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OldAligner.h
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OldAligner.h
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/*++
Module Name:
Aligner.h
Abstract:
Header for SNAP genome aligner
Authors:
Bill Bolosky, August, 2011
Environment:
User mode service.
This class is NOT thread safe. It's the caller's responsibility to ensure that
at most one thread uses an instance at any time.
Revision History:
Adapted from Matei Zaharia's Scala implementation.
--*/
#pragma once
#if 0
#include "options.h"
#include "Read.h"
#include "Seed.h"
#include "Genome.h"
#include "GenomeIndex.h"
#include "Histogram.h"
#include "Aligner.h"
#include "LandauVishkin.h"
#define USE_CAREFUL_BASE_STATUS 0 // Turning this off speeds up the aligner code path at the cost of a few possible extra lookups
class OldAligner: public Aligner {
public:
OldAligner(
GenomeIndex *i_genomeIndex,
unsigned i_confDiff,
unsigned i_maxHitsToConsider,
unsigned i_maxK,
unsigned i_maxReadSize,
unsigned i_maxSeedsToUse,
unsigned i_lvCutoff);
AlignmentResult
AlignRead(
Read *read,
unsigned *genomeLocation,
bool *hitIsRC,
int *finalScore = NULL);
//
// Statistics gathering.
//
void
ComputeHitDistribution(
Read *read,
unsigned correctGenomeLocation,
bool correctHitIsRC,
unsigned *hitCountBySeed,
unsigned *rcHitCountBySeed,
unsigned &nSeedsApplied,
unsigned &nRCSeedsApplied,
unsigned *hitsCountsContainingCorrectLocation);
_int64 getNHashTableLookups() const {return nHashTableLookups;}
_int64 getLocationsScored() const {return nLocationsScored;}
_int64 getNHitsIgnoredBecauseOfTooHighPopularity() const {return nHitsIgnoredBecauseOfTooHighPopularity;}
_int64 getNReadsIgnoredBecauseOfTooManyNs() const {return nReadsIgnoredBecauseOfTooManyNs;}
_int64 getNIndelsMerged() const {return nIndelsMerged;}
#if MAINTAIN_HISTOGRAMS
const Histogram *getLVHistogram() const {return lvHistogram;}
const Histogram *getLookupHistogram() const {return lookupHistogram;}
const Histogram *getLVHistogramForMulti() const {return lvHistogramForMulti;}
const Histogram *getLVHistogramWhenBestFound() const {return lvCountWhenBestFound;}
#endif // MAINTAIN_HISTOGRAMS
const char *getRCTranslationTable() const {return rcTranslationTable;}
~OldAligner();
inline int getMaxK() const {return maxK;}
inline int getConfDiff() const {return confDiff;}
const char *getName() const {return "Old Aligner";}
void addIgnoredReads(_int64 newlyIgnoredReads) {}
private:
LandauVishkin landauVishkin;
char rcTranslationTable[256];
#if MAINTAIN_HISTOGRAMS
Histogram *lvHistogram;
Histogram *lookupHistogram;
Histogram *lvHistogramForMulti;
Histogram *lvCountWhenBestFound;
#endif // MAINTAIN_HISTOGRAMS
_int64 nHashTableLookups;
_int64 nLocationsScored;
_int64 nHitsIgnoredBecauseOfTooHighPopularity;
_int64 nReadsIgnoredBecauseOfTooManyNs;
_int64 nIndelsMerged;
//
// A bitvector indexed by offset in the read indicating whether this seed is used.
// This is here to avoid doing a memory allocation in the aligner.
//
BYTE *seedUsed;
BYTE *seedUsedAsAllocated; // Use this for deleting seedUsed.
inline bool IsSeedUsed(unsigned indexInRead) const {
return (seedUsed[indexInRead / 8] & (1 << (indexInRead % 8))) != 0;
}
inline void SetSeedUsed(unsigned indexInRead) {
seedUsed[indexInRead / 8] |= (1 << (indexInRead % 8));
}
#if USE_CAREFUL_BASE_STATUS
struct BaseStatus {
unsigned nSeedsIncludingThisBase;
unsigned nRCSeedsIncludingThisBase;
};
//
// A table indexed by offset in the Read that describes what we've done with the (potential) seed that
// starts at this location.
//
BaseStatus *bases; // This is here just to avoid dynamically allocating this on every call to AlignRead
#endif // USE_CAREFUL_BASE_STATUS
struct Candidate {
unsigned genomeLocation;
unsigned weight;
unsigned minPossibleScore;
//
// In cases of insertions and deletions we might see
// several nearby hits, because the insertion or deletion
// messes up re-aligning the seed match with the read. If that
// happens, then we just add the new seed to the existing one
// by updating "minRange" and "maxRange" to include the new
// hit, and than scoring in that range.
unsigned minRange;
unsigned maxRange;
unsigned score;
bool scored;
bool isRC;
inline bool operator>(OldAligner::Candidate &peer) {
if (genomeLocation == peer.genomeLocation) {
return isRC > peer.isRC;
}
return genomeLocation > peer.genomeLocation;
}
inline bool operator>=(OldAligner::Candidate &peer) {
if (genomeLocation == peer.genomeLocation) {
return isRC >= peer.isRC;
}
return genomeLocation > peer.genomeLocation;
}
inline bool operator<(OldAligner::Candidate &peer) {
if (genomeLocation == peer.genomeLocation) {
return isRC < peer.isRC;
}
return genomeLocation < peer.genomeLocation;
}
inline bool operator<=(OldAligner::Candidate &peer) {
if (genomeLocation == peer.genomeLocation) {
return isRC <= peer.isRC;
}
return genomeLocation < peer.genomeLocation;
}
inline bool operator==(OldAligner::Candidate &peer) {
return genomeLocation == peer.genomeLocation && isRC == peer.isRC;
}
inline bool operator!=(OldAligner::Candidate &peer) {
return genomeLocation != peer.genomeLocation || isRC != peer.isRC;
}
};
static const unsigned UnusedScoreValue = 0xffff;
bool
score(
bool forceResult,
Read *read,
Read *rcRead,
AlignmentResult *result,
int *finalScore,
unsigned *singleHitGenomeLocation,
bool *hitIsRC,
unsigned nSeedsApplied,
unsigned nRCSeedsApplied,
unsigned mostSeedsContainingAnyParticularBase,
unsigned mostRCSeedsContainingAnyParticularBase,
unsigned &lowestPossibleScoreOfAnyUnseenLocation,
unsigned &lowestPossibleRCScoreOfAnyUnseenLocation,
Candidate *candidates,
unsigned &bestScore,
unsigned &bestScoreGenomeOffset,
unsigned &secondBestScore,
unsigned &lvScores,
unsigned &lvScoresAfterBestFound,
bool anyHitsSkippedBecauseOfTooHighPopularityThisRun);
inline void clearCandidates() {nCandidates = 0;}
Candidate *findCandidate(unsigned genomeLocation, bool isRC);
Candidate *allocateNewCandidate(unsigned genomeLocation, bool isRC);
void removeCandidateAtIndex(int index);
const Genome *genome;
GenomeIndex *genomeIndex;
unsigned seedLen;
unsigned confDiff;
unsigned maxHitsToConsider;
unsigned maxK;
unsigned maxReadSize;
unsigned maxSeedsToUse; // Max number of seeds to look up in the hash table
unsigned lvCutoff;
int nCandidates;
Candidate *candidates;
char *rcReadData;
unsigned nTable[256];
#if DBG
void AssertCandidatesAreSorted();
#else // DBG
inline void AssertCandidatesAreSorted() {}
#endif // DBG
inline unsigned getWrappedNextSeedToTest(unsigned wrapCount) {
if (0 == wrapCount) {
return 0;
}
switch (seedLen) {
case 23: {
switch (wrapCount) {
case 1: return 12;
case 2: return 6;
case 3: return 17;
case 4: return 3;
case 5: return 9;
case 6: return 20;
case 7: return 14;
case 8: return 1;
case 9: return 4;
case 10: return 7;
case 11: return 10;
case 12: return 15;
case 13: return 18;
case 14: return 21;
case 15: return 4;
case 16: return 2;
case 17: return 5;
case 18: return 11;
case 19: return 16;
case 20: return 19;
case 21: return 22;
case 22: return 8;
}
}
case 22: {
switch (wrapCount) {
case 1: return 11;
case 2: return 6;
case 3: return 16;
case 4: return 3;
case 5: return 9;
case 6: return 14;
case 7: return 19;
case 8: return 2;
case 9: return 7;
case 10: return 12;
case 11: return 17;
case 12: return 20;
case 13: return 4;
case 14: return 1;
case 15: return 10;
case 16: return 13;
case 17: return 15;
case 18: return 18;
case 19: return 21;
case 20: return 5;
case 21: return 8;
default: _ASSERT(!"NOTREACHED");
}
}
case 21: {
switch (wrapCount) {
case 1: return 11;
case 2: return 6;
case 3: return 16;
case 4: return 3;
case 5: return 9;
case 6: return 13;
case 7: return 17;
case 8: return 18;
case 9: return 2;
case 10: return 5;
case 11: return 8;
case 12: return 15;
case 13: return 20;
case 14: return 1;
case 15: return 4;
case 16: return 7;
case 17: return 10;
case 18: return 12;
case 19: return 14;
case 20: return 19;
default: _ASSERT(!"NOTREACHED");
}
}
case 20: {
switch (wrapCount) {
case 1: return 10;
case 2: return 5;
case 3: return 15;
case 4: return 2;
case 5: return 7;
case 6: return 12;
case 7: return 17;
case 8: return 3;
case 9: return 9;
case 10: return 11;
case 11: return 13;
case 12: return 19;
case 13: return 1;
case 14: return 4;
case 15: return 6;
case 16: return 8;
case 17: return 14;
case 18: return 18;
case 19: return 16;
default: _ASSERT(!"NOTREACHED");
}
}
case 19: {
switch (wrapCount) {
case 1: return 10;
case 2: return 4;
case 3: return 14;
case 4: return 2;
case 5: return 6;
case 6: return 8;
case 7: return 12;
case 8: return 16;
case 9: return 18;
case 10: return 1;
case 11: return 3;
case 12: return 5;
case 13: return 7;
case 14: return 9;
case 15: return 11;
case 16: return 13;
case 17: return 15;
case 18: return 17;
default: _ASSERT(!"NOTREACHED");
}
}
case 18: {
switch (wrapCount) {
case 1: return 9;
case 2: return 4;
case 3: return 13;
case 4: return 2;
case 5: return 6;
case 6: return 11;
case 7: return 15;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 8;
case 13: return 10;
case 14: return 12;
case 15: return 14;
case 16: return 16;
case 17: return 17;
default: _ASSERT(!"NOTREACHED");
}
}
case 17: {
switch (wrapCount) {
case 1: return 8;
case 2: return 4;
case 3: return 12;
case 4: return 2;
case 5: return 6;
case 6: return 10;
case 7: return 14;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 9;
case 13: return 11;
case 14: return 13;
case 15: return 15;
case 16: return 16;
default: _ASSERT(!"NOTREACHED");
}
}
case 16: {
switch (wrapCount) {
case 1: return 8;
case 2: return 4;
case 3: return 12;
case 4: return 2;
case 5: return 6;
case 6: return 10;
case 7: return 14;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 9;
case 13: return 11;
case 14: return 13;
case 15: return 15;
default: _ASSERT(!"NOTREACHED");
}
} // inner switch
default: fprintf(stderr,"OldAligner: Not set up to run with this seed size\n"); exit(1);
} // outer switch
}
};
#endif // 0