;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
int OutputType = qSetting->OutputType;
HSP * hsp = aIndex->hsp;
BWT * ceBwt = aIndex->bwt;
int * leftMostAligned = alignmentCase->leftMostAligned;
int * occMismatches = rOutput->Shared_AccMismatch;
unsigned long long * saPositions = rOutput->Shared_ReadPositions;
char * occQualities = rOutput->Shared_AccQualities;
unsigned long long extensionSeq[4];
unsigned int readPos;
int mismatch;
uint8_t minMismatch;
uint8_t maxMismatch;
int step,len,start,end,pos,newPosCount,swap,left,right,posCount;
int bufferCount;
int k=0;
unsigned long long saCount = 0;
step = alignmentCase->steps[stepInCase].step;
start = alignmentCase->steps[stepInCase].start;
pos = start + step * i;
int leftAlign = leftMostAligned[pos];
unsigned long long j;
int param_i = i;
int param_stepInCase = stepInCase;
int flag;
for (j=l;j<=r;j++) {
occMismatches[0]=occMismatch;
occQualities[0]=occQuality;
saPositions[0]=(*ceBwt->_bwtSaValue)(ceBwt,j)-leftAlign;
i = param_i;
stepInCase = param_stepInCase;
flag = 1;
mismatch = mismatchInserted;
while (alignmentCase->steps[stepInCase].type != SRA_STEP_TYPE_COMPLETE) {
minMismatch = alignmentCase->steps[stepInCase].MinError;
maxMismatch = alignmentCase->steps[stepInCase].MaxError;
step = alignmentCase->steps[stepInCase].step;
len = alignmentCase->steps[stepInCase].len;
start = alignmentCase->steps[stepInCase].start;
end = alignmentCase->steps[stepInCase].end;
pos = start + step * i;
swap = (pos - end) & -(pos < end);
left = end + swap;
right = pos - swap;
len = right - left + 1;
bufferCount = GetPackedPatternLong(convertedKey,left,len,extensionSeq);
mismatch += PackedDifferenceLong(extensionSeq,hsp,saPositions[0]+left,len);
if (mismatch>=minMismatch && mismatch<=maxMismatch) {
flag=1;
occMismatches[0]+=mismatch;
} else {
flag=0;
break;
}
stepInCase++;mismatch=0;
i=0;
}
if (flag==1) {
saCount+=OCCReportTextPositions(qInput, 1);
if (rOutput->IsClosed==1) {
return saCount;
}
}
}
return saCount;
}//*/
// BWTExactModelForward_Lookup lookup your pattern in lookup table, bi-directional and assuming forward
unsigned long long BWTExactModelForward_Lookup3 ( SRAQueryInput * qInput,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges, SingleAlgnResult * algnResult )
{
unsigned long long l_packedPattern = 0;
unsigned long long r_packedPattern = 0;
unsigned long long l = 0;
unsigned long long r = 0;
unsigned long long rev_l = 0;
unsigned long long rev_r = 0;
unsigned long long j;
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
unsigned int oCount[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
LT * lookupTable = aIndex->lookupTable;
LT * rev_lookupTable = aIndex->rev_lookupTable;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int step = alignmentCase->steps[stepInCase].step;
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
int pos = start;
int k;
int branchCount = 0;
char branchChar = 0;
uint8_t nbMismatch = 0;
unsigned int lookupLength = ( lookupTable->tableSize > len ) ? len : lookupTable->tableSize;
int i;
for ( i = 0; i < lookupLength ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
l_packedPattern |= ( convertedKey[pos++] & LOOKUP_CHAR_MASK );
}
r_packedPattern = l_packedPattern;
for ( i = lookupLength; i < lookupTable->tableSize ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern |= LOOKUP_CHAR_MASK ;
}
l = l_packedPattern ? lookupTable->table[l_packedPattern - 1] + 1 : 1;
r = lookupTable->table[r_packedPattern];
l_packedPattern = 0;
r_packedPattern = 0;
for ( i = 0; i < lookupLength ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
l_packedPattern |= ( convertedKey[--pos] & LOOKUP_CHAR_MASK );
}
r_packedPattern = l_packedPattern;
for ( i = lookupLength; i < rev_lookupTable->tableSize ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern |= LOOKUP_CHAR_MASK ;
}
rev_l = l_packedPattern ? rev_lookupTable->table[l_packedPattern - 1] + 1 : 1;
rev_r = rev_lookupTable->table[r_packedPattern];
if ( r - l < rev_r - rev_l )
{
rev_l = rev_r - ( r - l );
}
else if ( r - l > rev_r - rev_l )
{
l = r - ( rev_r - rev_l );
}
i = lookupLength;
pos = start + lookupLength;
while ( i < len && l <= r )
{
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[0] = l;
saRanges[1] = r;
return BWTMismatchModelAnyDirection_CE3 ( qInput, i, 0,
alignmentCase, stepInCase,
saRanges, 0, nbMismatch, 0, algnResult );
}
unsigned char c = convertedKey[pos];
BWTAllOccValue ( bwt, rev_l, oL );
BWTAllOccValue ( bwt, rev_r + 1, oR );
oCount[ALPHABET_SIZE - 1] = 0;
branchCount = ( oR[ALPHABET_SIZE - 1] > oL[ALPHABET_SIZE - 1] );
branchChar = ( ALPHABET_SIZE - 1 ) * branchCount;
for ( k = ALPHABET_SIZE - 2; k >= 0; k-- )
{
oCount[k] = oCount[k + 1] + oR[k + 1] - oL[k + 1];
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
// Non-branching Mismatch Handler
if ( oL[c] + 1 > oR[c] && branchCount == 1 && nbMismatch < qSetting->MaxNBMismatch )
{
rev_l = bwt->cumulativeFreq[branchChar] + oL[branchChar] + 1;
rev_r = bwt->cumulativeFreq[branchChar] + oR[branchChar];
r = r - oCount[branchChar];
l = r - ( rev_r - rev_l );
nbMismatch++;
}
else
{
rev_l = bwt->cumulativeFreq[c] + oL[c] + 1;
rev_r = bwt->cumulativeFreq[c] + oR[c];
r = r - oCount[c];
l = r - ( rev_r - rev_l );
}
i++;
pos++;
}
if ( l <= r )
{
//Next Step
saRanges[0] = l;
saRanges[1] = r;
saRanges[2] = rev_l;
saRanges[3] = rev_r;
if ( alignmentCase->steps[stepInCase + 1].type == SRA_STEP_TYPE_BACKWARD_ONLY_BWT )
{
//printf("[BWTExactModelForward_Lookup] BWTModelSwitchBackward\n");
return BWTModelSwitchBackward3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, 0, nbMismatch, 0, algnResult );
}
else
{
//printf("[BWTExactModelForward_Lookup] BWTModelSwitchAnyDirection\n");
return BWTModelSwitchAnyDirection3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, 0, nbMismatch, 0, algnResult );
}
}
return 0;
}
// BWTExactModelBackward_Lookup lookup your pattern in lookup table, single direction and assuming backward
unsigned long long BWTExactModelBackward_Lookup3 ( SRAQueryInput * qInput,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges, SingleAlgnResult * algnResult )
{
unsigned long long l_packedPattern = 0;
unsigned long long r_packedPattern = 0;
unsigned long long l = 0;
unsigned long long r = 0;
unsigned long long j = 0;
int k = 0;
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
LT * lookupTable = aIndex->lookupTable;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int step = alignmentCase->steps[stepInCase].step;
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
unsigned int lookupLength = ( lookupTable->tableSize > len ) ? len : lookupTable->tableSize;
int branchCount = 0;
unsigned char branchChar = 0;
uint8_t nbMismatch = 0;
int i;
int pos = start - lookupLength + 1;
for ( i = 0; i < lookupLength ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
l_packedPattern |= ( convertedKey[pos++] & LOOKUP_CHAR_MASK );
}
r_packedPattern = l_packedPattern;
for ( i = lookupLength; i < lookupTable->tableSize ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern |= LOOKUP_CHAR_MASK ;
}
l = l_packedPattern ? lookupTable->table[l_packedPattern - 1] + 1 : 1;
r = lookupTable->table[r_packedPattern];
i = lookupLength;
pos = start - lookupLength;
while ( i < len && l <= r )
{
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[0] = l;
saRanges[1] = r;
return BWTMismatchModelAnyDirection_CE3 ( qInput, i, 0,
alignmentCase, stepInCase,
saRanges, 0, nbMismatch, 0, algnResult );
}
unsigned char c = convertedKey[pos];
BWTAllOccValue ( bwt, l, oL );
BWTAllOccValue ( bwt, r + 1, oR );
branchCount = 0;
branchChar = 0;
for ( k = ALPHABET_SIZE - 1; k >= 0; k-- )
{
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
// Non-branching Mismatch Handler
if ( oL[c] + 1 > oR[c] && branchCount == 1 && nbMismatch < qSetting->MaxNBMismatch )
{
l = bwt->cumulativeFreq[branchChar] + oL[branchChar] + 1;
r = bwt->cumulativeFreq[branchChar] + oR[branchChar];
nbMismatch++;
}
else
{
l = bwt->cumulativeFreq[c] + oL[c] + 1;
r = bwt->cumulativeFreq[c] + oR[c];
}
i++;
pos--;
}
if ( l <= r )
{
//Next Step
saRanges[0] = l;
saRanges[1] = r;
return BWTModelSwitchBackward3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, 0, nbMismatch, 0, algnResult );
}
return 0;
}
// BWTExactModelBackwardAnyDirection_Lookup lookup your pattern in lookup table, bi-directional and assuming backward
unsigned long long BWTExactModelBackwardAnyDirection_Lookup3 ( SRAQueryInput * qInput,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges, SingleAlgnResult * algnResult )
{
unsigned long long l_packedPattern = 0;
unsigned long long r_packedPattern = 0;
unsigned long long l = 0;
unsigned long long r = 0;
unsigned long long rev_l = 0;
unsigned long long rev_r = 0;
unsigned long long j;
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
unsigned int oCount[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
LT * lookupTable = aIndex->lookupTable;
LT * rev_lookupTable = aIndex->rev_lookupTable;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int step = alignmentCase->steps[stepInCase].step;
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
int k;
int branchCount = 0;
char branchChar = 0;
uint8_t nbMismatch = 0;
unsigned int lookupLength = ( lookupTable->tableSize > len ) ? len : lookupTable->tableSize;
int i;
int pos = start - lookupLength + 1;
for ( i = 0; i < lookupLength ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
l_packedPattern |= ( convertedKey[pos++] & LOOKUP_CHAR_MASK );
}
r_packedPattern = l_packedPattern;
for ( i = lookupLength; i < lookupTable->tableSize ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern |= LOOKUP_CHAR_MASK ;
}
l = l_packedPattern ? lookupTable->table[l_packedPattern - 1] + 1 : 1;
r = lookupTable->table[r_packedPattern];
l_packedPattern = 0;
r_packedPattern = 0;
for ( i = 0; i < lookupLength ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
l_packedPattern |= ( convertedKey[--pos] & LOOKUP_CHAR_MASK );
}
r_packedPattern = l_packedPattern;
for ( i = lookupLength; i < rev_lookupTable->tableSize ; i++ )
{
l_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern <<= LOOKUP_BIT_PER_CHAR;
r_packedPattern |= LOOKUP_CHAR_MASK ;
}
rev_l = l_packedPattern ? rev_lookupTable->table[l_packedPattern - 1] + 1 : 1;
rev_r = rev_lookupTable->table[r_packedPattern];
if ( r - l < rev_r - rev_l )
{
rev_l = rev_r - ( r - l );
}
else if ( r - l > rev_r - rev_l )
{
l = r - ( rev_r - rev_l );
}
i = lookupLength;
pos = start - lookupLength;
while ( i < len && l <= r )
{
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[0] = l;
saRanges[1] = r;
return BWTMismatchModelAnyDirection_CE3 ( qInput, i, 0,
alignmentCase, stepInCase,
saRanges, 0, nbMismatch, 0, algnResult );
}
unsigned char c = convertedKey[pos];
BWTAllOccValue ( bwt, l, oL );
BWTAllOccValue ( bwt, r + 1, oR );
oCount[ALPHABET_SIZE - 1] = 0;
branchCount = ( oR[ALPHABET_SIZE - 1] > oL[ALPHABET_SIZE - 1] );
branchChar = ( ALPHABET_SIZE - 1 ) * branchCount;
for ( k = ALPHABET_SIZE - 2; k >= 0; k-- )
{
oCount[k] = oCount[k + 1] + oR[k + 1] - oL[k + 1];
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
// Non-branching Mismatch Handler
if ( oL[c] + 1 > oR[c] && branchCount == 1 && nbMismatch < qSetting->MaxNBMismatch )
{
l = bwt->cumulativeFreq[branchChar] + oL[branchChar] + 1;
r = bwt->cumulativeFreq[branchChar] + oR[branchChar];
rev_r = rev_r - oCount[branchChar];
rev_l = rev_r - ( r - l );
nbMismatch++;
}
else
{
l = bwt->cumulativeFreq[c] + oL[c] + 1;
r = bwt->cumulativeFreq[c] + oR[c];
rev_r = rev_r - oCount[c];
rev_l = rev_r - ( r - l );
}
i++;
pos--;
}
if ( l <= r )
{
//Next Step
saRanges[0] = l;
saRanges[1] = r;
saRanges[2] = rev_l;
saRanges[3] = rev_r;
if ( alignmentCase->steps[stepInCase + 1].type == SRA_STEP_TYPE_BACKWARD_ONLY_BWT )
{
//printf("[BWTExactModelForward_Lookup] BWTModelSwitchBackward\n");
return BWTModelSwitchBackward3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, 0, nbMismatch, 0, algnResult );
}
else
{
//printf("[BWTExactModelForward_Lookup] BWTModelSwitchAnyDirection\n");
return BWTModelSwitchAnyDirection3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, 0, nbMismatch, 0, algnResult );
}
}
return 0;
}
// BWTExactModelBackward matches pattern on text without using any other aux, e.g. lookup table.
unsigned long long BWTExactModelBackward3 ( SRAQueryInput * qInput, int i, int errorInserted,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges,
int occError, uint8_t nbMismatch, char occQuality, SingleAlgnResult * algnResult )
{
unsigned long long l = saRanges[0];
unsigned long long r = saRanges[1];
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
SRAQueryInfo * qInfo = qInput->QueryInfo;
SRASetting * qSetting = qInput->QuerySetting;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
uint8_t minError = alignmentCase->steps[stepInCase].MinError;
uint8_t maxError = alignmentCase->steps[stepInCase].MaxError;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
int step = -1;
int pos, k;
unsigned long long j;
pos = start + step * i;
step = -1;
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
int branchCount = 0;
char branchChar = 0;
//printf("[BWTExactModelBackward] from %d to %d allowing %u<%u<%u mismatches.\n", start,end, minError,errorInserted, maxError);
//printf("[BWTExactModelBackward] %d/%d\n", i,len);
while ( i < len && l <= r )
{
unsigned char c = convertedKey[pos];
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[0] = l;
saRanges[1] = r;
return BWTMismatchModelAnyDirection_CE3 ( qInput, i, errorInserted,
alignmentCase, stepInCase,
saRanges, occError, nbMismatch, occQuality, algnResult );
}
BWTAllOccValue ( bwt, l, oL );
BWTAllOccValue ( bwt, r + 1, oR );
branchCount = 0;
branchChar = 0;
for ( k = ALPHABET_SIZE - 1; k >= 0; k-- )
{
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
// Non-branching Mismatch Handler
if ( oL[c] + 1 > oR[c] && branchCount == 1 && nbMismatch < qSetting->MaxNBMismatch )
{
l = bwt->cumulativeFreq[branchChar] + oL[branchChar] + 1;
r = bwt->cumulativeFreq[branchChar] + oR[branchChar];
nbMismatch++;
}
else
{
l = bwt->cumulativeFreq[c] + oL[c] + 1;
r = bwt->cumulativeFreq[c] + oR[c];
}
i++;
pos += step;
}
if ( errorInserted >= minError && l <= r )
{
saRanges[0] = l;
saRanges[1] = r;
return BWTModelSwitchBackward3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, occError + errorInserted, nbMismatch, occQuality, algnResult );
}
return 0;
}
// BWTMismatchModelAnyDirection matches pattern on text without using any other aux, e.g. lookup table, with mismatches.
unsigned long long BWTExactModelAnyDirection3 ( SRAQueryInput * qInput, int i, int errorInserted,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges,
int occError, uint8_t nbMismatch, char occQuality, SingleAlgnResult * algnResult )
{
int step = alignmentCase->steps[stepInCase].step;
unsigned long long l = saRanges[ ( step < 0 ) * 2];
unsigned long long r = saRanges[ ( step < 0 ) * 2 + 1];
unsigned long long rev_l = saRanges[ ( step > 0 ) * 2];
unsigned long long rev_r = saRanges[ ( step > 0 ) * 2 + 1];
unsigned long long saCount = 0;
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
int k, pos;
uint8_t minError = alignmentCase->steps[stepInCase].MinError;
uint8_t maxError = alignmentCase->steps[stepInCase].MaxError;
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
unsigned long long err_rev_l;
unsigned long long err_rev_r;
unsigned long long err_r;
unsigned long long err_l;
unsigned long long errSaRange[4];
unsigned char c;
unsigned long long j;
int branchCount = 0;
char branchChar = 0;
//printf("Alignment from %d to %d allowing %u-%u mismatches.\n", start,end, minError, maxError);
//printf("[BWTExactModelAnyDirection] from %d to %d allowing %u<%u<%u mismatches.\n", start,end, minError,errorInserted, maxError);
//printf("[BWTExactModelAnyDirection] %d/%d\n", i,len);
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
unsigned int oCount[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
pos = start + step * i;
len -= ( minError - errorInserted - 1 ) * ( minError > errorInserted + 1 );
while ( i < len && l <= r )
{
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[ ( step < 0 ) * 2] = l;
saRanges[ ( step < 0 ) * 2 + 1] = r;
saRanges[ ( step > 0 ) * 2] = rev_l;
saRanges[ ( step > 0 ) * 2 + 1] = rev_r;
k = 0;
return BWTMismatchModelAnyDirection_CE3 ( qInput, i, errorInserted,
alignmentCase, stepInCase,
saRanges, occError, nbMismatch, occQuality, algnResult );
}
c = convertedKey[pos];
BWTAllOccValue ( bwt, rev_l, oL );
BWTAllOccValue ( bwt, rev_r + 1, oR );
oCount[ALPHABET_SIZE - 1] = 0;
branchCount = ( oR[ALPHABET_SIZE - 1] > oL[ALPHABET_SIZE - 1] );
branchChar = ( ALPHABET_SIZE - 1 ) * branchCount;
for ( k = ALPHABET_SIZE - 2; k >= 0; k-- )
{
oCount[k] = oCount[k + 1] + oR[k + 1] - oL[k + 1];
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
// Non-branching Mismatch Handler
if ( oL[c] + 1 > oR[c] && branchCount == 1 && nbMismatch < qSetting->MaxNBMismatch )
{
rev_l = bwt->cumulativeFreq[branchChar] + oL[branchChar] + 1;
rev_r = bwt->cumulativeFreq[branchChar] + oR[branchChar];
r = r - oCount[branchChar];
l = r - ( rev_r - rev_l );
nbMismatch++;
}
else
{
rev_l = bwt->cumulativeFreq[c] + oL[c] + 1;
rev_r = bwt->cumulativeFreq[c] + oR[c];
r = r - oCount[c];
l = r - ( rev_r - rev_l );
}
i += 1;
pos += step;
}
if ( errorInserted >= minError && l <= r )
{
//Next Step
saRanges[ ( step < 0 ) * 2] = l;
saRanges[ ( step < 0 ) * 2 + 1] = r;
saRanges[ ( step > 0 ) * 2] = rev_l;
saRanges[ ( step > 0 ) * 2 + 1] = rev_r;
return BWTModelSwitchAnyDirection3 ( qInput, 0, 0,
alignmentCase, stepInCase + 1,
saRanges, occError + errorInserted, nbMismatch, occQuality, algnResult );
}
return 0;
}
// BWTMismatchModelAnyDirection matches pattern on text without using any other aux, e.g. lookup table, with mismatches.
unsigned long long BWTMismatchModelAnyDirection3 ( SRAQueryInput * qInput, int i, int mismatchInserted,
SRACase * alignmentCase, int stepInCase,
unsigned long long * saRanges,
int occMismatch, uint8_t nbMismatch, char occQuality, SingleAlgnResult * algnResult )
{
int step = alignmentCase->steps[stepInCase].step;
unsigned long long l = saRanges[ ( step < 0 ) * 2];
unsigned long long r = saRanges[ ( step < 0 ) * 2 + 1];
unsigned long long rev_l = saRanges[ ( step > 0 ) * 2];
unsigned long long rev_r = saRanges[ ( step > 0 ) * 2 + 1];
unsigned long long saCount = 0;
SRAQueryInfo * qInfo = qInput->QueryInfo;
unsigned char * convertedKey = qInfo->ReadCode;
char * keyQuality = qInfo->ReadQuality;
SRAQueryResultCount * rOutput = qInput->QueryOutput;
SRASetting * qSetting = qInput->QuerySetting;
SRAIndex * aIndex = qInput->AlgnmtIndex;
int k, pos;
BWT * bwt = alignmentCase->steps[stepInCase].bwt;
uint8_t minMismatch = alignmentCase->steps[stepInCase].MinError;
uint8_t maxMismatch = alignmentCase->steps[stepInCase].MaxError;
int len = alignmentCase->steps[stepInCase].len;
int start = alignmentCase->steps[stepInCase].start;
int end = alignmentCase->steps[stepInCase].end;
int ceThreshold = alignmentCase->steps[stepInCase].ceThreshold;
int ceStart = alignmentCase->steps[stepInCase].ceStart;
int ceEnd = alignmentCase->steps[stepInCase].ceEnd;
unsigned long long err_rev_l;
unsigned long long err_rev_r;
unsigned long long err_r;
unsigned long long err_l;
unsigned long long errSaRange[4];
unsigned long long j;
unsigned char c;
int branchCount = 0;
char branchChar = 0;
//printf("Alignment from %d to %d allowing %u-%u mismatches.\n", start,end, minMismatch, maxMismatch);
//MARK_FOR_64_ENHANCEMENT ----
unsigned int oL[ALPHABET_SIZE];
unsigned int oR[ALPHABET_SIZE];
unsigned int oCount[ALPHABET_SIZE];
//MARK_FOR_64_ENHANCEMENT ---
pos = start + step * i;
len -= ( minMismatch - mismatchInserted - 1 ) * ( minMismatch > mismatchInserted + 1 );
while ( i < len && l <= r )
{
//printf("Current progress: %d(%d) within %d characters. stepping by %d.\n", i, pos, len, step);
if ( r - l < ceThreshold && pos >= ceStart && pos <= ceEnd )
{
saRanges[ ( step < 0 ) * 2] = l;
saRanges[ ( step < 0 ) * 2 + 1] = r;
saRanges[ ( step > 0 ) * 2] = rev_l;
saRanges[ ( step > 0 ) * 2 + 1] = rev_r;
saCount += BWTMismatchModelAnyDirection_CE3 ( qInput, i, mismatchInserted,
alignmentCase, stepInCase,
saRanges, occMismatch, nbMismatch, occQuality, algnResult );
return saCount;
}
c = convertedKey[pos];
BWTAllOccValue ( bwt, rev_l, oL );
BWTAllOccValue ( bwt, rev_r + 1, oR );
oCount[ALPHABET_SIZE - 1] = 0;
branchCount = ( oR[ALPHABET_SIZE - 1] > oL[ALPHABET_SIZE - 1] );
branchChar = ( ALPHABET_SIZE - 1 ) * branchCount;
for ( k = ALPHABET_SIZE - 2; k >= 0; k-- )
{
oCount[k] = oCount[k + 1] + oR[k + 1] - oL[k + 1];
branchCount += ( oR[k] > oL[k] );
branchChar |= k * ( oR[k] > oL[k] );
}
//if (mismatchInserted<maxMismatch) {
for ( k = 0; k < ALPHABET_SIZE; k++ )
{
if ( k != c )
{