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| /* | |
| * aligner_seed_mm.h | |
| */ | |
| #ifndef ALIGNER_SEED_MM_H_ | |
| #define ALIGNER_SEED_MM_H_ | |
| #include <utility> | |
| #include <vector> | |
| #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<EbwtRangeSource> TRangeSrcDr; | |
| typedef std::vector<TRangeSrcDr*> TRangeSrcDrPtrVec; | |
| typedef CostAwareRangeSourceDriver<EbwtRangeSource> TCostAwareRangeSrcDr; | |
| public: | |
| UnpairedSeedAlignerFactory( | |
| Ebwt<String<Dna> >& ebwtFw, | |
| Ebwt<String<Dna> >* 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<String<Dna5> >& 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<String<Dna> >* params = | |
| new EbwtSearchParams<String<Dna> >(*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<String<Dna> > *rchase = | |
| new RangeChaser<String<Dna> >(cacheLimit_, cacheFw_, cacheBw_, metrics_); | |
| return new UnpairedAlignerV2<EbwtRangeSource>( | |
| params, dr, rchase, | |
| sink_, sinkPtFactory_, sinkPt, os_, refs_, | |
| rangeMode_, verbose_, quiet_, maxBts_, pool_, btCnt, | |
| metrics_); | |
| } | |
| private: | |
| Ebwt<String<Dna> >& ebwtFw_; | |
| Ebwt<String<Dna> >* 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<String<Dna5> >& 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<EbwtRangeSource> TRangeSrcDr; | |
| typedef std::vector<TRangeSrcDr*> TRangeSrcDrPtrVec; | |
| typedef CostAwareRangeSourceDriver<EbwtRangeSource> TCostAwareRangeSrcDr; | |
| public: | |
| PairedSeedAlignerFactory( | |
| Ebwt<String<Dna> >& ebwtFw, | |
| Ebwt<String<Dna> >* 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<String<Dna5> >& 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<String<Dna> >* params = | |
| new EbwtSearchParams<String<Dna> >(*sinkPt, os_); | |
| EbwtSearchParams<String<Dna> >* paramsSe1 = NULL, * paramsSe2 = NULL; | |
| if(reportSe_) { | |
| sinkPtSe1 = sinkPtFactory_.create(); | |
| sinkPtSe2 = sinkPtFactory_.create(); | |
| paramsSe1 = | |
| new EbwtSearchParams<String<Dna> >(*sinkPtSe1, os_); | |
| paramsSe2 = | |
| new EbwtSearchParams<String<Dna> >(*sinkPtSe2, os_); | |
| } | |
| RefAligner<String<Dna5> >* refAligner = NULL; | |
| int *btCnt = new int[1]; | |
| *btCnt = maxBts_; | |
| if(seedMms_ == 0) { | |
| refAligner = new Seed0RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); | |
| } else if(seedMms_ == 1) { | |
| refAligner = new Seed1RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); | |
| } else if(seedMms_ == 2) { | |
| refAligner = new Seed2RefAligner<String<Dna5> >(color_, verbose_, quiet_, seedLen_, qualCutoff_, maqPenalty_); | |
| } else { | |
| refAligner = new Seed3RefAligner<String<Dna5> >(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<String<Dna> > *rchase = | |
| new RangeChaser<String<Dna> >(cacheLimit_, cacheFw_, cacheBw_); | |
| if(v1_) { | |
| PairedBWAlignerV1<EbwtRangeSource>* al = new PairedBWAlignerV1<EbwtRangeSource>( | |
| 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<EbwtRangeSource>* al = new PairedBWAlignerV2<EbwtRangeSource>( | |
| 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<String<Dna> >& ebwtFw_; | |
| Ebwt<String<Dna> >* 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<String<Dna5> >& 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_ */ |