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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_ */
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