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hi_aligner.h
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hi_aligner.h
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/*
* Copyright 2014, Daehwan Kim <[email protected]>
*
* 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 HI_ALIGNER_H_
#define HI_ALIGNER_H_
#include <iostream>
#include <utility>
#include <limits>
#include "qual.h"
#include "ds.h"
#include "sstring.h"
#include "alphabet.h"
#include "edit.h"
#include "read.h"
// Threading is necessary to synchronize the classes that dump
// intermediate alignment results to files. Otherwise, all data herein
// is constant and shared, or per-thread.
#include "threading.h"
#include "aligner_result.h"
#include "scoring.h"
#include "mem_ids.h"
#include "simple_func.h"
#include "group_walk.h"
/**
* Hit types for BWTHit class below
* Three hit types to anchor a read on the genome
*
*/
enum {
CANDIDATE_HIT = 1,
PSEUDOGENE_HIT,
ANCHOR_HIT,
};
/**
* Simple struct for holding a partial alignment for the read
* The alignment locations are represented by FM offsets [top, bot),
* and later genomic offsets are calculated when necessary
*/
template <typename index_t>
struct BWTHit {
BWTHit() { reset(); }
void reset() {
_top = _bot = 0;
_fw = true;
_bwoff = (index_t)OFF_MASK;
_len = 0;
_coords.clear();
_anchor_examined = false;
_hit_type = CANDIDATE_HIT;
}
void init(
index_t top,
index_t bot,
bool fw,
uint32_t bwoff,
uint32_t len,
index_t hit_type = CANDIDATE_HIT)
{
_top = top;
_bot = bot;
_fw = fw;
_bwoff = bwoff;
_len = len;
_coords.clear();
_anchor_examined = false;
_hit_type = hit_type;
}
bool hasGenomeCoords() const { return !_coords.empty(); }
/**
* Return true iff there is no hit.
*/
bool empty() const {
return _bot <= _top;
}
/**
* Higher score = higher priority.
*/
bool operator<(const BWTHit& o) const {
return _len > o._len;
}
/**
* Return the size of the alignments SA ranges.
*/
index_t size() const {
assert_leq(_top, _bot);
return _bot - _top;
}
index_t len() const {
// assert_gt(_len, 0);
return _len;
}
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
bool repOk(const Read& rd) const {
assert_gt(_bot, _top);
assert_neq(_bwoff, (index_t)OFF_MASK);
assert_gt(_len, 0);
return true;
}
#endif
index_t _top; // start of the range in the FM index
index_t _bot; // end of the range in the FM index
bool _fw; // whether read is forward or reverse complemented
index_t _bwoff; // current base of a read to search from the right end
index_t _len; // read length
EList<Coord> _coords; // genomic offsets corresponding to [_top, _bot)
bool _anchor_examined; // whether or not this hit is examined
index_t _hit_type; // hit type (anchor hit, pseudogene hit, or candidate hit)
};
/**
* Simple struct for holding alignments for the read
* The alignments are represented by chains of BWTHits
*/
template <typename index_t>
struct ReadBWTHit {
ReadBWTHit() { reset(); }
void reset() {
_fw = true;
_len = 0;
_cur = 0;
_done = false;
_numPartialSearch = 0;
_numUniqueSearch = 0;
_partialHits.clear();
}
void init(
bool fw,
index_t len)
{
_fw = fw;
assert_gt(len, 0);
_len = len;
_cur = 0;
_done = false;
_numPartialSearch = 0;
_numUniqueSearch = 0;
_partialHits.clear();
}
bool done() {
#ifndef NDEBUG
assert_gt(_len, 0);
if(_cur >= _len) {
assert(_done);
}
#endif
return _done;
}
void done(bool done) {
// assert(!_done);
assert(done);
_done = done;
}
index_t len() const { return _len; }
index_t cur() const { return _cur; }
size_t offsetSize() { return _partialHits.size(); }
size_t numPartialSearch() { return _numPartialSearch; }
size_t numActualPartialSearch()
{
assert_leq(_numUniqueSearch, _numPartialSearch);
return _numPartialSearch - _numUniqueSearch;
}
bool width(index_t offset_) {
assert_lt(offset_, _partialHits.size());
return _partialHits[offset_].size();
}
bool hasGenomeCoords(index_t offset_) {
assert_lt(offset_, _partialHits.size());
index_t width_ = width(offset_);
if(width_ == 0) {
return true;
} else {
return _partialHits[offset_].hasGenomeCoords();
}
}
bool hasAllGenomeCoords() {
if(_cur < _len) return false;
if(_partialHits.size() <= 0) return false;
for(size_t oi = 0; oi < _partialHits.size(); oi++) {
if(!_partialHits[oi].hasGenomeCoords())
return false;
}
return true;
}
/**
*
*/
index_t minWidth(index_t& offset) const {
index_t minWidth_ = (index_t)OFF_MASK;
index_t minWidthLen_ = 0;
for(size_t oi = 0; oi < _partialHits.size(); oi++) {
const BWTHit<index_t>& hit = _partialHits[oi];
if(hit.empty()) continue;
// if(!hit.hasGenomeCoords()) continue;
assert_gt(hit.size(), 0);
if((minWidth_ > hit.size()) ||
(minWidth_ == hit.size() && minWidthLen_ < hit.len())) {
minWidth_ = hit.size();
minWidthLen_ = hit.len();
offset = (index_t)oi;
}
}
return minWidth_;
}
// add policy for calculating a search score
int64_t searchScore(index_t minK) {
int64_t score = 0;
const int64_t penaltyPerOffset = minK * minK;
for(size_t i = 0; i < _partialHits.size(); i++) {
index_t len = _partialHits[i]._len;
score += (len * len);
}
assert_geq(_numPartialSearch, _partialHits.size());
index_t actualPartialSearch = numActualPartialSearch();
score -= (actualPartialSearch * penaltyPerOffset);
score -= (1 << (actualPartialSearch << 1));
return score;
}
BWTHit<index_t>& getPartialHit(index_t offset_) {
assert_lt(offset_, _partialHits.size());
return _partialHits[offset_];
}
bool adjustOffset(index_t minK) {
assert_gt(_partialHits.size(), 0);
const BWTHit<index_t>& hit = _partialHits.back();
if(hit.len() >= minK + 3) {
return false;
}
assert_geq(_cur, hit.len());
index_t origCur = _cur - hit.len();
_cur = origCur + max(hit.len(), minK + 1) - minK;
_partialHits.pop_back();
return true;
}
void setOffset(index_t offset) {
//assert_lt(offset, _len); //FIXME: assertion fails as offset == _len
_cur = offset;
}
#ifndef NDEBUG
/**
*/
bool repOk() const {
for(size_t i = 0; i < _partialHits.size(); i++) {
if(i == 0) {
assert_geq(_partialHits[i]._bwoff, 0);
}
if(i + 1 < _partialHits.size()) {
assert_leq(_partialHits[i]._bwoff + _partialHits[i]._len, _partialHits[i+1]._bwoff);
} else {
assert_eq(i+1, _partialHits.size());
assert_eq(_partialHits[i]._bwoff + _partialHits[i]._len, _cur);
}
}
return true;
}
#endif
bool _fw;
index_t _len;
index_t _cur;
bool _done;
index_t _numPartialSearch;
index_t _numUniqueSearch;
index_t _cur_local;
EList<BWTHit<index_t> > _partialHits;
};
/**
* this is per-thread data, which are shared by GenomeHit classes
* the main purpose of this struct is to avoid extensive use of memory related functions
* such as new and delete - those are really slow and lock based
*/
template <typename index_t>
struct SharedTempVars {
SStringExpandable<char> raw_refbuf;
SStringExpandable<char> raw_refbuf2;
EList<int64_t> temp_scores;
EList<int64_t> temp_scores2;
ASSERT_ONLY(SStringExpandable<uint32_t> destU32);
ASSERT_ONLY(BTDnaString editstr);
ASSERT_ONLY(BTDnaString partialseq);
ASSERT_ONLY(BTDnaString refstr);
ASSERT_ONLY(EList<index_t> reflens);
ASSERT_ONLY(EList<index_t> refoffs);
LinkedEList<EList<Edit> > raw_edits;
};
/**
* GenomeHit represents read alignment or alignment of a part of a read
* Two GenomeHits that represents alignments of different parts of a read
* can be combined together. Also, GenomeHit can be extended in both directions.
*/
template <typename index_t>
struct GenomeHit {
GenomeHit() :
_fw(false),
_rdoff((index_t)OFF_MASK),
_len((index_t)OFF_MASK),
_trim5(0),
_trim3(0),
_tidx((index_t)OFF_MASK),
_toff((index_t)OFF_MASK),
_edits(NULL),
_score(MIN_I64),
_hitcount(1),
_edits_node(NULL),
_sharedVars(NULL)
{
}
GenomeHit(const GenomeHit& otherHit) :
_fw(false),
_rdoff((index_t)OFF_MASK),
_len((index_t)OFF_MASK),
_trim5(0),
_trim3(0),
_tidx((index_t)OFF_MASK),
_toff((index_t)OFF_MASK),
_edits(NULL),
_score(MIN_I64),
_hitcount(1),
_edits_node(NULL),
_sharedVars(NULL)
{
init(otherHit._fw,
otherHit._rdoff,
otherHit._len,
otherHit._trim5,
otherHit._trim3,
otherHit._tidx,
otherHit._toff,
*(otherHit._sharedVars),
otherHit._edits,
otherHit._score,
otherHit._splicescore);
}
GenomeHit<index_t>& operator=(const GenomeHit<index_t>& otherHit) {
if(this == &otherHit) return *this;
init(otherHit._fw,
otherHit._rdoff,
otherHit._len,
otherHit._trim5,
otherHit._trim3,
otherHit._tidx,
otherHit._toff,
*(otherHit._sharedVars),
otherHit._edits,
otherHit._score,
otherHit._splicescore);
return *this;
}
~GenomeHit() {
if(_edits_node != NULL) {
assert(_edits != NULL);
assert(_sharedVars != NULL);
_sharedVars->raw_edits.delete_node(_edits_node);
_edits = NULL;
_edits_node = NULL;
_sharedVars = NULL;
}
}
void init(
bool fw,
index_t rdoff,
index_t len,
index_t trim5,
index_t trim3,
index_t tidx,
index_t toff,
SharedTempVars<index_t>& sharedVars,
EList<Edit>* edits = NULL,
int64_t score = 0,
double splicescore = 0.0)
{
_fw = fw;
_rdoff = rdoff;
_len = len;
_trim5 = trim5;
_trim3 = trim3;
_tidx = tidx;
_toff = toff;
_score = score;
_splicescore = splicescore;
assert(_sharedVars == NULL || _sharedVars == &sharedVars);
_sharedVars = &sharedVars;
if(_edits == NULL) {
assert(_edits_node == NULL);
_edits_node = _sharedVars->raw_edits.new_node();
assert(_edits_node != NULL);
_edits = &(_edits_node->payload);
}
assert(_edits != NULL);
_edits->clear();
if(edits != NULL) *_edits = *edits;
_hitcount = 1;
}
bool inited() const {
return _len >= 0 && _len < (index_t)OFF_MASK;
}
index_t rdoff() const { return _rdoff; }
index_t len() const { return _len; }
index_t trim5() const { return _trim5; }
index_t trim3() const { return _trim3; }
void trim5(index_t trim5) { _trim5 = trim5; }
void trim3(index_t trim3) { _trim3 = trim3; }
index_t ref() const { return _tidx; }
index_t refoff() const { return _toff; }
index_t fw() const { return _fw; }
index_t hitcount() const { return _hitcount; }
/**
* Leftmost coordinate
*/
Coord coord() const {
return Coord(_tidx, _toff, _fw);
}
const EList<Edit>& edits() const { return *_edits; }
bool operator== (const GenomeHit<index_t>& other) const {
if(_fw != other._fw ||
_rdoff != other._rdoff ||
_len != other._len ||
_tidx != other._tidx ||
_toff != other._toff ||
_trim5 != other._trim5 ||
_trim3 != other._trim3) {
return false;
}
if(_edits->size() != other._edits->size()) return false;
for(index_t i = 0; i < _edits->size(); i++) {
if(!((*_edits)[i] == (*other._edits)[i])) return false;
}
// daehwan - this may not be true when some splice sites are provided from outside
// assert_eq(_score, other._score);
return true;
}
bool contains(const GenomeHit<index_t>& other) const {
return (*this) == other;
}
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
bool repOk(const Read& rd, const BitPairReference& ref);
#endif
public:
bool _fw;
index_t _rdoff;
index_t _len;
index_t _trim5;
index_t _trim3;
index_t _tidx;
index_t _toff;
EList<Edit>* _edits;
int64_t _score;
double _splicescore;
index_t _hitcount; // for selection purposes
LinkedEListNode<EList<Edit> >* _edits_node;
SharedTempVars<index_t>* _sharedVars;
};
#ifndef NDEBUG
/**
* Check that hit is sane w/r/t read.
*/
template <typename index_t>
bool GenomeHit<index_t>::repOk(const Read& rd, const BitPairReference& ref)
{
assert(_sharedVars != NULL);
SStringExpandable<char>& raw_refbuf = _sharedVars->raw_refbuf;
SStringExpandable<uint32_t>& destU32 = _sharedVars->destU32;
BTDnaString& editstr = _sharedVars->editstr;
BTDnaString& partialseq = _sharedVars->partialseq;
BTDnaString& refstr = _sharedVars->refstr;
EList<index_t>& reflens = _sharedVars->reflens;
EList<index_t>& refoffs = _sharedVars->refoffs;
editstr.clear(); partialseq.clear(); refstr.clear();
reflens.clear(); refoffs.clear();
const BTDnaString& seq = _fw ? rd.patFw : rd.patRc;
partialseq.install(seq.buf() + this->_rdoff, (size_t)this->_len);
Edit::toRef(partialseq, *_edits, editstr);
index_t refallen = 0;
int64_t reflen = 0;
int64_t refoff = this->_toff;
refoffs.push_back(refoff);
size_t eidx = 0;
for(size_t i = 0; i < _len; i++, reflen++, refoff++) {
while(eidx < _edits->size() && (*_edits)[eidx].pos == i) {
const Edit& edit = (*_edits)[eidx];
if(edit.isReadGap()) {
reflen++;
refoff++;
} else if(edit.isRefGap()) {
reflen--;
refoff--;
}
if(edit.isSpliced()) {
assert_gt(reflen, 0);
refallen += reflen;
reflens.push_back((index_t)reflen);
reflen = 0;
refoff += edit.splLen;
assert_gt(refoff, 0);
refoffs.push_back((index_t)refoff);
}
eidx++;
}
}
assert_gt(reflen, 0);
refallen += (index_t)reflen;
reflens.push_back(reflen);
assert_gt(reflens.size(), 0);
assert_gt(refoffs.size(), 0);
assert_eq(reflens.size(), refoffs.size());
refstr.clear();
for(index_t i = 0; i < reflens.size(); i++) {
assert_gt(reflens[i], 0);
if(i > 0) {
assert_gt(refoffs[i], refoffs[i-1]);
}
raw_refbuf.resize(reflens[i] + 16);
raw_refbuf.clear();
int off = ref.getStretch(
reinterpret_cast<uint32_t*>(raw_refbuf.wbuf()),
(size_t)this->_tidx,
(size_t)max<TRefOff>(refoffs[i], 0),
reflens[i],
destU32);
assert_leq(off, 16);
for(index_t j = 0; j < reflens[i]; j++) {
char rfc = *(raw_refbuf.buf()+off+j);
refstr.append(rfc);
}
}
if(refstr != editstr) {
cerr << "Decoded nucleotides and edits don't match reference:" << endl;
//cerr << " score: " << score.score()
//<< " (" << gaps << " gaps)" << endl;
cerr << " edits: ";
Edit::print(cerr, *_edits);
cerr << endl;
cerr << " decoded nucs: " << partialseq << endl;
cerr << " edited nucs: " << editstr << endl;
cerr << " reference nucs: " << refstr << endl;
assert(0);
}
return true;
}
#endif
/**
* Encapsulates counters that measure how much work has been done by
* hierarchical indexing
*/
struct HIMetrics {
HIMetrics() : mutex_m() {
reset();
}
void reset() {
anchoratts = 0;
localatts = 0;
localindexatts = 0;
localextatts = 0;
localsearchrecur = 0;
globalgenomecoords = 0;
localgenomecoords = 0;
}
void init(
uint64_t localatts_,
uint64_t anchoratts_,
uint64_t localindexatts_,
uint64_t localextatts_,
uint64_t localsearchrecur_,
uint64_t globalgenomecoords_,
uint64_t localgenomecoords_)
{
localatts = localatts_;
anchoratts = anchoratts_;
localindexatts = localindexatts_;
localextatts = localextatts_;
localsearchrecur = localsearchrecur_;
globalgenomecoords = globalgenomecoords_;
localgenomecoords = localgenomecoords_;
}
/**
* Merge (add) the counters in the given HIMetrics object into this
* object. This is the only safe way to update a HIMetrics shared
* by multiple threads.
*/
void merge(const HIMetrics& r, bool getLock = false) {
ThreadSafe ts(&mutex_m, getLock);
localatts += r.localatts;
anchoratts += r.anchoratts;
localindexatts += r.localindexatts;
localextatts += r.localextatts;
localsearchrecur += r.localsearchrecur;
globalgenomecoords += r.globalgenomecoords;
localgenomecoords += r.localgenomecoords;
}
uint64_t localatts; // # attempts of local search
uint64_t anchoratts; // # attempts of anchor search
uint64_t localindexatts; // # attempts of local index search
uint64_t localextatts; // # attempts of extension search
uint64_t localsearchrecur;
uint64_t globalgenomecoords;
uint64_t localgenomecoords;
MUTEX_T mutex_m;
};
/**
* 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 HI_Aligner {
public:
/**
* Initialize with index.
*/
HI_Aligner(
const Ebwt<index_t>& ebwt,
bool secondary = false,
bool local = false,
uint64_t threads_rids_mindist = 0,
bool no_spliced_alignment = false) :
_secondary(secondary),
_local(local),
_gwstate(GW_CAT),
_gwstate_local(GW_CAT),
_thread_rids_mindist(threads_rids_mindist),
_no_spliced_alignment(no_spliced_alignment)
{
index_t genomeLen = ebwt.eh().len();
_minK = 0;
while(genomeLen > 0) {
genomeLen >>= 2;
_minK++;
}
_minK_local = 8;
}
HI_Aligner() {
}
/**
*/
void initRead(Read *rd, bool nofw, bool norc, TAlScore minsc, TAlScore maxpen, bool rightendonly = false) {
assert(rd != NULL);
_rds[0] = rd;
_rds[1] = NULL;
_paired = false;
_rightendonly = rightendonly;
_nofw[0] = nofw;
_nofw[1] = true;
_norc[0] = norc;
_norc[1] = true;
_minsc[0] = minsc;
_minsc[1] = OFF_MASK;
_maxpen[0] = maxpen;
_maxpen[1] = OFF_MASK;
for(size_t fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
_hits[0][fwi].init(fw, _rds[0]->length());
}
_genomeHits.clear();
_concordantPairs.clear();
_hits_searched[0].clear();
assert(!_paired);
}
/**
*/
void initReads(Read *rds[2], bool nofw[2], bool norc[2], TAlScore minsc[2], TAlScore maxpen[2]) {
assert(rds[0] != NULL && rds[1] != NULL);
_paired = true;
_rightendonly = false;
for(size_t rdi = 0; rdi < 2; rdi++) {
_rds[rdi] = rds[rdi];
_nofw[rdi] = nofw[rdi];
_norc[rdi] = norc[rdi];
_minsc[rdi] = minsc[rdi];
_maxpen[rdi] = maxpen[rdi];
for(size_t fwi = 0; fwi < 2; fwi++) {
bool fw = (fwi == 0);
_hits[rdi][fwi].init(fw, _rds[rdi]->length());
}
_hits_searched[rdi].clear();
}
_genomeHits.clear();
_concordantPairs.clear();
assert(_paired);
assert(!_rightendonly);
}
/**
* 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,
WalkMetrics& wlm,
PerReadMetrics& prm,
HIMetrics& him,
SpeciesMetrics& spm,
RandomSource& rnd,
AlnSinkWrap<index_t>& sink) = 0;
/**
* Align a part of a read without any edits
*/
size_t partialSearch(
const Ebwt<index_t>& ebwt, // BWT index
const Read& read, // read to align
const Scoring& sc, // scoring scheme
bool fw, // don't align forward read
size_t mineMax, // don't care about edit bounds > this
size_t& mineFw, // minimum # edits for forward read
size_t& mineRc, // minimum # edits for revcomp read
ReadBWTHit<index_t>& hit, // holds all the seed hits (and exact hit)
RandomSource& rnd);
protected:
Read * _rds[2];
bool _paired;
bool _rightendonly;
bool _nofw[2];
bool _norc[2];
TAlScore _minsc[2];
TAlScore _maxpen[2];
bool _secondary; // allow secondary alignments
bool _local; // perform local alignments
ReadBWTHit<index_t> _hits[2][2];
EList<index_t, 16> _offs;
SARangeWithOffs<EListSlice<index_t, 16> > _sas;
GroupWalk2S<index_t, EListSlice<index_t, 16>, 16> _gws;
GroupWalkState<index_t> _gwstate;
EList<local_index_t, 16> _offs_local;
SARangeWithOffs<EListSlice<local_index_t, 16> > _sas_local;
GroupWalk2S<local_index_t, EListSlice<local_index_t, 16>, 16> _gws_local;
GroupWalkState<local_index_t> _gwstate_local;
// temporary and shared variables used for GenomeHit
// this should be defined before _genomeHits and _hits_searched
SharedTempVars<index_t> _sharedVars;
// temporary and shared variables for AlnRes
LinkedEList<EList<Edit> > _rawEdits;
// temporary
EList<GenomeHit<index_t> > _genomeHits;
EList<bool> _genomeHits_done;
ELList<Coord> _coords;
EList<pair<index_t, index_t> > _concordantPairs;
size_t _minK; // log4 of the size of a genome
size_t _minK_local; // log4 of the size of a local index (8)
ELList<GenomeHit<index_t> > _local_genomeHits;
EList<uint8_t> _anchors_added;
uint64_t max_localindexatts;
uint64_t bwops_; // Burrows-Wheeler operations
uint64_t bwedits_; // Burrows-Wheeler edits
//
EList<GenomeHit<index_t> > _hits_searched[2];
uint64_t _thread_rids_mindist;
bool _no_spliced_alignment;
// For AlnRes::matchesRef
ASSERT_ONLY(EList<bool> raw_matches_);
ASSERT_ONLY(BTDnaString tmp_rf_);
ASSERT_ONLY(BTDnaString tmp_rdseq_);
ASSERT_ONLY(BTString tmp_qseq_);
};
#define HIER_INIT_LOCS(top, bot, tloc, bloc, e) { \
if(bot - top == 1) { \
tloc.initFromRow(top, (e).eh(), (e).ebwt()); \
bloc.invalidate(); \
} else { \
SideLocus<index_t>::initFromTopBot(top, bot, (e).eh(), (e).ebwt(), tloc, bloc); \
assert(bloc.valid()); \
} \
}
#define HIER_SANITY_CHECK_4TUP(t, b, tp, bp) { \
ASSERT_ONLY(cur_index_t tot = (b[0]-t[0])+(b[1]-t[1])+(b[2]-t[2])+(b[3]-t[3])); \
ASSERT_ONLY(cur_index_t totp = (bp[0]-tp[0])+(bp[1]-tp[1])+(bp[2]-tp[2])+(bp[3]-tp[3])); \
assert_eq(tot, totp); \
}
/**
* Sweep right-to-left and left-to-right using exact matching. Remember all
* the SA ranges encountered along the way. Report exact matches if there are
* any. Calculate a lower bound on the number of edits in an end-to-end
* alignment.
*/
template <typename index_t, typename local_index_t>
size_t HI_Aligner<index_t, local_index_t>::partialSearch(
const Ebwt<index_t>& ebwt, // BWT index
const Read& read, // read to align
const Scoring& sc, // scoring scheme
bool fw,
size_t mineMax, // don't care about edit bounds > this
size_t& mineFw, // minimum # edits for forward read
size_t& mineRc, // minimum # edits for revcomp read
ReadBWTHit<index_t>& hit, // holds all the seed hits (and exact hit)
RandomSource& rnd) // pseudo-random source
{
const index_t ftabLen = ebwt.eh().ftabChars();
SideLocus<index_t> tloc, bloc;
const index_t len = (index_t)read.length();
const BTDnaString& seq = fw ? read.patFw : read.patRc;
assert(!seq.empty());
size_t nelt = 0;
EList<BWTHit<index_t> >& partialHits = hit._partialHits;
index_t& cur = hit._cur;
assert_lt(cur, hit._len);
hit._numPartialSearch++;
index_t offset = cur;
index_t dep = offset;
index_t top = 0, bot = 0;
index_t topTemp = 0, botTemp = 0;
index_t left = len - dep;
assert_gt(left, 0);
if(left < ftabLen) {
cur = hit._len;
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
hit.done(true);
return 0;
}
// Does N interfere with use of Ftab?
for(index_t i = 0; i < ftabLen; i++) {
int c = seq[len-dep-1-i];
if(c > 3) {
cur += (i+1);
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
if(cur >= hit._len) {
hit.done(true);
}
return 0;
}
}
// Use ftab
ebwt.ftabLoHi(seq, len - dep - ftabLen, false, top, bot);
dep += ftabLen;
if(bot <= top) {
cur = dep;
partialHits.expand();
partialHits.back().init((index_t)OFF_MASK,
(index_t)OFF_MASK,
fw,
(uint32_t)offset,
(uint32_t)(cur - offset));
if(cur >= hit._len) {
hit.done(true);
}
return 0;
}
HIER_INIT_LOCS(top, bot, tloc, bloc, ebwt);
// Keep going
while(dep < len) {
int c = seq[len-dep-1];
if(c > 3) {
topTemp = botTemp = 0;
} else {
if(bloc.valid()) {
bwops_ += 2;
topTemp = ebwt.mapLF(tloc, c);
botTemp = ebwt.mapLF(bloc, c);
} else {
bwops_++;
topTemp = ebwt.mapLF1(top, tloc, c);
if(topTemp == (index_t)OFF_MASK) {
topTemp = botTemp = 0;
} else {
botTemp = topTemp + 1;
}
}
}
if(botTemp <= topTemp) {