forked from DaehwanKimLab/hisat2
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bp_aligner.h
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bp_aligner.h
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/*
* Copyright 2014, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT.
*
* HISAT is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* HISAT is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with HISAT. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef BP_ALIGNER_H_
#define BP_ALIGNER_H_
#include "hi_aligner.h"
/**
* With a hierarchical indexing, SplicedAligner provides several alignment strategies
* , which enable effective alignment of RNA-seq reads
*/
template <typename index_t, typename local_index_t>
class BP_Aligner : public HI_Aligner<index_t, local_index_t> {
public:
/**
* Initialize with index.
*/
BP_Aligner(
const Ebwt<index_t>& ebwt,
const EList<string>& refnames,
MUTEX_T* mutex,
uint64_t threads_rids_mindist = 0,
bool no_spliced_alignment = false) :
HI_Aligner<index_t, local_index_t>(ebwt,
threads_rids_mindist,
no_spliced_alignment),
_refnames(refnames),
_mutex(mutex),
_done(false)
{
}
~BP_Aligner() {
}
/**
* Aligns a read or a pair
* This funcion is called per read or pair
*/
virtual
int go(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink)
{
_done = false;
index_t rdi;
bool fw;
while(this->nextBWT(sc, ebwtFw, ebwtBw, ref, rdi, fw, wlm, prm, him, rnd, sink)) {
// given the partial alignment, try to extend it to full alignments
this->align(sc, ebwtFw, ebwtBw, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink);
if(_done) break;
}
return EXTEND_POLICY_FULFILLED;
}
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
virtual
void hybridSearch(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
bool fw,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink);
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
virtual
void hybridSearch_recur(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
const GenomeHit<index_t>& hit,
index_t hitoff,
index_t hitlen,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink,
index_t dep = 0);
private:
EList<string> _refnames;
MUTEX_T* _mutex;
bool _done;
};
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
template <typename index_t, typename local_index_t>
void BP_Aligner<index_t, local_index_t>::hybridSearch(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
bool fw,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink)
{
assert_lt(rdi, 2);
assert(this->_rds[rdi] != NULL);
him.localatts++;
// before further alignment using local search, extend the partial alignments directly
// by comparing with the corresponding genomic sequences
// this extension is performed without any mismatches allowed
for(index_t hi = 0; hi < this->_genomeHits.size(); hi++) {
GenomeHit<index_t>& genomeHit = this->_genomeHits[hi];
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)OFF_MASK;
genomeHit.extend(*(this->_rds[rdi]), ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, leftext, rightext);
}
// for the candidate alignments, examine the longest (best) one first
this->_genomeHits_done.resize(this->_genomeHits.size());
this->_genomeHits_done.fill(false);
for(size_t hi = 0; hi < this->_genomeHits.size(); hi++) {
index_t hj = 0;
for(; hj < this->_genomeHits.size(); hj++) {
if(!this->_genomeHits_done[hj]) break;
}
if(hj >= this->_genomeHits.size()) break;
for(index_t hk = hj + 1; hk < this->_genomeHits.size(); hk++) {
if(this->_genomeHits_done[hk]) continue;
GenomeHit<index_t>& genomeHit_j = this->_genomeHits[hj];
GenomeHit<index_t>& genomeHit_k = this->_genomeHits[hk];
if(genomeHit_k.hitcount() > genomeHit_j.hitcount() ||
(genomeHit_k.hitcount() == genomeHit_j.hitcount() && genomeHit_k.len() > genomeHit_j.len())) {
hj = hk;
}
}
// given a candidate partial alignment, extend it bidirectionally
him.anchoratts++;
GenomeHit<index_t>& genomeHit = this->_genomeHits[hj];
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
genomeHit,
genomeHit.rdoff(),
genomeHit.len(),
wlm,
prm,
swm,
him,
rnd,
sink);
this->_genomeHits_done[hj] = true;
if(_done) return;
}
}
/**
* Given a partial alignment of a read, try to further extend
* the alignment bidirectionally using a combination of
* local search, extension, and global search
*/
template <typename index_t, typename local_index_t>
void BP_Aligner<index_t, local_index_t>::hybridSearch_recur(
const Scoring& sc,
const Ebwt<index_t>& ebwtFw,
const Ebwt<index_t>& ebwtBw,
const BitPairReference& ref,
SwAligner& swa,
SpliceSiteDB& ssdb,
index_t rdi,
const GenomeHit<index_t>& hit,
index_t hitoff,
index_t hitlen,
WalkMetrics& wlm,
PerReadMetrics& prm,
SwMetrics& swm,
HIMetrics& him,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink,
index_t dep)
{
if(_done) return;
him.localsearchrecur++;
assert_lt(rdi, 2);
assert(this->_rds[rdi] != NULL);
const Read& rd = *(this->_rds[rdi]);
index_t rdlen = rd.length();
if(hit.score() < this->_minsc[rdi]) return;
// if it's already examined, just return
if(hitoff == hit.rdoff() - hit.trim5() && hitlen == hit.len() + hit.trim5() + hit.trim3()) {
if(this->isSearched(hit, rdi)) return;
this->addSearched(hit, rdi);
}
// for effective use of memory allocation and deallocation
if(this->_coords.size() <= dep) {
this->_coords.expand();
assert_leq(this->_local_genomeHits.size(), dep);
this->_local_genomeHits.expand();
assert_leq(this->_spliceSites.size(), dep);
this->_spliceSites.expand();
}
EList<Coord>& coords = this->_coords[dep];
EList<GenomeHit<index_t> >& local_genomeHits = this->_local_genomeHits[dep];
EList<SpliceSite>& spliceSites = this->_spliceSites[dep];
// daehwan - for debugging purposes
#if 0
cout << rd.name << "\t"
<< (hit.fw() ? "+" : "-") << "\t"
<< hitoff << "\t"
<< hitoff + hitlen << "\t"
<< "( " << hit.rdoff() << "\t"
<< hit.rdoff() + hit.len() << " )" << "\t"
<< hit.refoff() << "\t"
<< hit.getRightOff() << "\t"
<< hit.score() << "\t"
<< "dep: " << dep << "\t";
Edit::print(cout, hit.edits());
cout << endl;
#endif
assert_leq(hitoff + hitlen, rdlen);
// if this is a full alignment, report it
if(hitoff == 0 && hitlen == rdlen) {
if(!this->redundant(sink, rdi, hit)) {
// this->reportHit(sc, ebwtFw, ref, sink, rdi, hit);
return;
}
} else if(hitoff > 0 && (hitoff + hitlen == rdlen || hitoff + hitoff < rdlen - hitlen)) {
// extend the partial alignment in the left direction
index_t fragoff = 0, fraglen = 0, left = 0;
hit.getLeft(fragoff, fraglen, left);
const index_t minMatchLen = this->_minK_local;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen && left >= minMatchLen && !this->_no_spliced_alignment) {
spliceSites.clear();
ssdb.getLeftSpliceSites(hit.ref(), left + minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(left + fraglen - 1 < ss.right()) continue;
index_t frag2off = ss.left() - (ss.right() - left);
if(frag2off + 1 < hitoff) continue;
GenomeHit<index_t> tempHit;
tempHit.init(hit.fw(),
0,
hitoff,
0, // trim5
0, // trim3
hit.ref(),
frag2off + 1 - hitoff,
this->_sharedVars);
if(!tempHit.compatibleWith(hit, this->_no_spliced_alignment)) continue;
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, 1, 1, false);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(combined && tempHit.score() >= minsc) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
}
}
}
// choose a local index based on the genomic location of the partial alignment
const HierEbwt<index_t, local_index_t>* hierEbwtFw = (const HierEbwt<index_t, local_index_t>*)(&ebwtFw);
const LocalEbwt<local_index_t, index_t>* localEbwtFw = hierEbwtFw->getLocalEbwt(hit.ref(), hit.refoff());
assert_leq(localEbwtFw->_localOffset, hit.refoff());
bool success = false, first = true;
index_t count = 0;
// consider at most two local indexes
index_t max_count = 2;
int64_t prev_score = hit.score();
local_genomeHits.clear();
while(!success && count++ < max_count) {
if(him.localindexatts >= this->max_localindexatts) return;
if(first) {
first = false;
} else {
localEbwtFw = hierEbwtFw->prevLocalEbwt(localEbwtFw);
if(localEbwtFw == NULL || localEbwtFw->empty()) break;
}
// local index search
index_t extlen = 0;
local_index_t top = (local_index_t)OFF_MASK, bot = (local_index_t)OFF_MASK;
index_t extoff = hitoff - 1;
if(extoff > 0) extoff -= 1;
if(extoff < minAnchorLen) {
extoff = minAnchorLen;
}
index_t nelt = (index_t)OFF_MASK;
index_t max_nelt = std::max<index_t>(5, extlen);
bool no_extension = false;
bool uniqueStop;
// daehwan - for debugging purposes
// index_t minUniqueLen = this->_minK_local;
index_t minUniqueLen = (index_t)OFF_MASK;
for(; extoff < rdlen; extoff++) {
extlen = 0;
// daehwan - for debugging purposes
// uniqueStop = true;
uniqueStop = false;
him.localindexatts++;
nelt = this->localEbwtSearch(
localEbwtFw, // BWT index
NULL, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
false, // searchfw,
extoff,
extlen,
top,
bot,
rnd,
uniqueStop,
minUniqueLen);
if(extoff + 1 - extlen >= hitoff) {
no_extension = true;
break;
}
if(nelt <= max_nelt) break;
}
assert_leq(top, bot);
assert_eq(nelt, (index_t)(bot - top));
assert_leq(extlen, extoff + 1);
if(nelt > 0 &&
nelt <= max_nelt &&
extlen >= minAnchorLen &&
!no_extension) {
assert_leq(nelt, max_nelt);
coords.clear();
bool straddled = false;
// get genomic locations for this local search
this->getGenomeCoords_local(
*localEbwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,
him,
true, // reject straddled?
straddled);
assert_leq(coords.size(), nelt);
coords.sort();
for(int ri = coords.size() - 1; ri >= 0; ri--) {
const Coord& coord = coords[ri];
GenomeHit<index_t> tempHit;
tempHit.init(coord.orient(),
extoff + 1 - extlen,
extlen,
0, // trim5
0, // trim3
coord.ref(),
coord.off(),
this->_sharedVars);
// daehwan - for debugging purposes
if(coord.ref() == hit.ref() &&
coord.off() > hit.refoff() &&
coord.off() < hit.refoff() + 64000) {
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
index_t mm = 1;
tempHit.extend(
rd,
ref,
ssdb,
swa,
swm,
prm,
sc,
this->_minsc[rdi],
rnd,
this->_minK_local,
leftext,
rightext,
mm);
#if 0
cout << endl;
cout << rd.rdid << "\t" << rd.name << endl;
cout << "\ttype: " << 1 << endl;
cout << "\t" << hit.ref() << endl;
cout << "\t\ttempHit " << (tempHit.fw() ? "+" : "-") << "\t" << tempHit.refoff() << "\t" << tempHit.rdoff() << "\t" << tempHit.len() << "\t" << tempHit.score() << endl;
cout << "\t\tanchHit " << (hit.fw() ? "+" : "-") << "\t" << hit.refoff() << "\t" << hit.rdoff() << "\t" << hit.len() << "\t" << hit.score() << endl;
spliceSites.clear();
ssdb.getRightSpliceSites(hit.ref(), hit.refoff() - minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(ss.right() > tempHit.refoff()) {
index_t dist = ss.right() - 1 - (tempHit.refoff() + tempHit.len() - 1);
cout << rd.rdid << "s\t\t\t" << ss.left() + 1 << "\t" << ss.right() - 1 << "\t" << (ss.fw() ? "+" : "-") << "\t" << dist << endl;
}
}
spliceSites.clear();
ssdb.getLeftSpliceSites(tempHit.ref(), tempHit.getRightOff() + minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(ss.left() < hit.refoff()) {
index_t dist = hit.refoff() - (ss.left() + 1);
cout << rd.rdid << "s\t\t\t" << ss.left() + 1 << "\t" << ss.right() - 1 << "\t" << (ss.fw() ? "+" : "-") << "\t" << dist << endl;
}
}
if(tempHit.rdoff() + tempHit.len() + 1 >= hit.rdoff()) return;
#else
assert_lt(hit.ref(), _refnames.size());
{
ThreadSafe t(const_cast<MUTEX_T*>(_mutex), true);
cout << rd.name << "\t"
<< _refnames[hit.ref()] << "\t"
<< (tempHit.fw() ? "+" : "-") << "\t" << tempHit.refoff() << "\t" << tempHit.rdoff() << "\t" << tempHit.len() << "\t" << tempHit.score() << "\t"
<< (hit.fw() ? "+" : "-") << "\t" << hit.refoff() << "\t" << hit.rdoff() << "\t" << hit.len() << "\t" << hit.score()
<< endl;
}
_done = true;
return;
#endif
}
// check if the partial alignment is compatible with the new alignment using the local index
if(!tempHit.compatibleWith(hit, this->_no_spliced_alignment)) {
if(count == 1) continue;
else break;
}
if(uniqueStop) {
assert_eq(coords.size(), 1);
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, leftext, rightext);
}
// combine the partial alignment and the new alignment
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(combined && tempHit.score() >= minsc) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
if(tempHit.score() >= prev_score - sc.mmpMax) {
// extend the new partial alignment recursively
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
} else {
local_genomeHits.push_back(tempHit);
}
}
}
}
int64_t minsc = (rdi == 0 ? sink.bestUnp1() : sink.bestUnp2());
if(minsc >= prev_score - sc.mmpMax) success = true;
if(!success && (count == max_count || hierEbwtFw->prevLocalEbwt(localEbwtFw) == NULL)) {
for(index_t ti = 0; ti < local_genomeHits.size(); ti++) {
GenomeHit<index_t>& tempHit = local_genomeHits[ti];
int64_t minsc = this->_minsc[rdi];
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(tempHit.score() >= minsc) {
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
}
}
}
} // while(!success && count++ < 2)
if(!success) {
if(hitoff > this->_minK) {
index_t extlen = 0;
index_t top = (index_t)OFF_MASK, bot = (index_t)OFF_MASK;
index_t extoff = hitoff - 1;
bool uniqueStop = true;
// perform global search for long introns
index_t nelt = this->globalEbwtSearch(
ebwtFw, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
extoff,
extlen,
top,
bot,
rnd,
uniqueStop);
if(nelt <= 5 && extlen >= this->_minK) {
coords.clear();
bool straddled = false;
this->getGenomeCoords(
ebwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
bot - top,
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,
him,
true, // reject straddled?
straddled);
assert_leq(coords.size(), nelt);
coords.sort();
for(int ri = coords.size() - 1; ri >= 0; ri--) {
const Coord& coord = coords[ri];
GenomeHit<index_t> tempHit;
tempHit.init(coord.orient(),
extoff + 1 - extlen,
extlen,
0, // trim5
0, // trim3
coord.ref(),
coord.off(),
this->_sharedVars);
if(!tempHit.compatibleWith(hit, this->_no_spliced_alignment)) continue;
if(uniqueStop) {
assert_eq(coords.size(), 1);
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, leftext, rightext);
}
int64_t minsc = this->_minsc[rdi];
bool combined = tempHit.combineWith(hit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(combined && tempHit.score() >= minsc) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
}
}
}
}
GenomeHit<index_t> tempHit = hit;
if(tempHit.rdoff() <= 5) {
index_t trim5 = tempHit.rdoff();
tempHit.trim5(trim5);
assert_leq(tempHit.len() + tempHit.trim5() + tempHit.trim3(), rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
0,
tempHit.len() + tempHit.trim5() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
return;
}
// extend the partial alignment directly comparing with the corresponding genomic sequence
// with mismatches or a gap allowed
int64_t minsc = this->_minsc[rdi];
assert_geq(tempHit.score(), minsc);
index_t mm = (tempHit.score() - minsc) / sc.mmpMax;
index_t leftext = (index_t)OFF_MASK, rightext = (index_t)0;
index_t num_mismatch_allowed = 1;
if(hitoff <= this->_minK_local) {
num_mismatch_allowed = min<index_t>(tempHit.rdoff(), mm);
}
him.localextatts++;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, leftext, rightext, num_mismatch_allowed);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(tempHit.score() >= minsc && leftext >= min<index_t>(this->_minK_local, hit.rdoff())) {
assert_eq(tempHit.trim5(), 0);
assert_leq(tempHit.rdoff() + tempHit.len() + tempHit.trim3(), rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
tempHit,
tempHit.rdoff(),
tempHit.len() + tempHit.trim3(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
} else if(hitoff > this->_minK_local) {
// skip some bases of a read
index_t jumplen = hitoff > this->_minK ? this->_minK : this->_minK_local;
assert_leq(hitoff, hit.rdoff());
int64_t expected_score = hit.score() - (hit.rdoff() - hitoff) / jumplen * sc.mmpMax - sc.mmpMax;
if(expected_score >= minsc) {
assert_lt(hitlen + jumplen, rdlen);
assert_eq(hit.trim5(), 0);
assert_leq(hitoff + hitlen, rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
hit,
hitoff - jumplen,
hitlen + jumplen,
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
}
}
}
} else {
// extend the partial alignment in the right direction
assert_lt(hitoff + hitlen, rdlen);
index_t fragoff = 0, fraglen = 0, right = 0;
hit.getRight(fragoff, fraglen, right);
const index_t minMatchLen = this->_minK_local;
// make use of a list of known or novel splice sites to further align the read
if(fraglen >= minMatchLen && !this->_no_spliced_alignment) {
spliceSites.clear();
assert_gt(fraglen, 0);
ssdb.getRightSpliceSites(hit.ref(), right + fraglen - minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(!ss._fromfile && ss._readid + this->_thread_rids_mindist > rd.rdid) continue;
if(right > ss.left()) continue;
index_t frag2off = ss.right() - ss.left() + right + fraglen - 1;
GenomeHit<index_t> tempHit;
tempHit.init(hit.fw(),
fragoff + fraglen,
rdlen - fragoff - fraglen,
0, // trim5
0, // trim3
hit.ref(),
frag2off,
this->_sharedVars);
if(!hit.compatibleWith(tempHit, this->_no_spliced_alignment)) continue;
GenomeHit<index_t> combinedHit = hit;
int64_t minsc = this->_minsc[rdi];
bool combined = combinedHit.combineWith(tempHit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local, 1, 1, false);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());
if(combined && combinedHit.score() >= minsc) {
assert_leq(combinedHit.trim5(), combinedHit.rdoff());
assert_eq(combinedHit.rdoff() + combinedHit.len(), rdlen);
hybridSearch_recur(
sc,
ebwtFw,
ebwtBw,
ref,
swa,
ssdb,
rdi,
combinedHit,
combinedHit.rdoff() - combinedHit.trim5(),
combinedHit.len() + combinedHit.trim5(),
wlm,
prm,
swm,
him,
rnd,
sink,
dep + 1);
}
}
}
// choose a local index based on the genomic location of the partial alignment
const HierEbwt<index_t, local_index_t>* hierEbwtFw = (const HierEbwt<index_t, local_index_t>*)(&ebwtFw);
const LocalEbwt<local_index_t, index_t>* localEbwtFw = hierEbwtFw->getLocalEbwt(hit.ref(), hit.refoff());
bool success = false, first = true;
index_t count = 0;
index_t max_count = 2;
int64_t prev_score = hit.score();
local_genomeHits.clear();
while(!success && count++ < max_count) {
if(him.localindexatts >= this->max_localindexatts) return;
if(first) {
first = false;
} else {
localEbwtFw = hierEbwtFw->nextLocalEbwt(localEbwtFw);
if(localEbwtFw == NULL || localEbwtFw->empty()) break;
}
// local index search
index_t extlen = 0;
local_index_t top = (local_index_t)OFF_MASK, bot = (local_index_t)OFF_MASK;
// daehwan - for debugging purposes
// index_t extoff = hitoff + hitlen + this->_minK_local;
index_t extoff = hitoff + hitlen + this->_minK_local * 3;
if(extoff + 1 < rdlen) extoff += 1;
if(extoff >= rdlen) {
extoff = rdlen - 1;
}
index_t nelt = (index_t)OFF_MASK;
index_t max_nelt = std::max<index_t>(5, extlen);
bool no_extension = false;
bool uniqueStop;
// daehwan - for debugging purposes
// index_t minUniqueLen = this->_minK_local;
index_t minUniqueLen = (index_t)OFF_MASK;
index_t maxHitLen = max<index_t>(extoff + 1 - hitoff - hitlen, this->_minK_local);
for(; maxHitLen < extoff + 1 && extoff < rdlen;) {
extlen = 0;
uniqueStop = false;
him.localindexatts++;
nelt = this->localEbwtSearch(
localEbwtFw, // BWT index
NULL, // BWT index
rd, // read to align
sc, // scoring scheme
hit.fw(),
false, // searchfw,
extoff,
extlen,
top,
bot,
rnd,
uniqueStop,
minUniqueLen,
maxHitLen);
if(extoff < hitoff + hitlen) {
no_extension = true;
break;
}
if(nelt <= max_nelt) break;
if(extoff + 1 < rdlen) extoff++;
else {
if(extlen < maxHitLen) break;
else maxHitLen++;
}
}
assert_leq(top, bot);
assert_eq(nelt, (index_t)(bot - top));
assert_leq(extlen, extoff + 1);
assert_leq(extoff, rdlen);
if(nelt > 0 &&
nelt <= max_nelt &&
extlen >= minAnchorLen &&
!no_extension) {
assert_leq(nelt, max_nelt);
coords.clear();
bool straddled = false;
// get genomic locations for this local search
this->getGenomeCoords_local(
*localEbwtFw,
ref,
rnd,
top,
bot,
hit.fw(),
extoff + 1 - extlen,
extlen,
coords,
wlm,
prm,
him,
true, // reject straddled?
straddled);
assert_leq(coords.size(), nelt);
coords.sort();
for(index_t ri = 0; ri < coords.size(); ri++) {
const Coord& coord = coords[ri];
GenomeHit<index_t> tempHit;
tempHit.init(coord.orient(),
extoff + 1 - extlen,
extlen,
0, // trim5
0, // trim3
coord.ref(),
coord.off(),
this->_sharedVars);
// daehwan - for debugging purposes
if(coord.ref() == hit.ref() &&
coord.off() < hit.refoff() &&
coord.off() + 64000 > hit.refoff()) {
index_t leftext = (index_t)0, rightext = (index_t)OFF_MASK;
index_t mm = 1;
tempHit.extend(
rd,
ref,
ssdb,
swa,
swm,
prm,
sc,
this->_minsc[rdi],
rnd,
this->_minK_local,
leftext,
rightext,
mm);
#if 0
cout << endl;
cout << rd.rdid << "\t" << rd.name << endl;
cout << "\ttype: " << 2 << endl;
cout << "\t" << hit.ref() << endl;
cout << "\t\ttempHit " << (tempHit.fw() ? "+" : "-") << "\t" << tempHit.refoff() << "\t" << tempHit.rdoff() << "\t" << tempHit.len() << "\t" << tempHit.score() << endl;
cout << "\t\tanchHit " << (hit.fw() ? "+" : "-") << "\t" << hit.refoff() << "\t" << hit.rdoff() << "\t" << hit.len() << "\t" << hit.score() << endl;
spliceSites.clear();
ssdb.getRightSpliceSites(tempHit.ref(), tempHit.refoff() - minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(ss.right() > hit.getRightOff()) {
index_t dist = ss.right() - 1 - hit.getRightOff();
cout << rd.rdid << "s\t\t\t" << ss.left() + 1 << "\t" << ss.right() - 1 << "\t" << (ss.fw() ? "+" : "-") << "\t" << dist << endl;
}
}
spliceSites.clear();
ssdb.getLeftSpliceSites(hit.ref(), hit.getRightOff() + minMatchLen, minMatchLen * 2, spliceSites);
for(size_t si = 0; si < spliceSites.size(); si++) {
const SpliceSite& ss = spliceSites[si];
if(ss.left() < tempHit.refoff()) {
index_t dist = tempHit.refoff() - (ss.left() + 1);
cout << rd.rdid << "s\t\t\t" << ss.left() + 1 << "\t" << ss.right() - 1 << "\t" << (ss.fw() ? "+" : "-") << "\t" << dist << endl;
}
}
if(hit.rdoff() + hit.len() - 1 <= tempHit.rdoff()) return;
#else
assert_lt(hit.ref(), _refnames.size());
{
ThreadSafe t(const_cast<MUTEX_T*>(_mutex), true);
cout << rd.name << "\t"
<< _refnames[hit.ref()] << "\t"
<< (hit.fw() ? "+" : "-") << "\t" << hit.refoff() << "\t" << hit.rdoff() << "\t" << hit.len() << "\t" << hit.score() << "\t"
<< (tempHit.fw() ? "+" : "-") << "\t" << tempHit.refoff() << "\t" << tempHit.rdoff() << "\t" << tempHit.len() << "\t" << tempHit.score()
<< endl;
}
_done = true;
return;
#endif
}
// check if the partial alignment is compatible with the new alignment using the local index
if(!hit.compatibleWith(tempHit, this->_no_spliced_alignment)) {
if(count == 1) continue;
else break;
}
index_t leftext = (index_t)0, rightext = (index_t)OFF_MASK;
tempHit.extend(rd, ref, ssdb, swa, swm, prm, sc, this->_minsc[rdi], rnd, this->_minK_local, leftext, rightext);
GenomeHit<index_t> combinedHit = hit;
int64_t minsc = this->_minsc[rdi];
// combine the partial alignment and the new alignment
bool combined = combinedHit.combineWith(tempHit, rd, ref, ssdb, swa, swm, sc, minsc, rnd, this->_minK_local);
if(rdi == 0) minsc = max(minsc, sink.bestUnp1());
else minsc = max(minsc, sink.bestUnp2());