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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 CLASSIFIER_H_
#define CLASSIFIER_H_
#include "hi_aligner.h"
struct IDCount {
uint32_t id;
uint32_t count;
uint32_t weightedCount;
uint32_t timeStamp ;
};
/**
* 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 Classifier : public HI_Aligner<index_t, local_index_t> {
public:
/**
* Initialize with index.
*/
Classifier(const Ebwt<index_t>& ebwt,
const EList<string>& refnames) :
HI_Aligner<index_t, local_index_t>(
ebwt,
0, // don't make use of splice sites found by earlier reads
true), // no spliced alignment
_refnames(refnames)
{
}
~Classifier() {
}
/**
* 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)
{
_speciesMap.clear();
_genusMap.clear();
const index_t increment = 10;
const index_t minPartialLen = 22;
size_t bestScore = 0, secondBestScore = 0 ;
for(index_t rdi = 0; rdi < (this->_paired ? 2 : 1); rdi++) {
assert(this->_rds[rdi] != NULL);
const Read& rd = *(this->_rds[rdi]);
index_t rdlen = rd.length();
index_t fwi;
bool done[2] = {false, false};
size_t cur[2] = {0, 0 } ;
const size_t maxDiff = ( rdlen / 2 > 2 * minPartialLen ) ? rdlen / 2 : ( 2 * minPartialLen ) ;
while(!done[0] || !done[1]) {
for(fwi = 0; fwi < 2; fwi++) {
if(done[fwi]) continue;
size_t mineFw = 0, mineRc = 0;
bool fw = (fwi == 0);
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
bool pseudogeneStop = false, anchorStop = false;
this->partialSearch(
ebwtFw,
rd,
sc,
fw,
0,
mineFw,
mineRc,
hit,
rnd,
pseudogeneStop,
anchorStop);
if(hit.done()) {
done[fwi] = true;
cur[fwi] = rdlen ;
continue;
}
cur[fwi] = hit.cur() ;
BWTHit<index_t>& lastHit = hit.getPartialHit(hit.offsetSize() - 1);
if(lastHit.len() > increment) {
if ( lastHit.len() < minPartialLen )
hit.setOffset(hit.cur() - increment);
else
hit.setOffset( hit.cur() + 1 ) ;
}
if(hit.cur() + minPartialLen >= rdlen) {
hit.done(true);
done[fwi] = true;
continue;
}
}
//ReadBWTHit<index_t>& lastHitForward = (this->_hits[rdi][0] ).getPartialHit(hit.offsetSize() - 1).cur() ;
//ReadBWTHit<index_t>& lastHitBackward = (this->_hits[rdi][1] ).getPartialHit(hit.offsetSize() - 1).cur() ;
//size_t curForward = this->_hits[rdi][0].cur() ;
//size_t curBackward = this->_hits[rdi][1].cur() ;
//cout<< cur[0] << " " << cur[1] << " " << done[0] << " " << done[1] << endl ;
if ( cur[0] > cur[1] + maxDiff )
{
this->_hits[rdi][1].done( true ) ;
done[1] = true ;
}
else if ( cur[1] > cur[0] + maxDiff )
{
this->_hits[rdi][0].done( true ) ;
done[0] = true ;
}
}
// choose fw or rc of a read
index_t avgHitLength[2] = {0, 0};
index_t totalHitLength[2] = {0, 0};
for(fwi = 0; fwi < 2; fwi++) {
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
index_t numHits = 0;
for(size_t i = 0; i < hit.offsetSize(); i++) {
if(hit.getPartialHit(i).len() < minPartialLen) continue;
totalHitLength[fwi] += hit.getPartialHit(i).len();
numHits++;
}
if(numHits > 0) {
avgHitLength[fwi] = totalHitLength[fwi] / numHits;
}
}
if(avgHitLength[0] > avgHitLength[1]) {
fwi = 0;
} else {
fwi = 1;
}
bool fw = (fwi == 0);
const ReportingParams& rp = sink.reportingParams();
ReadBWTHit<index_t>& hit = this->_hits[rdi][fwi];
assert(hit.done());
// choose candidate partial alignments for further alignment
const index_t maxGenomeHitSize = rp.khits;
index_t offsetSize = hit.offsetSize();
this->_genomeHits.clear();
int hitLen[100] ;
int hitSize[100] ;
size_t hiMap[100] ;
for ( size_t hi = 0 ; hi < offsetSize ; ++hi )
{
hitLen[hi] = hit.getPartialHit(hi).len() ;
hitSize[hi] = hit.getPartialHit(hi).size() ;
hiMap[hi] = hi ;
}
// Change to quicksort in future
for ( size_t hi = 0 ; hi < offsetSize ; ++hi )
{
for ( size_t hj = hi + 1 ; hj < offsetSize ; ++hj )
{
//if ( hitLen[ hiMap[hi] ] < hitLen[ hiMap[hj] ] )
if ( hitSize[ hiMap[hi] ] > hitSize[ hiMap[hj] ] ) // When use size()
{
size_t tmp = hiMap[hi] ;
hiMap[hi] = hiMap[hj] ;
hiMap[hj] = tmp ;
}
else if ( hitSize[ hiMap[hi] ] == hitSize[ hiMap[hj] ] && hitLen[ hiMap[hi] ] < hitLen[ hiMap[hj] ] )
{
size_t tmp = hiMap[hi] ;
hiMap[hi] = hiMap[hj] ;
hiMap[hj] = tmp ;
}
}
}
size_t usedPortion = 0 ;
size_t genomeHitCnt = 0 ;
for(size_t hi = 0; hi < offsetSize; hi++) {
/*index_t hj = 0;
for(; hj < offsetSize; hj++) {
BWTHit<index_t>& partialHit_j = hit.getPartialHit(hj);
if(partialHit_j.empty() ||
partialHit_j.hasGenomeCoords() ||
partialHit_j.len() < minPartialLen) continue;
else break;
}
if(hj >= offsetSize) break;
for(index_t hk = hj + 1; hk < offsetSize; hk++) {
BWTHit<index_t>& partialHit_j = hit.getPartialHit(hj);
BWTHit<index_t>& partialHit_k = hit.getPartialHit(hk);
if(partialHit_k.empty() ||
partialHit_k.hasGenomeCoords() ||
partialHit_k.len() < minPartialLen) continue;
if(partialHit_j.size() > partialHit_k.size() ||
(partialHit_j.size() == partialHit_k.size() && partialHit_j.len() < partialHit_k.len())) {
hj = hk;
}
}*/
BWTHit<index_t>& partialHit = hit.getPartialHit( hiMap[ hi ] );
if ( partialHit.len() < minPartialLen )
continue ;
//break ;
assert(!partialHit.hasGenomeCoords());
usedPortion += partialHit.len() ;
bool straddled = false;
this->getGenomeIdx(
ebwtFw,
ref,
rnd,
partialHit._top,
partialHit._bot,
fw,
maxGenomeHitSize - genomeHitCnt, // this->_genomeHits.size(),
hit._len - partialHit._bwoff - partialHit._len,
partialHit._len,
partialHit._coords,
wlm,
prm,
him,
false, // reject straddled
straddled);
if(!partialHit.hasGenomeCoords()) continue;
EList<Coord>& coords = partialHit._coords;
assert_gt(coords.size(), 0);
//const index_t genomeHit_size = this->_genomeHits.size();
if(genomeHitCnt + coords.size() >= maxGenomeHitSize) {
coords.shufflePortion(0, coords.size(), rnd);
}
for(index_t k = 0; k < coords.size(); k++, ++genomeHitCnt) {
//cout << genomeHitCnt << " " << maxGenomeHitSize << endl ;
if ( genomeHitCnt >= maxGenomeHitSize )
break ;
const Coord& coord = coords[k] ;
assert_lt(coord.ref(), _refnames.size());
const string& refName = _refnames[coord.ref()];
uint64_t id = 0;
for(size_t ni = 0; ni < refName.length(); ni++) {
if(refName[ni] < '0' || refName[ni] > '9') break;
id *= 10;
id += (refName[ni] - '0');
}
uint32_t speciesID = (uint32_t)(id >> 32);
uint32_t genusID = (uint32_t)(id & 0xffffffff);
assert_gt(partialHit.len(), 15);
uint32_t addWeight = (uint32_t)((partialHit.len() - 15) * (partialHit.len() - 15));
bool found = false;
uint32_t newScore = 0 ;
for(size_t mi = 0; mi < _speciesMap.size(); mi++) {
if(_speciesMap[mi].id == speciesID) {
found = true;
if ( _speciesMap[mi].timeStamp != hi )
{
_speciesMap[mi].count += 1;
_speciesMap[mi].weightedCount += addWeight;
_speciesMap[mi].timeStamp = hi;
//newScore = _speciesMap[mi].weightedCount ;
}
break;
}
}
if(!found) {
_speciesMap.expand();
_speciesMap.back().id = speciesID;
_speciesMap.back().count = 1;
_speciesMap.back().timeStamp = hi ;
_speciesMap.back().weightedCount = addWeight;
//newScore = addWeight ;
}
found = false;
for(size_t mi = 0; mi < _genusMap.size(); mi++) {
if(_genusMap[mi].id == genusID) {
found = true;
if(_genusMap[mi].timeStamp != hi ) {
_genusMap[mi].count += 1;
_genusMap[mi].weightedCount += addWeight;
_genusMap[mi].timeStamp = hi ;
newScore = _genusMap[mi].weightedCount ;
}
break;
}
}
if(!found) {
_genusMap.expand();
_genusMap.back().id = genusID;
_genusMap.back().count = 1;
_genusMap.back().weightedCount = addWeight;
_genusMap.back().timeStamp = hi ;
newScore = addWeight ;
}
// classification of bacterial sequences
#ifndef NDEBUG
cout << this->_rds[rdi]->name << "\t"
// << refName << "\t"
<< speciesID << "\t"
<< genusID << "\t"
<< genomeHit.refoff() << "\t"
<< genomeHit.len() << "M" << endl;
#endif
if ( newScore > bestScore )
{
secondBestScore = bestScore ;
bestScore = newScore ;
}
else if ( newScore > secondBestScore )
{
secondBestScore = newScore ;
}
} // for k
if ( genomeHitCnt >= maxGenomeHitSize )
break ;
//cout<< bestScore << " " << secondBestScore << " " << totalHitLength[fwi] << " " << usedPortion << endl ;
if ( rdi == (this->_paired ? 2: 1) - 1 && bestScore > secondBestScore +
( totalHitLength[fwi] - usedPortion - 15 ) * ( totalHitLength[fwi] - usedPortion - 15 ) )
{
//cout << "saved\n" ;
break ;
}
} // for hi
} // for rdi
uint32_t speciesID = 0xffffffff, genusID = 0xffffffff;
uint32_t speciesWeightedCount = 0, genusWeightedCount = 0;
for(size_t mi = 0; mi < _speciesMap.size(); mi++) {
if(_speciesMap[mi].weightedCount > speciesWeightedCount) {
speciesID = _speciesMap[mi].id;
speciesWeightedCount = _speciesMap[mi].weightedCount;
}
}
for(size_t mi = 0; mi < _genusMap.size(); mi++) {
if(_genusMap[mi].weightedCount > genusWeightedCount) {
genusID = _genusMap[mi].id;
genusWeightedCount = _genusMap[mi].weightedCount;
}
}
if(genusID != 0xffffffff) {
cout << this->_rds[0]->name << "\t"
<< speciesID << "\t"
<< genusID << endl;
}
return EXTEND_POLICY_FULFILLED;
}
bool getGenomeIdx(
const Ebwt<index_t>& ebwt,
const BitPairReference& ref,
RandomSource& rnd,
index_t top,
index_t bot,
bool fw,
index_t maxelt,
index_t rdoff,
index_t rdlen,
EList<Coord>& coords,
WalkMetrics& met,
PerReadMetrics& prm,
HIMetrics& him,
bool rejectStraddle,
bool& straddled)
{
straddled = false;
assert_gt(bot, top);
index_t nelt = bot - top;
nelt = min<index_t>(nelt, maxelt);
coords.clear();
him.globalgenomecoords += (bot - top);
this->_offs.resize(nelt);
this->_offs.fill(std::numeric_limits<index_t>::max());
this->_sas.init(top, rdlen, EListSlice<index_t, 16>(this->_offs, 0, nelt));
this->_gws.init(ebwt, ref, this->_sas, rnd, met);
for(index_t off = 0; off < nelt; off++) {
WalkResult<index_t> wr;
this->_gws.advanceElement(
off,
ebwt, // forward Bowtie index for walking left
ref, // bitpair-encoded reference
this->_sas, // SA range with offsets
this->_gwstate, // GroupWalk state; scratch space
wr, // put the result here
met, // metrics
prm); // per-read metrics
// Coordinate of the seed hit w/r/t the pasted reference string
coords.expand();
coords.back().init(wr.toff, 0, fw);
}
return true;
}
private:
EList<string> _refnames;
EList<IDCount> _speciesMap;
EList<IDCount> _genusMap;
};
#endif /*CLASSIFIER_H_*/
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