/* * aligner_seed_mm.h */ #ifndef ALIGNER_SEED_MM_H_ #define ALIGNER_SEED_MM_H_ #include #include #include "aligner.h" #include "hit.h" #include "row_chaser.h" #include "range_chaser.h" #include "aligner_metrics.h" /** * Concrete factory class for constructing unpaired exact aligners. */ class UnpairedSeedAlignerFactory : public AlignerFactory { typedef RangeSourceDriver TRangeSrcDr; typedef std::vector TRangeSrcDrPtrVec; typedef CostAwareRangeSourceDriver TCostAwareRangeSrcDr; public: UnpairedSeedAlignerFactory( Ebwt >& ebwtFw, Ebwt >* ebwtBw, bool doFw, bool doRc, uint32_t seedMms, uint32_t seedLen, int qualCutoff, int maxBts, HitSink& sink, const HitSinkPerThreadFactory& sinkPtFactory, RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, ChunkPool *pool, BitPairReference* refs, vector >& os, bool maqPenalty, bool qualOrder, bool strandFix, bool rangeMode, bool verbose, bool quiet, uint32_t seed, AlignerMetrics *metrics) : ebwtFw_(ebwtFw), ebwtBw_(ebwtBw), doFw_(doFw), doRc_(doRc), seedMms_(seedMms), seedLen_(seedLen), qualCutoff_(qualCutoff), maxBts_(maxBts), sink_(sink), sinkPtFactory_(sinkPtFactory), cacheFw_(cacheFw), cacheBw_(cacheBw), cacheLimit_(cacheLimit), pool_(pool), refs_(refs), os_(os), strandFix_(strandFix), maqPenalty_(maqPenalty), qualOrder_(qualOrder), rangeMode_(rangeMode), verbose_(verbose), quiet_(quiet), metrics_(metrics) { assert(ebwtFw.isInMemory()); } /** * Create a new UnpairedExactAlignerV1s. */ virtual Aligner* create() const { HitSinkPerThread* sinkPt = sinkPtFactory_.create(); EbwtSearchParams >* params = new EbwtSearchParams >(*sinkPt, os_); int *btCnt = new int[1]; *btCnt = maxBts_; TRangeSrcDrPtrVec *drVec = new TRangeSrcDrPtrVec(); if(seedMms_ == 0) { const int halfAndHalf = 0; bool mate1 = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, true, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, false, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * driverFw = new EbwtRangeSourceDriver( *params, rFw_Bw, true, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * driverRc = new EbwtRangeSourceDriver( *params, rRc_Fw, false, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 if(doFw_) drVec->push_back(driverFw); if(doRc_) drVec->push_back(driverRc); } else if(seedMms_ == 1) { const int halfAndHalf = 0; bool fw = true; bool mate1 = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, true); if(doFw_) { drVec->push_back(drFw_Bw); drVec->push_back(drFw_Seed); } if(doRc_) { drVec->push_back(drRc_Fw); drVec->push_back(drRc_Seed); } } else if(seedMms_ == 2) { bool fw = true; bool mate1 = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rFw_BwHalf = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriver * drFw_BwHalf = new EbwtRangeSourceDriver( *params, rFw_BwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_FwHalf = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, // no mismatches in hi half PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, // up to 2 in lo half PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, // no mismatches in lo half PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, // up to 2 in hi half PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, true); EbwtRangeSourceDriver * drRc_FwHalf = new EbwtRangeSourceDriver( *params, rRc_FwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); if(doFw_) { drVec->push_back(drFw_Bw); drVec->push_back(drFw_Seed); drVec->push_back(drFw_BwHalf); } if(doRc_) { drVec->push_back(drRc_Fw); drVec->push_back(drRc_Seed); drVec->push_back(drRc_FwHalf); } } else if(seedMms_ > 2) { bool fw = true; bool mate1 = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); // Partial and full aligners for alignments with 0 // mismatches in the lo-half and up to 3 mismatches in the // hi-half EbwtRangeSourceFactory *rFw_BwSeed03 = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rFw_FwSeedGen03 = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_, metrics_); // Partial and full aligners for alignments with 1 // mismatch in the lo-half and up to 2 mismatches in the // hi-half EbwtRangeSourceFactory *rFw_BwSeed12 = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); // Note: the following is half-and-half (unlike the 03 version) EbwtRangeSource *rFw_FwSeedGen12 = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rFw_BwHalf12 = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, true, // nudgeLeft PIN_TO_HI_HALF_EDGE, // 0 mismatches in hi-half PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, // up to 3 mismatches in lo-half os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drFw_BwSeed03 = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed03, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drFw_FwSeedGen03 = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen03, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drFw_Seed03 = new EbwtSeededRangeSourceDriver( drFw_BwSeed03, drFw_FwSeedGen03, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drFw_BwSeed12 = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drFw_FwSeedGen12 = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, // 1-mismatch in lo-half PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, // 1 or 2 mismatches in hi-half os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drFw_Seed12 = new EbwtSeededRangeSourceDriver( drFw_BwSeed12, drFw_FwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriver * drFw_BwHalf12 = new EbwtRangeSourceDriver( *params, rFw_BwHalf12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); // Partial and full aligners for alignments with 0 // mismatches in the lo-half and up to 3 mismatches in the // hi-half EbwtRangeSourceFactory *rRc_FwSeed03 = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_BwSeedGen03 = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_, metrics_); // Partial and full aligners for alignments with 1 // mismatch in the lo-half and up to 2 mismatches in the // hi-half EbwtRangeSourceFactory *rRc_FwSeed12 = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_BwSeedGen12 = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_, metrics_); EbwtRangeSource *rRc_FwHalf12 = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_, metrics_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drRc_FwSeed03 = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed03, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drRc_BwSeedGen03 = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen03, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drRc_Seed03 = new EbwtSeededRangeSourceDriver( drRc_FwSeed03, drRc_BwSeedGen03, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drRc_FwSeed12 = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drRc_BwSeedGen12 = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drRc_Seed12 = new EbwtSeededRangeSourceDriver( drRc_FwSeed12, drRc_BwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriver * drRc_FwHalf12 = new EbwtRangeSourceDriver( *params, rRc_FwHalf12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); if(doFw_) { drVec->push_back(drFw_Bw); drVec->push_back(drFw_Seed03); drVec->push_back(drFw_Seed12); drVec->push_back(drFw_BwHalf12); } if(doRc_) { drVec->push_back(drRc_Fw); drVec->push_back(drRc_Seed03); drVec->push_back(drRc_Seed12); drVec->push_back(drRc_FwHalf12); } } else { cerr << "Unsupported --stateful mode: " << seedMms_ << endl; } TCostAwareRangeSrcDr* dr = new TCostAwareRangeSrcDr(strandFix_, drVec, verbose_, quiet_, false); delete drVec; // Set up a RangeChaser RangeChaser > *rchase = new RangeChaser >(cacheLimit_, cacheFw_, cacheBw_, metrics_); return new UnpairedAlignerV2( params, dr, rchase, sink_, sinkPtFactory_, sinkPt, os_, refs_, rangeMode_, verbose_, quiet_, maxBts_, pool_, btCnt, metrics_); } private: Ebwt >& ebwtFw_; Ebwt >* ebwtBw_; bool doFw_; bool doRc_; const uint32_t seedMms_; const uint32_t seedLen_; const int qualCutoff_; const int maxBts_; HitSink& sink_; const HitSinkPerThreadFactory& sinkPtFactory_; RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; ChunkPool *pool_; BitPairReference* refs_; vector >& os_; bool strandFix_; bool maqPenalty_; bool qualOrder_; bool rangeMode_; bool verbose_; bool quiet_; AlignerMetrics *metrics_; }; /** * Concrete factory class for constructing unpaired exact aligners. */ class PairedSeedAlignerFactory : public AlignerFactory { typedef RangeSourceDriver TRangeSrcDr; typedef std::vector TRangeSrcDrPtrVec; typedef CostAwareRangeSourceDriver TCostAwareRangeSrcDr; public: PairedSeedAlignerFactory( Ebwt >& ebwtFw, Ebwt >* ebwtBw, bool color, bool v1, bool doFw, bool doRc, uint32_t seedMms, uint32_t seedLen, int qualCutoff, int maxBts, HitSink& sink, const HitSinkPerThreadFactory& sinkPtFactory, bool mate1fw, bool mate2fw, uint32_t peInner, uint32_t peOuter, bool dontReconcile, uint32_t symCeil, uint32_t mixedThresh, uint32_t mixedAttemptLim, RangeCache* cacheFw, RangeCache* cacheBw, uint32_t cacheLimit, ChunkPool *pool, BitPairReference* refs, vector >& os, bool reportSe, bool maqPenalty, bool qualOrder, bool strandFix, bool rangeMode, bool verbose, bool quiet, uint32_t seed) : ebwtFw_(ebwtFw), ebwtBw_(ebwtBw), color_(color), v1_(v1), doFw_(doFw), doRc_(doRc), seedMms_(seedMms), seedLen_(seedLen), qualCutoff_(qualCutoff), maxBts_(maxBts), sink_(sink), sinkPtFactory_(sinkPtFactory), mate1fw_(mate1fw), mate2fw_(mate2fw), peInner_(peInner), peOuter_(peOuter), dontReconcile_(dontReconcile), symCeil_(symCeil), mixedThresh_(mixedThresh), mixedAttemptLim_(mixedAttemptLim), cacheFw_(cacheFw), cacheBw_(cacheBw), cacheLimit_(cacheLimit), pool_(pool), refs_(refs), os_(os), reportSe_(reportSe), maqPenalty_(maqPenalty), qualOrder_(qualOrder), strandFix_(strandFix), rangeMode_(rangeMode), verbose_(verbose), quiet_(quiet) { assert(ebwtFw.isInMemory()); assert(ebwtBw->isInMemory()); } /** * Create a new UnpairedExactAlignerV1s. */ virtual Aligner* create() const { HitSinkPerThread* sinkPt = sinkPtFactory_.createMult(2); HitSinkPerThread* sinkPtSe1 = NULL, * sinkPtSe2 = NULL; EbwtSearchParams >* params = new EbwtSearchParams >(*sinkPt, os_); EbwtSearchParams >* paramsSe1 = NULL, * paramsSe2 = NULL; if(reportSe_) { sinkPtSe1 = sinkPtFactory_.create(); sinkPtSe2 = sinkPtFactory_.create(); paramsSe1 = new EbwtSearchParams >(*sinkPtSe1, os_); paramsSe2 = new EbwtSearchParams >(*sinkPtSe2, os_); } RefAligner >* refAligner = NULL; int *btCnt = new int[1]; *btCnt = maxBts_; if(seedMms_ == 0) { refAligner = new Seed0RefAligner >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); } else if(seedMms_ == 1) { refAligner = new Seed1RefAligner >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); } else if(seedMms_ == 2) { refAligner = new Seed2RefAligner >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); } else { refAligner = new Seed3RefAligner >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); } bool do1Fw = true; bool do1Rc = true; bool do2Fw = true; bool do2Rc = true; if(!doFw_) { if(mate1fw_) do1Fw = false; else do1Rc = false; if(mate2fw_) do2Fw = false; else do2Rc = false; } if(!doRc_) { if(mate1fw_) do1Rc = false; else do1Fw = false; if(mate2fw_) do2Rc = false; else do2Fw = false; } TRangeSrcDrPtrVec *dr1FwVec = new TRangeSrcDrPtrVec(); TRangeSrcDrPtrVec *dr1RcVec; TRangeSrcDrPtrVec *dr2FwVec; TRangeSrcDrPtrVec *dr2RcVec; if(v1_) { dr1RcVec = new TRangeSrcDrPtrVec(); dr2FwVec = new TRangeSrcDrPtrVec(); dr2RcVec = new TRangeSrcDrPtrVec(); } else { dr1RcVec = dr1FwVec; dr2FwVec = dr1FwVec; dr2RcVec = dr1FwVec; } if(seedMms_ == 0) { const int halfAndHalf = 0; if(do1Fw) { bool mate1 = true; bool fw = true; EbwtRangeSource *r1Fw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver *dr1Fw_Bw = new EbwtRangeSourceDriver( *params, r1Fw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 dr1FwVec->push_back(dr1Fw_Bw); } if(do2Fw) { bool mate1 = false; bool fw = true; EbwtRangeSource *r2Fw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver *dr2Fw_Bw = new EbwtRangeSourceDriver( *params, r2Fw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 dr2FwVec->push_back(dr2Fw_Bw); } if(do1Rc) { bool mate1 = true; bool fw = false; EbwtRangeSource *r1Rc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver *dr1Rc_Fw = new EbwtRangeSourceDriver( *params, r1Rc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 dr1RcVec->push_back(dr1Rc_Fw); } if(do2Rc) { bool mate1 = false; bool fw = false; EbwtRangeSource *r2Rc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver *dr2Rc_Fw = new EbwtRangeSourceDriver( *params, r2Rc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft (not applicable) PIN_TO_SEED_EDGE, // whole alignment is unrevisitable PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " PIN_TO_SEED_EDGE, // " os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 dr2RcVec->push_back(dr2Rc_Fw); } } else if(seedMms_ == 1) { const int halfAndHalf = 0; if(do1Fw) { bool mate1 = true; bool fw = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); dr1FwVec->push_back(drFw_Bw); dr1FwVec->push_back(drFw_Seed); } if(do2Fw) { bool mate1 = false; bool fw = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); dr2FwVec->push_back(drFw_Bw); dr2FwVec->push_back(drFw_Seed); } if(do1Rc) { bool mate1 = true; bool fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); dr1RcVec->push_back(drRc_Fw); dr1RcVec->push_back(drRc_Seed); } if(do2Rc) { bool mate1 = false; bool fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, halfAndHalf, false, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, halfAndHalf, true, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, NULL); // no backtrack limit for -n 1/2 EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); dr2RcVec->push_back(drRc_Fw); dr2RcVec->push_back(drRc_Seed); } } else if(seedMms_ > 1) { bool two = seedMms_ == 2; if(do1Fw) { bool mate1 = true; bool fw = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_BwHalf = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drFw_BwSeed12 = NULL; if(!two) { EbwtRangeSourceFactory *rFw_BwSeed12 = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); drFw_BwSeed12 = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtRangeSourceDriver * drFw_FwSeedGen12 = NULL; if(!two) { EbwtRangeSource *rFw_FwSeedGen12 = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_); drFw_FwSeedGen12 = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtSeededRangeSourceDriver * drFw_Seed12 = NULL; if(!two) { drFw_Seed12 = new EbwtSeededRangeSourceDriver( drFw_BwSeed12, drFw_FwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); } EbwtRangeSourceDriver * drFw_BwHalf = new EbwtRangeSourceDriver( *params, rFw_BwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); dr1FwVec->push_back(drFw_Bw); dr1FwVec->push_back(drFw_Seed); if(drFw_Seed12 != NULL) { dr1FwVec->push_back(drFw_Seed12); } dr1FwVec->push_back(drFw_BwHalf); } if(do2Fw) { bool mate1 = false; bool fw = true; EbwtRangeSource *rFw_Bw = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rFw_BwSeed = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_FwSeedGen = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_); EbwtRangeSource *rFw_BwHalf = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drFw_Bw = new EbwtRangeSourceDriver( *params, rFw_Bw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drFw_BwSeed = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drFw_FwSeedGen = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drFw_Seed = new EbwtSeededRangeSourceDriver( drFw_BwSeed, drFw_FwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drFw_BwSeed12 = NULL; if(!two) { EbwtRangeSourceFactory *rFw_BwSeed12 = new EbwtRangeSourceFactory( ebwtBw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); drFw_BwSeed12 = new EbwtRangeSourceDriverFactory( *params, rFw_BwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtRangeSourceDriver * drFw_FwSeedGen12 = NULL; if(!two) { EbwtRangeSource *rFw_FwSeedGen12 = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_); drFw_FwSeedGen12 = new EbwtRangeSourceDriver( *params, rFw_FwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtSeededRangeSourceDriver * drFw_Seed12 = NULL; if(!two) { drFw_Seed12 = new EbwtSeededRangeSourceDriver( drFw_BwSeed12, drFw_FwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); } EbwtRangeSourceDriver * drFw_BwHalf = new EbwtRangeSourceDriver( *params, rFw_BwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); dr2FwVec->push_back(drFw_Bw); dr2FwVec->push_back(drFw_Seed); if(drFw_Seed12 != NULL) { dr2FwVec->push_back(drFw_Seed12); } dr2FwVec->push_back(drFw_BwHalf); } if(do1Rc) { bool mate1 = true; bool fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_FwHalf = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drRc_FwSeed12 = NULL; if(!two) { EbwtRangeSourceFactory *rRc_FwSeed12 = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); drRc_FwSeed12 = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtRangeSourceDriver * drRc_BwSeedGen12 = NULL; if(!two) { EbwtRangeSource *rRc_BwSeedGen12 = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_); drRc_BwSeedGen12 = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtSeededRangeSourceDriver * drRc_Seed12 = NULL; if(!two) { drRc_Seed12 = new EbwtSeededRangeSourceDriver( drRc_FwSeed12, drRc_BwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); } EbwtRangeSourceDriver * drRc_FwHalf = new EbwtRangeSourceDriver( *params, rRc_FwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); dr1RcVec->push_back(drRc_Fw); dr1RcVec->push_back(drRc_Seed); if(drRc_Seed12 != NULL) { dr1RcVec->push_back(drRc_Seed12); } dr1RcVec->push_back(drRc_FwHalf); } if(do2Rc) { bool mate1 = false; bool fw = false; EbwtRangeSource *rRc_Fw = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSourceFactory *rRc_FwSeed = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_BwSeedGen = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 0, true, maqPenalty_, qualOrder_); EbwtRangeSource *rRc_FwHalf = new EbwtRangeSource( &ebwtFw_, fw, qualCutoff_, false, verbose_, quiet_, 2, false, maqPenalty_, qualOrder_); EbwtRangeSourceDriver * drRc_Fw = new EbwtRangeSourceDriver( *params, rRc_Fw, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriverFactory * drRc_FwSeed = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtRangeSourceDriver * drRc_BwSeedGen = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); EbwtSeededRangeSourceDriver * drRc_Seed = new EbwtSeededRangeSourceDriver( drRc_FwSeed, drRc_BwSeedGen, fw, seedLen_, verbose_, quiet_, mate1); EbwtRangeSourceDriverFactory * drRc_FwSeed12 = NULL; if(!two) { EbwtRangeSourceFactory *rRc_FwSeed12 = new EbwtRangeSourceFactory( &ebwtFw_, fw, qualCutoff_, true, verbose_, quiet_, 0, false, maqPenalty_, qualOrder_); drRc_FwSeed12 = new EbwtRangeSourceDriverFactory( *params, rRc_FwSeed12, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtRangeSourceDriver * drRc_BwSeedGen12 = NULL; if(!two) { EbwtRangeSource *rRc_BwSeedGen12 = new EbwtRangeSource( ebwtBw_, fw, qualCutoff_, false, verbose_, quiet_, 3, true, maqPenalty_, qualOrder_); drRc_BwSeedGen12 = new EbwtRangeSourceDriver( *params, rRc_BwSeedGen12, fw, true, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen false, // nudgeLeft PIN_TO_BEGINNING, PIN_TO_HI_HALF_EDGE, PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); } EbwtSeededRangeSourceDriver * drRc_Seed12 = NULL; if(!two) { drRc_Seed12 = new EbwtSeededRangeSourceDriver( drRc_FwSeed12, drRc_BwSeedGen12, fw, seedLen_, verbose_, quiet_, mate1); } EbwtRangeSourceDriver * drRc_FwHalf = new EbwtRangeSourceDriver( *params, rRc_FwHalf, fw, false, maqPenalty_, qualOrder_, sink_, sinkPt, seedLen_, // seedLen true, // nudgeLeft PIN_TO_BEGINNING, // nothing's unrevisitable PIN_TO_HI_HALF_EDGE, two ? PIN_TO_SEED_EDGE : PIN_TO_HI_HALF_EDGE, PIN_TO_SEED_EDGE, os_, verbose_, quiet_, mate1, pool_, btCnt); dr2RcVec->push_back(drRc_Fw); dr2RcVec->push_back(drRc_Seed); if(drRc_Seed12 != NULL) { dr2RcVec->push_back(drRc_Seed12); } dr2RcVec->push_back(drRc_FwHalf); } } else { cerr << "Unsupported --stateful mode: " << seedMms_ << endl; } // Set up a RangeChaser RangeChaser > *rchase = new RangeChaser >(cacheLimit_, cacheFw_, cacheBw_); if(v1_) { PairedBWAlignerV1* al = new PairedBWAlignerV1( params, new TCostAwareRangeSrcDr(strandFix_, dr1FwVec, verbose_, quiet_, false), new TCostAwareRangeSrcDr(strandFix_, dr1RcVec, verbose_, quiet_, false), new TCostAwareRangeSrcDr(strandFix_, dr2FwVec, verbose_, quiet_, false), new TCostAwareRangeSrcDr(strandFix_, dr2RcVec, verbose_, quiet_, false), refAligner, rchase, sink_, sinkPtFactory_, sinkPt, mate1fw_, mate2fw_, peInner_, peOuter_, dontReconcile_, symCeil_, mixedThresh_, mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_, maxBts_, pool_, btCnt); delete dr1FwVec; delete dr1RcVec; delete dr2FwVec; delete dr2RcVec; return al; } else { // We dumped all the drivers into dr1FwVec PairedBWAlignerV2* al = new PairedBWAlignerV2( params, paramsSe1, paramsSe2, new TCostAwareRangeSrcDr(strandFix_, dr1FwVec, verbose_, quiet_, true), refAligner, rchase, sink_, sinkPtFactory_, sinkPt, sinkPtSe1, sinkPtSe2, mate1fw_, mate2fw_, peInner_, peOuter_, mixedAttemptLim_, refs_, rangeMode_, verbose_, quiet_, maxBts_, pool_, btCnt); delete dr1FwVec; return al; } } private: Ebwt >& ebwtFw_; Ebwt >* ebwtBw_; bool color_; const bool v1_; // whether to use V1 PairedAligner const bool doFw_; const bool doRc_; const uint32_t seedMms_; const uint32_t seedLen_; const int qualCutoff_; const int maxBts_; HitSink& sink_; const HitSinkPerThreadFactory& sinkPtFactory_; const bool mate1fw_; const bool mate2fw_; const uint32_t peInner_; const uint32_t peOuter_; const bool dontReconcile_; const uint32_t symCeil_; const uint32_t mixedThresh_; const uint32_t mixedAttemptLim_; RangeCache *cacheFw_; RangeCache *cacheBw_; const uint32_t cacheLimit_; ChunkPool *pool_; BitPairReference* refs_; vector >& os_; const bool reportSe_; const bool maqPenalty_; const bool qualOrder_; const bool strandFix_; const bool rangeMode_; const bool verbose_; const bool quiet_; }; #endif /* ALIGNER_SEED_MM_H_ */