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ChimericPairedEndAligner.cpp
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ChimericPairedEndAligner.cpp
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/*++
Module Name:
ChimericPairedEndAligner.cpp
Abstract:
A paired-end aligner calls into a different paired-end aligner, and if
it fails to find an alignment, aligns each of the reads singly. This handles
chimeric reads that would otherwise be unalignable.
Authors:
Bill Bolosky, June, 2013
Environment:
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "ChimericPairedEndAligner.h"
#include "mapq.h"
#include "directions.h"
#include "BigAlloc.h"
#include "Util.h"
using namespace std;
#ifdef TRACE_PAIRED_ALIGNER
#define TRACE printf
#else
#define TRACE(...) {}
#endif
ChimericPairedEndAligner::ChimericPairedEndAligner(
GenomeIndex *index_,
unsigned maxReadSize,
unsigned maxHits,
unsigned maxK,
unsigned maxSeedsFromCommandLine,
double seedCoverage,
unsigned minWeightToCheck,
bool forceSpacing_,
unsigned extraSearchDepth_,
bool noUkkonen,
bool noOrderedEvaluation,
bool noTruncation,
bool useAffineGap_,
bool ignoreAlignmentAdjustmentsForOm,
bool altAwareness,
bool emitALTAlignments_,
PairedEndAligner *underlyingPairedEndAligner_,
unsigned minReadLength_,
int maxSecondaryAlignmentsPerContig,
int maxScoreGapToPreferNonAltAlignment,
int flattenMAPQAtOrBelow_,
bool useSoftClipping_,
unsigned matchReward,
unsigned subPenalty,
unsigned gapOpenPenalty,
unsigned gapExtendPenalty,
unsigned fivePrimeEndBonus,
unsigned threePrimeEndBonus,
int minScoreRealignment_,
int minScoreGapRealignmentALT_,
int minAGScoreImprovement_,
bool enableHammingScoringBaseAligner_,
BigAllocator *allocator)
: underlyingPairedEndAligner(underlyingPairedEndAligner_), forceSpacing(forceSpacing_), index(index_), minReadLength(minReadLength_), emitALTAlignments(emitALTAlignments_),
maxKSingleEnd(maxK / 2), maxKPairedEnd(maxK), extraSearchDepth(extraSearchDepth_),
minScoreRealignment(minScoreRealignment_), minScoreGapRealignmentALT(minScoreGapRealignmentALT_), minAGScoreImprovement(minAGScoreImprovement_), useSoftClipping(useSoftClipping_),
flattenMAPQAtOrBelow(flattenMAPQAtOrBelow_), enableHammingScoringBaseAligner(enableHammingScoringBaseAligner_), useAffineGap(useAffineGap_)
{
// Create single-end aligners.
singleAligner = new (allocator) BaseAligner(index, maxHits, maxK / 2 /* allocate half to each end instead of letting it float like when they're aligned together */, maxReadSize,
maxSeedsFromCommandLine, seedCoverage, minWeightToCheck, extraSearchDepth,
noUkkonen, noOrderedEvaluation, noTruncation, useAffineGap,
ignoreAlignmentAdjustmentsForOm, altAwareness, emitALTAlignments, maxScoreGapToPreferNonAltAlignment,
maxSecondaryAlignmentsPerContig, &lv, &reverseLV,
matchReward, subPenalty, gapOpenPenalty, gapExtendPenalty, fivePrimeEndBonus, threePrimeEndBonus,
NULL, allocator);
underlyingPairedEndAligner->setLandauVishkin(&lv, &reverseLV);
ag.init(matchReward, subPenalty, gapOpenPenalty, gapExtendPenalty, fivePrimeEndBonus, threePrimeEndBonus);
reverseAG.init(matchReward, subPenalty, gapOpenPenalty, gapExtendPenalty, fivePrimeEndBonus, threePrimeEndBonus);
underlyingPairedEndAligner->setAffineGap(&ag, &reverseAG);
singleSecondary[0] = singleSecondary[1] = NULL;
}
size_t
ChimericPairedEndAligner::getBigAllocatorReservation(
GenomeIndex * index,
unsigned maxReadSize,
unsigned maxHits,
unsigned seedLen,
unsigned maxSeedsFromCommandLine,
double seedCoverage,
unsigned maxEditDistanceToConsider,
unsigned maxExtraSearchDepth,
unsigned maxCandidatePoolSize,
int maxSecondaryAlignmentsPerContig)
{
return BaseAligner::getBigAllocatorReservation(index, false, maxHits, maxReadSize, seedLen, maxSeedsFromCommandLine, seedCoverage, maxSecondaryAlignmentsPerContig, maxExtraSearchDepth) + sizeof(ChimericPairedEndAligner)+sizeof(_uint64);
}
ChimericPairedEndAligner::~ChimericPairedEndAligner()
{
singleAligner->~BaseAligner();
}
#ifdef _DEBUG
extern bool _DumpAlignments;
#endif // _DEBUG
bool ChimericPairedEndAligner::align(
Read *read0,
Read *read1,
PairedAlignmentResult *result,
PairedAlignmentResult *firstALTResult,
int maxEditDistanceForSecondaryResults,
_int64 secondaryResultBufferSize,
_int64 *nSecondaryResults,
PairedAlignmentResult *secondaryResults, // The caller passes in a buffer of secondaryResultBufferSize and it's filled in by AlignRead()
_int64 singleSecondaryBufferSize,
_int64 maxSecondaryAlignmentsToReturn,
_int64 *nSingleEndSecondaryResultsForFirstRead,
_int64 *nSingleEndSecondaryResultsForSecondRead,
SingleAlignmentResult *singleEndSecondaryResults, // Single-end secondary alignments for when the paired-end alignment didn't work properly
_int64 maxPairedCandidatesForAffineGapBufferSize,
_int64 *nPairedCandidatesForAffineGap,
PairedAlignmentResult *pairedCandidatesForAffineGap,
_int64 maxSingleCandidatesForAffineGapBufferSize,
_int64 *nSingleCandidatesForAffineGapFirstRead,
_int64 *nSingleCandidatesForAffineGapSecondRead,
SingleAlignmentResult *singleCandidatesForAffineGap,
int maxK
)
{
result->status[0] = result->status[1] = NotFound;
*nSecondaryResults = 0;
*nSingleEndSecondaryResultsForFirstRead = 0;
*nSingleEndSecondaryResultsForSecondRead = 0;
result->usedAffineGapScoring[0] = result->usedAffineGapScoring[1] = false;
result->basesClippedBefore[0] = result->basesClippedBefore[1] = 0;
result->basesClippedAfter[0] = result->basesClippedAfter[1] = 0;
result->clippingForReadAdjustment[0] = result->clippingForReadAdjustment[1] = 0;
result->agScore[0] = result->agScore[1] = 0;
result->liftover[0] = result->liftover[1] = false;
result->agForcedSingleAlignerCall = false;
firstALTResult->status[0] = firstALTResult->status[1] = NotFound;
*nPairedCandidatesForAffineGap = 0;
*nSingleCandidatesForAffineGapFirstRead = 0;
*nSingleCandidatesForAffineGapSecondRead = 0;
if (read0->getDataLength() < minReadLength && read1->getDataLength() < minReadLength) {
TRACE("Reads are both too short -- returning");
for (int whichRead = 0; whichRead < NUM_READS_PER_PAIR; whichRead++) {
result->location[whichRead] = InvalidGenomeLocation;
result->mapq[whichRead] = 0;
result->score[whichRead] = 0;
result->status[whichRead] = NotFound;
}
result->alignedAsPair = false;
result->nanosInAlignTogether = 0;
result->nLVCalls = 0;
result->nSmallHits = 0;
return true;
}
_int64 start = timeInNanos();
int pairAGScore = 0, sumPairScore = 0, sumPairScoreAlt = 0;
bool compareWithSingleEndAlignment = false;
if (read0->getDataLength() >= minReadLength && read1->getDataLength() >= minReadLength) {
//
// Let the LVs use the cache that we built up.
//
bool fitInSecondaryBuffer =
underlyingPairedEndAligner->align(read0, read1, result, firstALTResult, maxEditDistanceForSecondaryResults, secondaryResultBufferSize, nSecondaryResults, secondaryResults,
singleSecondaryBufferSize, maxSecondaryAlignmentsToReturn, nSingleEndSecondaryResultsForFirstRead, nSingleEndSecondaryResultsForSecondRead,
singleEndSecondaryResults, maxPairedCandidatesForAffineGapBufferSize, nPairedCandidatesForAffineGap, pairedCandidatesForAffineGap, maxSingleCandidatesForAffineGapBufferSize,
nSingleCandidatesForAffineGapFirstRead, nSingleCandidatesForAffineGapSecondRead, singleCandidatesForAffineGap, maxKPairedEnd);
if (*nPairedCandidatesForAffineGap > maxPairedCandidatesForAffineGapBufferSize) {
*nSecondaryResults = *nSingleEndSecondaryResultsForFirstRead = *nSingleEndSecondaryResultsForSecondRead = 0;
*nPairedCandidatesForAffineGap = maxPairedCandidatesForAffineGapBufferSize + 1; // So the caller knows it's the paired LV candidate buffer that overflowed
return false;
}
if (!fitInSecondaryBuffer) {
*nSingleEndSecondaryResultsForFirstRead = *nSingleEndSecondaryResultsForSecondRead = 0;
*nPairedCandidatesForAffineGap = 0;
*nSecondaryResults = secondaryResultBufferSize + 1; // So the caller knows it's the paired secondary buffer that overflowed
return false;
}
_int64 end = timeInNanos();
result->nanosInAlignTogether = end - start;
result->alignedAsPair = true;
if (forceSpacing) {
if (result->status[0] == NotFound) {
result->alignedAsPair = false;
} else {
_ASSERT(result->status[1] != NotFound); // If one's not found, so is the other
}
return true;
}
int maxScore = __max(result->score[0], result->score[1]);
sumPairScore = result->score[0] + result->score[1];
sumPairScoreAlt = firstALTResult->score[0] + firstALTResult->score[1];
//
// If the command line requests zeroing out low mapqs, do it now. There's one other place we need to check below.
//
result->mapq[0] = result->mapq[0] <= flattenMAPQAtOrBelow ? 0 : result->mapq[0];
result->mapq[1] = result->mapq[1] <= flattenMAPQAtOrBelow ? 0 : result->mapq[1];
// If we have already seen a good ALT pair, don't separate them by running the single end aligner
bool seenBetterAltResult = (firstALTResult->status[0] != NotFound)
&& (firstALTResult->status[1] != NotFound)
&& (sumPairScoreAlt <= sumPairScore - minScoreGapRealignmentALT);
bool useAltLiftover = result->liftover[0] && result->liftover[1];
if ((result->usedAffineGapScoring[0] || result->usedAffineGapScoring[1]) && maxScore >= minScoreRealignment && !seenBetterAltResult && !useAltLiftover) {
compareWithSingleEndAlignment = true;
}
if (result->status[0] != NotFound && result->status[1] != NotFound && (!compareWithSingleEndAlignment)) {
//
// Not a chimeric read.
//
return true;
}
}
int scoreLimitLeft = maxKSingleEnd;
if (compareWithSingleEndAlignment) {
scoreLimitLeft = sumPairScore;
if (result->status[0] != NotFound && result->status[1] != NotFound) {
result->agForcedSingleAlignerCall = true; // Only set this if we wouldn't have done it anyway.
}
}
//
// If the intersecting aligner didn't find an alignment for these reads (or we're double checking because of affine gap alignments), then they may be
// chimeric and so we should just align them with the single end aligner and apply a MAPQ penalty.
//
Read *read[NUM_READS_PER_PAIR] = {read0, read1};
_int64 *resultCount[2] = {nSingleEndSecondaryResultsForFirstRead, nSingleEndSecondaryResultsForSecondRead};
_int64 *affineCandidates[2] = { nSingleCandidatesForAffineGapFirstRead, nSingleCandidatesForAffineGapSecondRead };
SingleAlignmentResult singleResult[NUM_READS_PER_PAIR];
SingleAlignmentResult firstSingleALTResult[NUM_READS_PER_PAIR];
int singleEndAGScore = 0;
bool chooseSingleEndMapq = true;
for (int r = 0; r < NUM_READS_PER_PAIR; r++) {
_int64 singleEndSecondaryResultsThisTime = 0;
_int64 singleEndAffineCandidatesThisTime = 0;
if (compareWithSingleEndAlignment) {
pairAGScore += result->agScore[r];
}
// Reset max edit distance for single end aligner
singleAligner->setMaxK(maxKSingleEnd);
if (read[r]->getDataLength() < minReadLength) {
result->status[r] = NotFound;
result->mapq[r] = 0;
result->direction[r] = FORWARD;
result->location[r] = InvalidGenomeLocation;
result->score[r] = 0;
result->usedAffineGapScoring[r] = false;
result->basesClippedBefore[r] = 0;
result->basesClippedAfter[r] = 0;
result->agScore[r] = 0;
result->alignedAsPair = false;
result->clippingForReadAdjustment[r] = 0;
firstALTResult->status[r] = NotFound; // Don't need to fill in the rest, this suppresses writing it
chooseSingleEndMapq = false;
} else {
if (compareWithSingleEndAlignment) {
// Single-end alignments are not good enough to be considered
if (scoreLimitLeft < 0) {
break;
}
int maxKForRead = __min(maxKSingleEnd, __min(result->score[r], scoreLimitLeft));
singleAligner->setMaxK(maxKForRead);
}
// We're using *nSingleEndSecondaryResultsForFirstRead because it's either 0 or what all we've seen (i.e., we know NUM_READS_PER_PAIR is 2)
bool fitInSecondaryBuffer =
singleAligner->AlignRead(read[r], &singleResult[r], &firstSingleALTResult[r], maxEditDistanceForSecondaryResults,
singleSecondaryBufferSize - *nSingleEndSecondaryResultsForFirstRead, &singleEndSecondaryResultsThisTime,
maxSecondaryAlignmentsToReturn, singleEndSecondaryResults + *nSingleEndSecondaryResultsForFirstRead,
maxSingleCandidatesForAffineGapBufferSize - *nSingleCandidatesForAffineGapFirstRead, &singleEndAffineCandidatesThisTime,
singleCandidatesForAffineGap + *nSingleCandidatesForAffineGapFirstRead);
if (singleEndAffineCandidatesThisTime > (maxSingleCandidatesForAffineGapBufferSize - *nSingleCandidatesForAffineGapFirstRead)) {
*nSecondaryResults = *nSingleEndSecondaryResultsForFirstRead = *nSingleEndSecondaryResultsForSecondRead = 0;
*nSingleCandidatesForAffineGapFirstRead = maxSingleCandidatesForAffineGapBufferSize + 1; // So the caller knows it's the single end candidate buffer that overflowed
return false;
}
if (!fitInSecondaryBuffer) {
*nSecondaryResults = 0;
*nSingleEndSecondaryResultsForFirstRead = singleSecondaryBufferSize + 1;
*nSingleEndSecondaryResultsForSecondRead = 0;
*nSingleCandidatesForAffineGapFirstRead = 0;
return false;
}
bool usedHammingScoreingBaseAligner = false;
if (useSoftClipping && enableHammingScoringBaseAligner) {
//
// Try Hamming distance scoring to align any unmapped reads
//
if (singleResult[r].status == NotFound && result->status[r] == NotFound) {
usedHammingScoreingBaseAligner = true;
singleAligner->AlignRead(read[r], &singleResult[r], &firstSingleALTResult[r], maxEditDistanceForSecondaryResults,
singleSecondaryBufferSize - *nSingleEndSecondaryResultsForFirstRead, &singleEndSecondaryResultsThisTime,
maxSecondaryAlignmentsToReturn, singleEndSecondaryResults + *nSingleEndSecondaryResultsForFirstRead,
maxSingleCandidatesForAffineGapBufferSize - *nSingleCandidatesForAffineGapFirstRead, &singleEndAffineCandidatesThisTime,
singleCandidatesForAffineGap + *nSingleCandidatesForAffineGapFirstRead, true);
if (singleEndAffineCandidatesThisTime > (maxSingleCandidatesForAffineGapBufferSize - *nSingleCandidatesForAffineGapFirstRead)) {
*nSecondaryResults = *nSingleEndSecondaryResultsForFirstRead = *nSingleEndSecondaryResultsForSecondRead = 0;
*nSingleCandidatesForAffineGapFirstRead = maxSingleCandidatesForAffineGapBufferSize + 1; // So the caller knows it's the single end candidate buffer that overflowed
return false;
}
if (!fitInSecondaryBuffer) {
*nSecondaryResults = 0;
*nSingleEndSecondaryResultsForFirstRead = singleSecondaryBufferSize + 1;
*nSingleEndSecondaryResultsForSecondRead = 0;
*nSingleCandidatesForAffineGapFirstRead = 0;
return false;
}
_ASSERT(useAffineGap);
singleAligner->alignAffineGap(read[r], &singleResult[r], &firstSingleALTResult[r],
singleEndAffineCandidatesThisTime, singleCandidatesForAffineGap + *nSingleCandidatesForAffineGapFirstRead);
}
}
*(resultCount[r]) = singleEndSecondaryResultsThisTime;
*(affineCandidates[r]) = singleEndAffineCandidatesThisTime;
if (compareWithSingleEndAlignment) {
//
// Do not lower scoreLimit for mate if we used Hamming scoring for the base aligner
//
if (!usedHammingScoreingBaseAligner) {
if (singleResult[r].score != ScoreAboveLimit && singleResult[r].score != BaseAligner::UnusedScoreValue) {
scoreLimitLeft -= singleResult[r].score;
} else {
scoreLimitLeft = ScoreAboveLimit;
}
}
singleEndAGScore += singleResult[r].agScore;
if (result->agScore[r] >= singleResult[r].agScore) {
chooseSingleEndMapq = false;
}
}
} // Not too short
} // For each read in the pair
if (chooseSingleEndMapq) {
for (int r = 0; r < NUM_READS_PER_PAIR; r++) {
//
// If the single-end aligner returns a lower MAPQ choose that for the result
//
result->mapq[r] = __min(result->mapq[r], singleResult[r].mapq);
//
// If the command line requests zeroing out low mapqs, do it now. There's one other place we need to check below.
//
if (result->mapq[r] <= flattenMAPQAtOrBelow) {
result->mapq[r] = 0;
} // if we flatten
} // for each read
} // choose single end mapq
if (!compareWithSingleEndAlignment || (singleEndAGScore >= pairAGScore + minAGScoreImprovement)) {
for (int r = 0; r < NUM_READS_PER_PAIR; r++) {
if (read[r]->getDataLength() < minReadLength) {
result->status[r] = NotFound;
result->mapq[r] = 0;
result->direction[r] = FORWARD;
result->location[r] = InvalidGenomeLocation;
result->score[r] = 0;
result->usedAffineGapScoring[r] = false;
result->basesClippedBefore[r] = 0;
result->basesClippedAfter[r] = 0;
result->agScore[r] = 0;
result->clippingForReadAdjustment[r] = 0;
firstALTResult->status[r] = NotFound; // Don't need to fill in the rest, this suppresses writing it
} else {
result->status[r] = singleResult[r].status;
result->mapq[r] = singleResult[r].mapq / 3; // Heavy quality penalty for chimeric reads
result->mapq[r] = result->mapq[r] <= 3 ? 0 : result->mapq[r];
result->direction[r] = singleResult[r].direction;
result->location[r] = singleResult[r].location;
result->score[r] = singleResult[r].score;
result->scorePriorToClipping[r] = singleResult[r].scorePriorToClipping;
result->usedAffineGapScoring[r] = singleResult[r].usedAffineGapScoring;
result->basesClippedBefore[r] = singleResult[r].basesClippedBefore;
result->basesClippedAfter[r] = singleResult[r].basesClippedAfter;
result->agScore[r] = singleResult[r].agScore;
_ASSERT(result->basesClippedAfter[r] >= 0);
_ASSERT(result->basesClippedBefore[r] >= 0);
}
}
result->alignedAsPair = false;
}
#ifdef _DEBUG
if (_DumpAlignments) {
printf("ChimericPairedEndAligner: (%s:%llu, %s:%llu) score (%d, %d), MAPQ (%d, %d)\n\n\n",
index->getGenome()->getContigAtLocation(result->location[0])->name, result->location[0] - index->getGenome()->getContigAtLocation(result->location[0])->beginningLocation,
index->getGenome()->getContigAtLocation(result->location[1])->name, result->location[1] - index->getGenome()->getContigAtLocation(result->location[1])->beginningLocation,
result->score[0], result->score[1], result->mapq[0], result->mapq[1]);
}
#endif // _DEBUG
return true;
}