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OutputDPResult.cpp
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OutputDPResult.cpp
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/*
*
* OutputDPResult.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 "OutputDPResult.h"
void getReadInfo ( SRAQueryInput * qInput, unsigned int readID, unsigned int displayID,
unsigned char * upkdQueries, char * upkdQueryNames, unsigned int * upkdReadLengths,
unsigned int maxReadLength, int maxReadNameLength )
{
SRAQueryInfo * qInfo = qInput->QueryInfo;
qInfo->ReadName = upkdQueryNames + ( unsigned long long ) readID * maxReadNameLength;
qInfo->ReadCode = upkdQueries + ( unsigned long long ) readID * maxReadLength;
qInfo->ReadLength = upkdReadLengths[readID];
qInfo->ReadId = displayID;
}
void getReadInfoPackedSeq ( SRAQueryInput * qInput, unsigned int readID, unsigned int displayID,
unsigned int * queries, unsigned int * readLengths, unsigned int * upkdReadIDs, char * upkdQueryNames,
unsigned int word_per_query, unsigned char * unpackedQueries, char * upkdQualities,
unsigned int maxReadLength, int maxReadNameLength )
{
SRAQueryInfo * qInfo = qInput->QueryInfo;
qInfo->ReadName = upkdQueryNames + ( unsigned long long ) ( upkdReadIDs[readID] - 1 ) * maxReadNameLength;
retrieve2BWTQueryFormat ( queries, readID, word_per_query, unpackedQueries );
qInfo->ReadCode = unpackedQueries;
qInfo->ReadLength = readLengths[readID];
qInfo->ReadId = displayID;
qInfo->ReadQuality = upkdQualities + ( unsigned long long ) ( upkdReadIDs[readID] - 1 ) * maxReadLength;
}
void getAlgnInfo ( PEPairs & pePair, AlgnmtDPResult & dpResult, int peStrandLeftLeg, int peStrandRightLeg )
{
pePair.algnmt_1 = dpResult.algnmt_1;
pePair.strand_1 = dpResult.strand_1;
pePair.mismatch_1 = dpResult.score_1;
pePair.algnmt_2 = dpResult.algnmt_2;
pePair.strand_2 = dpResult.strand_2;
pePair.mismatch_2 = dpResult.score_2;
}
void getAlgnInfo2 ( PEPairs & pePair, DeepDPAlignResult & dpResult, int peStrandLeftLeg, int peStrandRightLeg )
{
pePair.algnmt_1 = dpResult.algnmt_1;
pePair.strand_1 = dpResult.strand_1;
pePair.mismatch_1 = dpResult.score_1;
pePair.algnmt_2 = dpResult.algnmt_2;
pePair.strand_2 = dpResult.strand_2;
pePair.mismatch_2 = dpResult.score_2;
}
// output a set of default DP alignment results
void outputRead ( AlgnmtDPResult * algnResult, unsigned int algnNum, unsigned char * upkdQueries, char * upkdQueryNames,
unsigned int * upkdReadLengths, unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index, int peStrandLeftLeg, int peStrandRightLeg )
{
// output a set of alignment results
// the alignments of the same pair of reads have to be together
// algnNum: the number of results in "algnResult"
if ( algnNum == 0 )
{ return; }
HSPAux * hspaux = index->sraIndex->hspaux;
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.AlgnmtIndex = &aIndex;
qInput.QueryInfo = &qInfo;
OCC * occ = qInput.QuerySetting->occ;
unsigned int currReadID;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int displayID;
PEPairs pePair;
for ( unsigned int i = 0; i < algnNum; i++ )
{
// check the readID
/*
if (algnResult[i].readID%2 > 0) {
fprintf(stderr, "ERROR! The read ID is not even! i=%u readID=%u\n", i, algnResult[i].readID);
}*/
int isFirstUnaligned = ( algnResult[i].algnmt_1 == 0xFFFFFFFF );
int isSecondUnaligned = ( algnResult[i].algnmt_2 == 0xFFFFFFFF );
int properlyPaired = ( ( !isFirstUnaligned ) && ( !isSecondUnaligned ) );
unsigned int readLen1 = upkdReadLengths[algnResult[i].readID]; // length of the first read
unsigned int readLen2 = upkdReadLengths[algnResult[i].readID + 1]; // length of the second read
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT ) && ( algnResult[i].readID != preReadID )
&& properlyPaired )
{
// output the information of the (second) read
currReadID = algnResult[i].readID + 1;
displayID = ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN ) ? ( currReadID + accumReadNum ) / 2 + 1 : currReadID + accumReadNum + 1;
getReadInfo ( &qInput, currReadID, displayID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
OCCReportDelimitorDP ( &qInput );
preReadID = algnResult[i].readID;
}
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT )
&& properlyPaired )
{
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
algnResult[i].strand_2 = 2;
#endif
// for plain and binary, we only output the answer for properly aligned pairs
// output the alignment of the first read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_1;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_1;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_1;
if ( algnResult[i].whichFromDP == 0 )
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString;
}
else
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 0;
}
occ->occPositionCache[occ->occPositionCacheCount].len = readLen1;
occ->occPositionCacheCount++;
// output the alignment of the second read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_2;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_2;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_2;
if ( algnResult[i].whichFromDP == 1 )
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString;
}
else
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 0;
}
occ->occPositionCache[occ->occPositionCacheCount].len = readLen2;
occ->occPositionCacheCount++;
}
else if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
// SAM format
getAlgnInfo ( pePair, algnResult[i], peStrandLeftLeg, peStrandRightLeg );
// output the alignment of the first read
currReadID = algnResult[i].readID;
getReadInfo ( &qInput, currReadID, currReadID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
if ( algnResult[i].whichFromDP == 0 )
{
// this should be properly paired
OCCDirectWritePairOccSAMAPIwCIGAR ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen2, algnResult[i].cigarString );
}
else
{
OCCDirectWritePairOccSAMAPI ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen2, properlyPaired );
}
// output the alignment of the second read
currReadID = algnResult[i].readID + 1;
getReadInfo ( &qInput, currReadID, currReadID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
if ( algnResult[i].whichFromDP == 1 )
{
// this should be properly paired
OCCDirectWritePairOccSAMAPI2wCIGAR ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen1, algnResult[i].cigarString );
}
else
{
OCCDirectWritePairOccSAMAPI2 ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen1, properlyPaired );
}
}
}
OCCFlushCacheDP ( &qInput );
OCCFree ( qSetting.occ );
}
void outputRead2 ( AlgnmtDPResult * algnResult, unsigned int algnNum,
unsigned int * queries, unsigned int * readLengths, unsigned int * upkdReadIDs, char * upkdQueryNames, char * upkdQualities,
unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index, int peStrandLeftLeg, int peStrandRightLeg )
{
if ( algnNum == 0 )
{
return;
}
HSPAux * hspaux = index->sraIndex->hspaux;
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.AlgnmtIndex = &aIndex;
qInput.QueryInfo = &qInfo;
OCC * occ = qSetting.occ;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int upkdReadID;
unsigned int displayID;
AlgnmtDPResult * bestAlgn = NULL;
AlgnmtDPResult * currAlgn = NULL;
char minNumMismatch, currNumMismatch;
int maxScore, currScore;
unsigned char upkdPosQuery[MAX_READ_LENGTH];
unsigned char upkdPosQuery2[MAX_READ_LENGTH];
char * qualities1, *qualities2;
unsigned int readLen1, readLen2;
char * queryName1, *queryName2;
unsigned int word_per_query = getWordPerQuery ( maxReadLength );
unsigned int startIndex = 0;
DynamicUint8Array * charArray = NULL;
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{ charArray = DynamicUint8ArrayConstruct (); }
for ( unsigned int i = 0; i < algnNum; i++ )
{
int isFirstUnaligned = ( algnResult[i].algnmt_1 == 0xFFFFFFFF );
int isSecondUnaligned = ( algnResult[i].algnmt_2 == 0xFFFFFFFF );
int properlyPaired = ( ( !isFirstUnaligned ) && ( !isSecondUnaligned ) );
if ( algnResult[i].readID != preReadID )
{
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
if ( preReadID != 0xFFFFFFFF )
{
pairDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, i - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
}
// reset the bestAlgn
bestAlgn = & ( algnResult[i] );
if ( isFirstUnaligned && !isSecondUnaligned )
{
minNumMismatch = bestAlgn->score_2;
maxScore = -127;
}
else if ( isSecondUnaligned && !isFirstUnaligned )
{
minNumMismatch = bestAlgn->score_1;
maxScore = -127;
}
else if ( properlyPaired )
{
minNumMismatch = ( bestAlgn->whichFromDP == 1 ) ? bestAlgn->score_1 : bestAlgn->score_2;
maxScore = ( bestAlgn->whichFromDP == 1 ) ? bestAlgn->score_2 : bestAlgn->score_1;
}
}
// get the information of both reads
readLen1 = readLengths[algnResult[i].readID]; // length of the first read
readLen2 = readLengths[algnResult[i].readID + 1]; // length of the second read
// name of the first read
queryName1 = upkdQueryNames + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID] - 1 ) * hspaux->maxLenReadName;
// name of the second read
queryName2 = upkdQueryNames + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID + 1] - 1 ) * hspaux->maxLenReadName;
// sequence the first read
retrieve2BWTQueryFormat ( queries, algnResult[i].readID, word_per_query, upkdPosQuery );
// sequence the second read
retrieve2BWTQueryFormat ( queries, algnResult[i].readID + 1, word_per_query, upkdPosQuery2 );
// base qualities of the first read
qualities1 = upkdQualities + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID] - 1 ) * maxReadLength;
// base qualities of the second read
qualities2 = upkdQualities + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID + 1] - 1 ) * maxReadLength;
// set qInput for the second read
qInfo.ReadName = queryName2;
qInfo.ReadCode = upkdPosQuery2;
qInfo.ReadLength = readLen2;
qInfo.ReadQuality = qualities2;
upkdReadID = upkdReadIDs[algnResult[i].readID + 1];
displayID = ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN ) ? ( upkdReadID + accumReadNum ) / 2 : upkdReadID + accumReadNum;
qInfo.ReadId = displayID;
startIndex = i;
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT ) && properlyPaired )
{
OCCReportDelimitorDP ( &qInput );
}
preReadID = algnResult[i].readID;
}
else if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
// SAM format
// update the bestAlgn
if ( isFirstUnaligned && !isSecondUnaligned )
{
if ( algnResult[i].score_2 < minNumMismatch )
{
bestAlgn = & ( algnResult[i] );
minNumMismatch = bestAlgn->score_2;
maxScore = -127;
}
}
else if ( isSecondUnaligned && !isFirstUnaligned )
{
if ( algnResult[i].score_1 < minNumMismatch )
{
bestAlgn = & ( algnResult[i] );
minNumMismatch = bestAlgn->score_1;
maxScore = -127;
}
}
else if ( properlyPaired )
{
currAlgn = & ( algnResult[i] );
currNumMismatch = ( currAlgn->whichFromDP == 1 ) ? currAlgn->score_1 : currAlgn->score_2;
currScore = ( currAlgn->whichFromDP == 1 ) ? currAlgn->score_2 : currAlgn->score_1;
if ( ( currNumMismatch == minNumMismatch && currScore > maxScore ) ||
( currNumMismatch < minNumMismatch ) )
{
bestAlgn = currAlgn;
minNumMismatch = currNumMismatch;
maxScore = currScore;
}
}
}
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT )
&& properlyPaired )
{
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
algnResult[i].strand_2 = 2;
#endif
// for plain and binary, we only output the answer for properly aligned pairs
// output the alignment of the first read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_1;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_1;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_1;
if ( algnResult[i].whichFromDP == 0 )
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString;
}
else
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 0;
}
occ->occPositionCache[occ->occPositionCacheCount].len = readLen1;
occ->occPositionCacheCount++;
// output the alignment of the second read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_2;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_2;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_2;
if ( algnResult[i].whichFromDP == 1 )
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString;
}
else
{
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 0;
}
occ->occPositionCache[occ->occPositionCacheCount].len = readLen2;
occ->occPositionCacheCount++;
}
}
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API && preReadID != 0xFFFFFFFF )
{
pairDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, algnNum - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
}
if ( outputFormat != SRA_OUTPUT_FORMAT_SAM_API )
{ OCCFlushCacheDP ( &qInput ); }
OCCFree ( qSetting.occ );
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{ DynamicUint8ArrayFree ( charArray ); }
}
// output a set of deep DP alignment results
void outputDeepDPResult ( DeepDPAlignResult * algnResult, unsigned int algnNum, unsigned char * upkdQueries, char * upkdQueryNames,
unsigned int * upkdReadLengths, unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index, int peStrandLeftLeg, int peStrandRightLeg )
{
// output a set of alignment results
// the alignments of the same pair of reads have to be together
// algnNum: the number of results in "algnResult"
if ( algnNum == 0 )
{ return; }
HSPAux * hspaux = index->sraIndex->hspaux;
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.QueryInfo = &qInfo;
qInput.AlgnmtIndex = &aIndex;
OCC * occ = qSetting.occ;
unsigned int currReadID;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int displayID;
PEPairs pePair;
for ( unsigned int i = 0; i < algnNum; i++ )
{
// check the readID
/*
if (algnResult[i].readID%2 > 0) {
fprintf(stderr, "ERROR! The read ID is not even! i=%u readID=%u\n", i, algnResult[i].readID);
}*/
int isFirstUnaligned = ( algnResult[i].algnmt_1 == 0xFFFFFFFF );
int isSecondUnaligned = ( algnResult[i].algnmt_2 == 0xFFFFFFFF );
int properlyPaired = ( ( !isFirstUnaligned ) & ( !isSecondUnaligned ) );
unsigned int readLen1 = upkdReadLengths[algnResult[i].readID]; // length of the first read
unsigned int readLen2 = upkdReadLengths[algnResult[i].readID + 1]; // length of the second read
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT ) && ( algnResult[i].readID != preReadID )
&& properlyPaired )
{
// output the information of the (second) read
currReadID = algnResult[i].readID + 1;
displayID = ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN ) ? ( currReadID + accumReadNum ) / 2 + 1 : currReadID + accumReadNum + 1;
getReadInfo ( &qInput, currReadID, displayID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
OCCReportDelimitorDP ( &qInput );
preReadID = algnResult[i].readID;
}
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT )
&& properlyPaired )
{
// output the alignment of the first read
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
algnResult[i].strand_2 = 2;
#endif
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_1;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_1;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_1;
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString_1 );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString_1;
occ->occPositionCache[occ->occPositionCacheCount].len = readLen1;
occ->occPositionCacheCount++;
// output the alignment of the second read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_2;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_2;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_2;
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString_2 );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString_2;
occ->occPositionCache[occ->occPositionCacheCount].len = readLen2;
occ->occPositionCacheCount++;
}
else if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
// SAM format
getAlgnInfo2 ( pePair, algnResult[i], peStrandLeftLeg, peStrandRightLeg );
// output the alignment of the first read
currReadID = algnResult[i].readID;
getReadInfo ( &qInput, currReadID, currReadID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
if ( properlyPaired )
{ OCCDirectWritePairOccSAMAPIwCIGAR ( &qInput, &pePair, 0, 0, readLen2, algnResult[i].cigarString_1 ); }
else
{ OCCDirectWritePairOccSAMAPI ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen2, properlyPaired ); }
// output the alignment of the second read
currReadID = algnResult[i].readID + 1;
getReadInfo ( &qInput, currReadID, currReadID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
if ( properlyPaired )
{ OCCDirectWritePairOccSAMAPI2wCIGAR ( &qInput, &pePair, 0, 0, readLen1, algnResult[i].cigarString_2 ); }
else
{ OCCDirectWritePairOccSAMAPI2 ( &qInput, &pePair, isFirstUnaligned, isSecondUnaligned, readLen1, properlyPaired ); }
}
}
OCCFlushCacheDP ( &qInput );
OCCFree ( qSetting.occ );
}
void outputDeepDPResult2 ( DeepDPAlignResult * algnResult, unsigned int algnNum,
unsigned int * queries, unsigned int * readLengths, unsigned int * upkdReadIDs, char * upkdQueryNames, char * upkdQualities,
unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index, int peStrandLeftLeg, int peStrandRightLeg )
{
if ( algnNum == 0 )
{
return;
}
BWT * bwt = index->sraIndex->bwt;
HSPAux * hspaux = index->sraIndex->hspaux;
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.QueryInfo = &qInfo;
qInput.AlgnmtIndex = &aIndex;
OCC * occ = qSetting.occ;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int upkdReadID;
unsigned int displayID;
DeepDPAlignResult * bestAlgn = NULL;
int maxScore;
unsigned char upkdPosQuery[MAX_READ_LENGTH];
unsigned char upkdPosQuery2[MAX_READ_LENGTH];
char * qualities1, *qualities2;
unsigned int readLen1, readLen2;
char * queryName1, *queryName2;
unsigned int word_per_query = getWordPerQuery ( maxReadLength );
unsigned int startIndex = 0;
DynamicUint8Array * charArray = NULL;
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{ charArray = DynamicUint8ArrayConstruct (); }
for ( unsigned int i = 0; i < algnNum; i++ )
{
int isFirstUnaligned = ( algnResult[i].algnmt_1 == 0xFFFFFFFF );
int isSecondUnaligned = ( algnResult[i].algnmt_2 == 0xFFFFFFFF );
int properlyPaired = ( ( !isFirstUnaligned ) && ( !isSecondUnaligned ) );
if ( algnResult[i].readID != preReadID )
{
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
if ( preReadID != 0xFFFFFFFF )
{
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
// ==========================================================
// for those not properly paired, needs to perform deep-dp for unaligned reads,
// ==========================================================
if ( bestAlgn->algnmt_1 == 0xFFFFFFFF && bestAlgn->algnmt_2 == 0xFFFFFFFF && ( ( AllHits * ) hspaux->allHits )->readNum < MAX_UNALIGN_READS_NUM_FOR_DEEP_DP )
{
int readID = preReadID;
int first_read_no_hit = ( ( hspaux->sa_num[readID] == 0 ) && ( hspaux->occ_num[readID] == 0 ) );
int second_read_no_hit = ( ( hspaux->sa_num[readID + 1] == 0 ) && ( hspaux->occ_num[readID + 1] == 0 ) );
if ( first_read_no_hit )
{
addReadIDToBothUnalignedPairs ( ( ( UnalignedSinglesArrays * ) ( hspaux->readsIDForSingleDP ) )->array[0], readID );
}
else
{
inputSoap3AnsToArray ( ( AllHits * ) hspaux->allHits, readID, hspaux, bwt, readLen1 );
}
if ( second_read_no_hit || ( !first_read_no_hit ) )
{
addReadIDToBothUnalignedPairs ( ( ( UnalignedSinglesArrays * ) ( hspaux->readsIDForSingleDP ) )->array[0], readID + 1 );
}
else
{
inputSoap3AnsToArray ( ( AllHits * ) hspaux->allHits, readID + 1, hspaux, bwt, readLen2 );
}
}
else
{
pairDeepDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, i - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
}
// ==========================================================
#else
pairDeepDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, i - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
#endif
}
// reset the bestAlgn
bestAlgn = & ( algnResult[i] );
if ( isFirstUnaligned && ( !isSecondUnaligned ) )
{
maxScore = bestAlgn->score_2;
}
else if ( isSecondUnaligned && ( !isFirstUnaligned ) )
{
maxScore = bestAlgn->score_1;
}
else if ( properlyPaired )
{
maxScore = bestAlgn->score_1 + bestAlgn->score_2;
}
else
{
maxScore = -127;
}
}
// get the information of both reads
readLen1 = readLengths[algnResult[i].readID]; // length of the first read
readLen2 = readLengths[algnResult[i].readID + 1]; // length of the second read
// name of the first read
queryName1 = upkdQueryNames + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID] - 1 ) * hspaux->maxLenReadName;
// name of the second read
queryName2 = upkdQueryNames + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID + 1] - 1 ) * hspaux->maxLenReadName;
// sequence the first read
retrieve2BWTQueryFormat ( queries, algnResult[i].readID, word_per_query, upkdPosQuery );
// sequence the second read
retrieve2BWTQueryFormat ( queries, algnResult[i].readID + 1, word_per_query, upkdPosQuery2 );
// base qualities of the first read
qualities1 = upkdQualities + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID] - 1 ) * maxReadLength;
// base qualities of the second read
qualities2 = upkdQualities + ( unsigned long long ) ( upkdReadIDs[algnResult[i].readID + 1] - 1 ) * maxReadLength;
// set qInput for the second read
qInfo.ReadName = queryName2;
qInfo.ReadCode = upkdPosQuery2;
qInfo.ReadLength = readLen2;
qInfo.ReadQuality = qualities2;
upkdReadID = upkdReadIDs[algnResult[i].readID + 1];
displayID = ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN ) ? ( upkdReadID + accumReadNum ) / 2 : upkdReadID + accumReadNum;
qInfo.ReadId = displayID;
startIndex = i;
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT ) && properlyPaired )
{
OCCReportDelimitorDP ( &qInput );
}
preReadID = algnResult[i].readID;
}
else if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{
// SAM format
// update the bestAlgn
if ( isFirstUnaligned && !isSecondUnaligned )
{
if ( algnResult[i].score_2 > maxScore )
{
bestAlgn = & ( algnResult[i] );
maxScore = algnResult[i].score_2;
}
}
else if ( isSecondUnaligned && !isFirstUnaligned )
{
if ( algnResult[i].score_1 > maxScore )
{
bestAlgn = & ( algnResult[i] );
maxScore = algnResult[i].score_1;
}
}
else if ( properlyPaired )
{
if ( algnResult[i].score_1 + algnResult[i].score_2 > maxScore )
{
bestAlgn = & ( algnResult[i] );
maxScore = algnResult[i].score_1 + algnResult[i].score_2;
}
}
}
if ( ( outputFormat == SRA_OUTPUT_FORMAT_PLAIN || outputFormat == SRA_OUTPUT_FORMAT_DEFAULT )
&& properlyPaired )
{
#ifdef BGS_FWD_FOR_FIRST_REV_FOR_SECOND
algnResult[i].strand_2 = 2;
#endif
// for plain and binary, we only output the answer for properly aligned pairs
// output the alignment of the first read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_1;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_1;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_1;
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString_1 );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString_1;
occ->occPositionCache[occ->occPositionCacheCount].len = readLen1;
occ->occPositionCacheCount++;
// output the alignment of the second read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt_2;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand_2;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score_2;
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
convertToCigarStr2 ( algnResult[i].cigarString_2 );
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString_2;
occ->occPositionCache[occ->occPositionCacheCount].len = readLen2;
occ->occPositionCacheCount++;
}
}
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API && preReadID != 0xFFFFFFFF )
{
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
// ==========================================================
// for those not properly paired, needs to perform deep-dp for unaligned reads,
// ==========================================================
if ( bestAlgn->algnmt_1 == 0xFFFFFFFF && bestAlgn->algnmt_2 == 0xFFFFFFFF && ( ( AllHits * ) hspaux->allHits )->readNum < MAX_UNALIGN_READS_NUM_FOR_DEEP_DP )
{
int readID = preReadID;
int first_read_no_hit = ( ( hspaux->sa_num[readID] == 0 ) && ( hspaux->occ_num[readID] == 0 ) );
int second_read_no_hit = ( ( hspaux->sa_num[readID + 1] == 0 ) && ( hspaux->occ_num[readID + 1] == 0 ) );
if ( first_read_no_hit )
{
addReadIDToBothUnalignedPairs ( ( ( UnalignedSinglesArrays * ) ( hspaux->readsIDForSingleDP ) )->array[0], readID );
}
else
{
inputSoap3AnsToArray ( ( AllHits * ) hspaux->allHits, readID, hspaux, bwt, readLen1 );
}
if ( second_read_no_hit || ( !first_read_no_hit ) )
{
addReadIDToBothUnalignedPairs ( ( ( UnalignedSinglesArrays * ) ( hspaux->readsIDForSingleDP ) )->array[0], readID + 1 );
}
else
{
inputSoap3AnsToArray ( ( AllHits * ) hspaux->allHits, readID + 1, hspaux, bwt, readLen2 );
}
}
else
{
pairDeepDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, algnNum - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
}
// ==========================================================
#else
pairDeepDPOutputSAMAPI ( &qInput, algnResult, bestAlgn,
startIndex, algnNum - startIndex,
upkdPosQuery, upkdPosQuery2, qualities1, qualities2,
readLen1, readLen2, queryName1, queryName2,
charArray );
#endif
}
if ( outputFormat != SRA_OUTPUT_FORMAT_SAM_API )
{ OCCFlushCacheDP ( &qInput ); }
OCCFree ( qSetting.occ );
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{ DynamicUint8ArrayFree ( charArray ); }
}
// output DP single-end alignment results
void outputDPSingleResult ( SingleAlgnmtResult * algnResult, unsigned int algnNum, unsigned char * upkdQueries, char * upkdQueryNames,
unsigned int * upkdReadLengths, unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index )
{
// output a set of alignment results
// the alignments of the same pair of reads have to be together
// algnNum: the number of results in "algnResult"
if ( algnNum == 0 )
{ return; }
HSP * hsp = index->sraIndex->hsp;
HSPAux * hspaux = index->sraIndex->hspaux;
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.QueryInfo = &qInfo;
qInput.AlgnmtIndex = &aIndex;
OCC * occ = qSetting.occ;
unsigned int currReadID;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int displayID;
for ( unsigned int i = 0; i < algnNum; i++ )
{
// check the readID
int isUnaligned = ( algnResult[i].algnmt == 0xFFFFFFFF );
unsigned int readLen = upkdReadLengths[algnResult[i].readID]; // length of the read
int needOutput = ( ( !isUnaligned ) || ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API ) );
if ( ( algnResult[i].readID != preReadID ) && needOutput && outputDPFile != NULL )
{
// output the information of the read
currReadID = algnResult[i].readID;
displayID = currReadID + accumReadNum + 1;
getReadInfo ( &qInput, currReadID, displayID, upkdQueries, upkdQueryNames, upkdReadLengths, maxReadLength, hspaux->maxLenReadName );
OCCReportDelimitorDP ( &qInput );
preReadID = algnResult[i].readID;
}
if ( needOutput && outputDPFile != NULL )
{
// output the alignment of the read
if ( occ->occPositionCacheCount >= OCC_CACHE_SIZE ) {OCCFlushCacheDP ( &qInput );}
if ( !isUnaligned )
{
occ->occPositionCache[occ->occPositionCacheCount].tp = algnResult[i].algnmt;
occ->occPositionCache[occ->occPositionCacheCount].ReadStrand = algnResult[i].strand;
occ->occPositionCache[occ->occPositionCacheCount].ChromId = 0;
occ->occPositionCache[occ->occPositionCacheCount].occMismatch = algnResult[i].score;
occ->occPositionCache[occ->occPositionCacheCount].resultSource = 1;
occ->occPositionCache[occ->occPositionCacheCount].cigarString = algnResult[i].cigarString;
occ->occPositionCache[occ->occPositionCacheCount].len = readLen;
occ->occPositionCacheCount++;
}
else
{
OCCReportNoAlignment ( &qInput );
}
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API )
{ OCCFlushCacheDP ( &qInput ); }
}
if ( ( !isUnaligned ) && outputDPFile == NULL )
{
// output the alignment to the array
addOCCToArray ( hspaux->algnResultArrays->algnArrays[hspaux->algnResultArrays->numArrays - 1], currReadID, algnResult[i].algnmt, algnResult[i].strand,
2, algnResult[i].score );
}
}
if ( outputDPFile != NULL )
{ OCCFlushCacheDP ( &qInput ); }
OCCFree ( qSetting.occ );
}
void outputDPSingleResult2 ( SingleAlgnmtResult * algnResult, unsigned int algnNum,
unsigned int * queries, unsigned int * readLengths, unsigned int * upkdReadIDs, char * upkdQueryNames, char * upkdQualities,
unsigned int maxReadLength, unsigned int accumReadNum, int outputFormat,
FILE * outputDPFile, samfile_t * samOutputDPFilePtr, Soap3Index * index )
{
if ( algnNum == 0 )
{ return; }
HSPAux * hspaux = index->sraIndex->hspaux;
#ifdef PERFORM_DEEP_DP_FOR_UNALIGN_READS
if ( hspaux->readType == PAIR_END_READ )
{
// preforming deep dp for the unaligned pair-end reads
// save all the alignment results to array
inputAlgnmtsToArray ( ( AllHits * ) hspaux->allHits, algnResult, algnNum );
return;
}
#endif
SRAIndex aIndex;
// Copy SRAIndex
memcpy ( & ( aIndex ), index->sraIndex, sizeof ( SRAIndex ) );
SRASetting qSetting;
qSetting.OutFilePtr = outputDPFile;
qSetting.occ = OCCConstruct ();
qSetting.OutFileFormat = outputFormat;
qSetting.SAMOutFilePtr = samOutputDPFilePtr;
SRAQueryInput qInput;
SRAQueryInfo qInfo;
qInput.QuerySetting = &qSetting;
qInput.QueryInfo = &qInfo;
qInput.AlgnmtIndex = &aIndex;
// check whether the answers are outputted to file
// or stored into the global array
int isAnsToFile = ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API ) || ( outputDPFile != NULL );
OCC * occ = qSetting.occ;
unsigned int currReadID;
unsigned int preReadID = 0xFFFFFFFF;
unsigned int displayID;
unsigned int startIndex = 0;
unsigned char upkdPosQuery[MAX_READ_LENGTH];
unsigned int word_per_query = getWordPerQuery ( maxReadLength );
DynamicUint8Array * charArray = NULL;
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API && isAnsToFile )
{ charArray = DynamicUint8ArrayConstruct (); }
for ( unsigned int i = 0; i < algnNum; i++ )
{
// check the readID
int isUnaligned = ( algnResult[i].algnmt == 0xFFFFFFFF );
unsigned int readLen = readLengths[algnResult[i].readID]; // length of the read
int needOutput = ( ( !isUnaligned ) || ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API ) );
if ( ( algnResult[i].readID != preReadID ) && needOutput && isAnsToFile )
{
// For SAM output format
if ( outputFormat == SRA_OUTPUT_FORMAT_SAM_API && preReadID != 0xFFFFFFFF )
{
SingleDPOutputSAMAPI ( &qInput, algnResult,
startIndex, i - startIndex, charArray );