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|
// ==========================================================================
// STELLAR - SwifT Exact LocaL AligneR
// https://www.seqan.de/apps/stellar
// ==========================================================================
// Copyright (C) 2010-2026 by Birte Kehr
//
// This program is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 3 of the License, or (at your options) any later version.
//
// This program 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <https://www.gnu.org/licenses/>.
//
// ==========================================================================
// Author: Birte Kehr <birte.kehr@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_STELLAR_H
#define SEQAN_HEADER_STELLAR_H
#include <iostream>
#include <seqan/index.h>
#include <seqan/seeds.h>
#include "stellar_types.h"
#include "stellar_extension.h"
using namespace seqan2;
struct VerifyAllLocal_;
typedef Tag<VerifyAllLocal_> const AllLocal;
struct VerifyBestLocal_;
typedef Tag<VerifyBestLocal_> const BestLocal;
struct VerifyBandedGlobal_;
typedef Tag<VerifyBandedGlobal_> const BandedGlobal;
struct VerifyBandedGlobalExtend_;
typedef Tag<VerifyBandedGlobalExtend_> const BandedGlobalExtend;
///////////////////////////////////////////////////////////////////////////////
inline bool _verifyFast(BestLocal) {
return true;
}
template<typename TTag>
inline bool _verifyFast(TTag) {
return false;
}
///////////////////////////////////////////////////////////////////////////////
// Appends a segment of only error positions from align to queue.
template<typename TAlign, typename TPos, typename TScoreValue>
inline void
_appendNegativeSegment(TAlign const & align,
TPos & pos, TPos len,
Score<TScoreValue> const & scoreMatrix,
String<Triple<TPos, TPos, TScoreValue> > & queue) {
typedef Triple<TPos, TPos, TScoreValue> TMerger;
TPos beginPos = pos;
TScoreValue score = 0;
while (pos < len) {
if (isGap(row(align, 0), pos) || isGap(row(align, 1), pos)) {
score += scoreGap(scoreMatrix);
} else if (value(row(align, 0), pos) != value(row(align, 1), pos)) {
score += scoreMismatch(scoreMatrix);
} else {
break;
}
++pos;
}
if (pos == len) appendValue(queue, TMerger(beginPos, pos, MinValue<TScoreValue>::VALUE + 1));
else appendValue(queue, TMerger(beginPos, pos, score));
}
///////////////////////////////////////////////////////////////////////////////
// Appends a segment of only matching positions from align to queue.
template<typename TAlign, typename TPos, typename TScoreValue>
inline void
_appendPositiveSegment(TAlign const & align,
TPos & pos, TPos len,
Score<TScoreValue> const & scoreMatrix,
String<Triple<TPos, TPos, TScoreValue> > & queue) {
if (pos == len) return;
typedef Triple<TPos, TPos, TScoreValue> TMerger;
TPos beginPos = pos;
TScoreValue score = 0;
while ((pos < len) &&
(!isGap(row(align, 0), pos) &&
!isGap(row(align, 1), pos) &&
(value(row(align, 0), pos) == value(row(align, 1), pos)))) {
score += scoreMatch(scoreMatrix);
++pos;
}
appendValue(queue, TMerger(beginPos, pos, score));
}
///////////////////////////////////////////////////////////////////////////////
// See Lemma 5 in Zhang et al., 1999.
template<typename TMerger>
inline bool
_negativeMerge(String<TMerger> & queue) {
typedef typename Value<TMerger, 1>::Type TPos;
TPos len = length(queue);
if (len < 3) return false;
TMerger cd = value(queue, len-1);
TMerger bc = value(queue, len-2);
TMerger ab = value(queue, len-3);
if ((bc.i3 < 0) || (bc.i3 >= abs(_max(ab.i3, cd.i3)))) {
return false;
} else {
String<TMerger> newMerger;
appendValue(newMerger, TMerger(ab.i1, cd.i2, ab.i3 + bc.i3 + cd.i3));
replace(queue, len-3, len, newMerger);
return true;
}
}
///////////////////////////////////////////////////////////////////////////////
// See Lemma 6 in Zhang et al., 1999.
template<typename TMerger>
inline bool
_positiveMerge(String<TMerger> & queue) {
typedef typename Value<TMerger, 1>::Type TPos;
TPos len = length(queue);
if (len < 5) return false;
TMerger ef = value(queue, len-1);
TMerger de = value(queue, len-2);
TMerger cd = value(queue, len-3);
TMerger bc = value(queue, len-4);
TMerger ab = value(queue, len-5);
if ((cd.i3 >= 0) || (cd.i3 < _max(ab.i3, ef.i3))) {
return false;
} else {
String<TMerger> newMerger;
appendValue(newMerger, TMerger(bc.i1, de.i2, bc.i3 + cd.i3 + de.i3));
replace(queue, len-4, len-1, newMerger);
return true;
}
}
///////////////////////////////////////////////////////////////////////////////
// Implements the algorithm from Zhang et al. in Bioinformatics, 1999: "Post-processing long pairwise alignments".
// Splits an alignment into sub-alignments that contain no x-Drop.
template<typename TAlign, typename TScoreValue, typename TScoreValue1, typename TScoreValue2>
void
_splitAtXDrops(TAlign & align,
Score<TScoreValue> & scoreMatrix,
TScoreValue1 scoreDropOff,
TScoreValue2 minScore,
String<TAlign> & alignmentString) {
typedef typename Position<Row<TAlign> >::Type TPos;
typedef Triple<TPos, TPos, TScoreValue> TMerger;
// initialization
String<TMerger> queue;
TPos pos = _min(toViewPosition(row(align, 0), beginPosition(row(align, 0))),
toViewPosition(row(align, 1), beginPosition(row(align, 1))));
appendValue(queue, TMerger(pos, pos, MinValue<TScoreValue1>::VALUE + 1));
TPos aliLength = _max(toViewPosition(row(align, 0), endPosition(row(align, 0))),
toViewPosition(row(align, 1), endPosition(row(align, 1))));
TPos len;
while ((pos < aliLength) || (length(queue) > 1)) {
// construct useful tree
if (!_negativeMerge(queue)) {
if (!_positiveMerge(queue)) {
_appendPositiveSegment(align, pos, aliLength, scoreMatrix, queue);
_appendNegativeSegment(align, pos, aliLength, scoreMatrix, queue);
}
}
// check for x-Drop
len = length(queue);
if ((len == 3) && (value(queue, 2).i3 < scoreDropOff * (-1))) {
if (value(queue, 1).i3 >= minScore) {
// create new sub-alignment
TAlign ali(align);
// std::cerr << "SEQ0 " << source(row(ali, 0)) << "\n";
// std::cerr << "SEQ1 " << source(row(ali, 1)) << "\n";
// std::cerr << "ROW0\n" << row(ali, 0) << "\nqueue[1].i1 == " << queue[1].i1 << ", queue[1].i2 == " << queue[1].i2 << "\n";
// std::cerr << "ROW1\n" << row(ali, 1) << "\nqueue[1].i1 == " << queue[1].i1 << ", queue[1].i2 == " << queue[1].i2 <<
// "\n";
setClippedBeginPosition(row(ali, 0), queue[1].i1 + clippedBeginPosition(row(align, 0)));
setClippedBeginPosition(row(ali, 1), queue[1].i1 + clippedBeginPosition(row(align, 1)));
setClippedEndPosition(row(ali, 0), queue[1].i2 + clippedBeginPosition(row(align, 0)));
setClippedEndPosition(row(ali, 1), queue[1].i2 + clippedBeginPosition(row(align, 1)));
// TPos begin0 = toSourcePosition(row(ali, 0), value(queue, 1).i1);
// TPos begin1 = toSourcePosition(row(ali, 1), value(queue, 1).i1);
// TPos end0 = toSourcePosition(row(ali, 0), value(queue, 1).i2);
// TPos end1 = toSourcePosition(row(ali, 1), value(queue, 1).i2);
// setClippedBeginPosition(row(ali, 0), begin0);
// setClippedBeginPosition(row(ali, 1), begin1);
// setBeginPosition(row(ali, 0), 0);
// setBeginPosition(row(ali, 1), 0);
// setClippedEndPosition(row(ali, 0), end0);
// setClippedEndPosition(row(ali, 1), end1);
// append sub-alignment
appendValue(alignmentString, ali);
}
replace(queue, 0, 2, String<TMerger>());
}
}
}
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////
// Checks whether two matches overlap *in seq2* and
// whether the non-overlaping parts are shorter than minLength.
template<typename TMatch, typename TSize>
bool
checkOverlap(TMatch & matchA, TMatch & matchB, TSize minLength) {
// check id and orienation
if (matchA.id != matchB.id || matchA.orientation != matchB.orientation) return false;
if (matchA.id == TMatch::INVALID_ID || matchB.id == TMatch::INVALID_ID) return false;
// check overlap in seq2
if (matchA.begin2 >= matchB.begin2) {
if (matchA.end2 >= matchB.end2) {
// check length of non-overlapping parts of both matches
if ((TSize)matchA.begin2 - (TSize)matchB.begin2 >= minLength &&
(TSize)matchA.end2 - (TSize)matchB.end2 >= minLength) {
return false;
}
}
// check whether offset is the same in both sequences
if (toViewPosition(matchA.row2, matchA.begin2) - toViewPosition(matchB.row2, matchB.begin2) !=
toViewPosition(matchA.row1, matchA.begin1) - toViewPosition(matchB.row1, matchB.begin1)) {
return false;
}
} else {
if (matchA.end2 < matchB.end2) {
// check length of non-overlapping parts of both matches
if ((TSize)matchB.begin2 - (TSize)matchA.begin2 >= minLength &&
(TSize)matchB.end2 - (TSize)matchA.end2 >= minLength) {
return false;
}
}
// check whether offset is the same in both sequences
if (toViewPosition(matchB.row2, matchB.begin2) - toViewPosition(matchA.row2, matchA.begin2) !=
toViewPosition(matchB.row1, matchB.begin1) - toViewPosition(matchA.row1, matchA.begin1)) {
return false;
}
}
return true;
}
template<typename TRow, typename TPosition>
TPosition
projectedPosition(TRow & rowA, TRow & rowB, TPosition pos)
{
return toSourcePosition(rowB, toViewPosition(rowA, pos));
}
///////////////////////////////////////////////////////////////////////////////
// Checks all alignment columns of two overlapping matches.
// It is assumed that matchA.begin1 < matchB.begin1.
template<typename TMatch, typename TSize>
bool
_checkAlignColOverlap(TMatch & matchA, TMatch & matchB, TSize minLength)
{
TSize diffCols = 0;
for (typename TMatch::TPos pos = matchB.begin1; pos < _min(matchA.end1, matchB.end1); ++pos)
{
diffCols += (projectedPosition(matchA.row1, matchA.row2, pos) != projectedPosition(matchB.row1, matchB.row2, pos));
}
if (diffCols >= minLength) return false;
return true;
}
///////////////////////////////////////////////////////////////////////////////
// Marks matches that overlap in both sequences with a longer match as invalid.
template<typename TSequence, typename TId, typename TSize>
void maskOverlaps(String<StellarMatch<TSequence, TId> > & matches, TSize minLength)
{
typedef StellarMatch<TSequence, TId> TMatch;
typedef typename TMatch::TPos TPos;
typedef typename Iterator<String<TMatch>, Rooted>::Type TIter;
typedef typename Iterator<String<TSize>, Rooted>::Type TOverlapIter;
// sort matches by begin position in row0
sortMatches(matches, LessPos<TMatch>());
// iterate all matches
TIter it = begin(matches);
// list of matches that potentially overlap with the current match in row0 and
// start earlier (including matches that overlap but have a unique part of at
// least minLength) sorted by descending end positions
String<TSize> overlaps;
for (; it != end(matches); ++it)
{
if ((*it).id == TMatch::INVALID_ID) continue;
TPos insertPos = 0;
// iterate potentially overlapping matches
TOverlapIter overlapIt = begin(overlaps);
for (; overlapIt != end(overlaps); ++overlapIt)
{
TMatch & o = matches[*overlapIt];
// determine position for inserting *it into overlaps after checking
if ((*it).end1 < o.end1) insertPos++;
// check if matches overlap in row0 - if not, then break
if (o.end1 <= (*it).begin1) break;
// check if unique parts of the two matches in row0 are longer than minLength - if yes, then continue
if ((*it).begin1 - o.begin1 >= (TPos)minLength &&
(*it).end1 > o.end1 && (*it).end1 - o.end1 >= (TPos)minLength) continue;
// check if matches overlap in row1 - if not, then continue
if (!checkOverlap(*it, o, minLength)) continue;
// check exact alignment columns for overlap
if (!_checkAlignColOverlap(o, *it, minLength)) continue;
// set shorter match invalid
if (length(*it) > length(o))
o.id = TMatch::INVALID_ID;
else
(*it).id = TMatch::INVALID_ID;
}
// remove all matches from overlaps that end earlier than current match begins
resize(overlaps, position(overlapIt));
if ((*it).id != TMatch::INVALID_ID)
insertValue(overlaps, insertPos, position(it));
}
}
///////////////////////////////////////////////////////////////////////////////
// Removes matches that are marked as invalid, and then keeps only the numMatches best matches.
template<typename TSequence, typename TId, typename TSize>
void
compactMatches(String<StellarMatch<TSequence, TId> > & matches, TSize numMatches) {
typedef StellarMatch<TSequence, TId> TMatch;
typedef typename Iterator<String<TMatch>, Standard>::Type TIterator;
// sort matches by length (and validity)
sortMatches(matches, LessLength<TMatch>());
// count valid matches
TSize num = 0;
TIterator it = begin(matches, Standard());
TIterator itEnd = end(matches, Standard());
for(; it != itEnd; ++it) {
if ((*it).id != TMatch::INVALID_ID)
++num;
}
// keep only valid and longest matches
resize(matches, _min(num, numMatches));
}
///////////////////////////////////////////////////////////////////////////////
// Appends a match to matches container and removes overlapping matches if threshold is reached.
template<typename TSource, typename TId, typename TSize, typename TSize1>
inline bool
_insertMatch(QueryMatches<StellarMatch<TSource, TId> > & queryMatches,
StellarMatch<TSource, TId> const & match,
TSize minLength,
TSize1 disableThresh,
TSize1 & compactThresh,
TSize1 numMatches) {
appendValue(queryMatches.matches, match);
// std::cerr << "Inserting match \n-------------\n" << match.row1 <<"\n" << match.row2 << "----------------\n";
if (length(queryMatches.matches) > disableThresh) {
queryMatches.disabled = true;
clear(queryMatches.matches);
return false;
}
if (length(queryMatches.matches) > compactThresh) {
maskOverlaps(queryMatches.matches, minLength); // remove overlaps and duplicates
compactMatches(queryMatches.matches, numMatches); // keep only the <numMatches> longest matches
// raise compact threshold if many matches are kept
if ((length(queryMatches.matches) << 1) > compactThresh)
compactThresh += (compactThresh >> 1);
}
return true;
}
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////
// Conducts banded alignment on swift hit and extracts longest contained eps-match.
template<typename TInfix, typename TEpsilon, typename TSize, typename TDelta,
typename TDrop, typename TSize1, typename TSource, typename TId>
void
verifySwiftHit(Segment<TInfix, InfixSegment> const & infH,
Segment<TInfix, InfixSegment> const & infV,
TEpsilon eps,
TSize minLength,
TDrop /*xDrop*/,
TDelta delta,
TSize1 disableThresh,
TSize1 & compactThresh,
TSize1 numMatches,
TId & databaseId,
bool dbStrand,
QueryMatches<StellarMatch<TSource, TId> > & matches,
BandedGlobal) {
typedef Segment<TInfix, InfixSegment> TSegment;
typedef typename StellarMatch<TSource, TId>::TAlign TAlign;
// define a scoring scheme
typedef int TScore;
TScore match = 1;
TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH)));
Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel);
// diagonals for banded alignment
int64_t upperDiag = 0;
int64_t lowerDiag = endPosition(infH) - (int64_t)endPosition(infV) - beginPosition(infH) + beginPosition(infV);
if (beginPosition(infV) == 0) upperDiag = lowerDiag + delta;
if (endPosition(infV) == endPosition(host(infV))) lowerDiag = -(int64_t)delta;
// banded alignment on parallelogram
Align<TSegment> bandedAlign;
resize(rows(bandedAlign), 2);
assignSource(row(bandedAlign, 0), infH);
assignSource(row(bandedAlign, 1), infV);
globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch());
longestEpsMatch(bandedAlign, minLength, eps);
// integrate alignment in object of type TAlign
TAlign align;
resize(rows(align), 2);
setSource(row(align, 0), host(host(infH)));
setSource(row(align, 1), host(host(infV)));
integrateAlign(align, bandedAlign);
// TODO(holtgrew): The following has not been adapted to the new clipping interface yet!
// set begin and end positions of align
SEQAN_FAIL("TODO(bkehr): Adapt to new clipping interface!");
setClippedBeginPosition(row(align, 0), beginPosition(infH) + clippedBeginPosition(row(bandedAlign, 0)));
setClippedBeginPosition(row(align, 1), beginPosition(infV) + beginPosition(host(infV)) + clippedBeginPosition(row(bandedAlign, 1)));
setBeginPosition(row(align, 0), 0);
setBeginPosition(row(align, 1), 0);
setClippedEndPosition(row(align, 0), beginPosition(infH) + clippedEndPosition(row(bandedAlign, 0)));
setClippedEndPosition(row(align, 1), beginPosition(infV) + beginPosition(host(infV)) + clippedEndPosition(row(bandedAlign, 1)));
if ((TSize)length(row(align, 0)) < minLength)
return;
// insert eps-match in matches string
StellarMatch<TSource, TId> m(align, databaseId, dbStrand);
_insertMatch(matches, m, minLength, disableThresh, compactThresh, numMatches);
}
///////////////////////////////////////////////////////////////////////////////
// Conducts banded alignment on swift hit, extends alignment, and extracts longest contained eps-match.
template<typename TInfix, typename TEpsilon, typename TSize, typename TDelta,
typename TDrop, typename TSize1, typename TSource, typename TId>
void
verifySwiftHit(Segment<TInfix, InfixSegment> const & infH,
Segment<TInfix, InfixSegment> const & infV,
TEpsilon eps,
TSize minLength,
TDrop xDrop,
TDelta delta,
TSize1 disableThresh,
TSize1 & compactThresh,
TSize1 numMatches,
TId & databaseId,
bool dbStrand,
QueryMatches<StellarMatch<TSource, TId> > & matches,
BandedGlobalExtend) {
typedef Segment<TInfix, InfixSegment> TSegment;
typedef typename StellarMatch<TSource, TId>::TAlign TAlign;
// define a scoring scheme
typedef int TScore;
TScore match = 1;
TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH)));
Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel);
TScore scoreDropOff = (TScore) _max((TScore) xDrop * (-mismatchIndel), MinValue<TScore>::VALUE + 1);
// diagonals for banded alignment
int64_t upperDiag = 0;
int64_t lowerDiag = endPosition(infH) - (int64_t)endPosition(infV) - beginPosition(infH) + beginPosition(infV);
if (beginPosition(infV) == 0) upperDiag = lowerDiag + delta;
if (endPosition(infV) == endPosition(host(infV))) lowerDiag = -(int64_t)delta;
// banded alignment on parallelogram
Align<TSegment> bandedAlign;
resize(rows(bandedAlign), 2);
assignSource(row(bandedAlign, 0), infH);
assignSource(row(bandedAlign, 1), infV);
globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch());
// create alignment object for the complete sequences
TAlign align;
resize(rows(align), 2);
setSource(row(align, 0), host(host(infH)));
setSource(row(align, 1), host(host(infV)));
// extend alignment and obtain longest contained eps-match
// TODO: something is wrong here, e.g. extract around seed, but also something else
if (!_extendAndExtract(bandedAlign, scoreDropOff, scoreMatrix, infH, infV, EXTEND_BOTH, minLength, eps, align))
return;
// insert eps-match in matches string
StellarMatch<TSource, TId> m(align, databaseId, dbStrand);
_insertMatch(matches, m, minLength, disableThresh, compactThresh, numMatches);
}
///////////////////////////////////////////////////////////////////////////////
// Conducts banded local alignment on swift hit (= computes eps-cores),
// splits eps-cores at X-drops, and calls _extendAndExtract for extension of eps-cores
template<typename TInfix, typename TEpsilon, typename TSize, typename TDelta, typename TDrop,
typename TSize1, typename TId, typename TSource, typename TTag>
void
verifySwiftHit(Segment<TInfix, InfixSegment> const & infH,
Segment<TInfix, InfixSegment> const & infV,
TEpsilon eps,
TSize minLength,
TDrop xDrop,
TDelta delta,
TSize1 disableThresh,
TSize1 & compactThresh,
TSize1 numMatches,
TId & databaseId,
bool dbStrand,
QueryMatches<StellarMatch<TSource, TId> > & matches,
TTag tag) {
typedef Segment<TInfix, InfixSegment> TSegment;
typedef typename StellarMatch<TSource, TId>::TAlign TAlign;
TSize maxLength = 1000000000;
if ((TSize)length(infH) > maxLength) {
std::cerr << "Warning: SWIFT hit <" << beginPosition(infH) << "," << endPosition(infH);
std::cerr << "> , <" << beginPosition(infV) << "," << endPosition(infV);
std::cerr << "> too long. Verification skipped.\n" << std::flush;
return;
}
// define a scoring scheme
typedef int TScore;
TScore match = 1;
TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH)));
Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel);
TScore scoreDropOff = (TScore) _max((TScore) xDrop * (-mismatchIndel), MinValue<TScore>::VALUE + 1);
// calculate minimal score for local alignments
TEpsilon e = floor(eps*minLength);
TSize minLength1 = _max(0, (TSize)ceil((e+1) / eps));
TEpsilon e1 = floor(eps*minLength1);
TSize minScore = _min((TSize)ceil((minLength-e) / (e+1)), (TSize)ceil((minLength1-e1) / (e1+1)));
// diagonals for banded local alignment
int64_t upperDiag = 0;
int64_t lowerDiag = endPosition(infH) - (int64_t)endPosition(infV) - beginPosition(infH) + beginPosition(infV);
if (beginPosition(infV) == 0) {
if (endPosition(infV) == endPosition(host(infV))) {
// TODO: is it possible to get a smaller band in this case?
upperDiag = delta;
lowerDiag = -(int64_t)delta;
} else
upperDiag = lowerDiag + delta;
} else if (endPosition(infV) == endPosition(host(infV)))
lowerDiag = -(int64_t)delta;
// banded local alignment
LocalAlignmentEnumerator<Score<TScore>, Banded> enumerator(scoreMatrix, lowerDiag, upperDiag, minScore);
Align<TSegment> localAlign;
resize(rows(localAlign), 2);
assignSource(row(localAlign, 0), infH);
assignSource(row(localAlign, 1), infV);
while (nextLocalAlignment(localAlign, enumerator)) {
// while (localAlignment(localAlign, finder, scoreMatrix, minScore, lowerDiag, upperDiag, BandedWatermanEggert())) {
// std::cerr << "localAlign == \n" << localAlign << "\n";
// split local alignments containing an X-drop
String<Align<TSegment> > seedAlignments;
_splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments);
typename Iterator<String<Align<TSegment> > >::Type aliIt = begin(seedAlignments);
while (aliIt != end(seedAlignments)) {
// std::cerr << "aliIt == \n" << row(*aliIt, 0) << "\n" << row(*aliIt, 1) << "\n";
// create alignment object for the complete sequences
TAlign align;
resize(rows(align), 2);
setSource(row(align, 0), host(host(infH)));
setSource(row(align, 1), host(host(infV)));
// determine extension direction
ExtensionDirection direction;
if (length(seedAlignments) == 1) direction = EXTEND_BOTH;
else if (aliIt == begin(seedAlignments)) direction = EXTEND_RIGHT;
else if (aliIt == end(seedAlignments)-1) direction = EXTEND_LEFT;
else direction = EXTEND_NONE;
// extend alignment and obtain longest contained eps-match
if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) {
aliIt++;
continue;
}
// insert eps-match in matches string
StellarMatch<TSource, TId> m(align, databaseId, dbStrand);
length(m); // DEBUG: Contains assertion on clipping.
if(!_insertMatch(matches, m, minLength, disableThresh, compactThresh, numMatches)) return;
++aliIt;
}
if (_verifyFast(tag)) break;
}
}
///////////////////////////////////////////////////////////////////////////////
// Calls swift filter and verifies swift hits. = Computes eps-matches.
template<typename TText, typename TStringSetSpec, typename TIndexSpec, typename TSize, typename TDrop, typename TSize1,
typename TMode, typename TSource, typename TId, typename TTag>
void stellar(Finder<TText, Swift<SwiftLocal> > & finder,
Pattern<Index<StringSet<TText, TStringSetSpec>, TIndexSpec>, Swift<SwiftLocal> > & pattern,
double epsilon,
TSize minLength,
TDrop xDrop,
TSize1 disableThresh,
TSize1 & compactThresh,
TSize1 numMatches,
TMode verbose,
TId & databaseID,
bool dbStrand,
StringSet<QueryMatches<StellarMatch<TSource, TId> > > & matches,
TTag tag) {
typedef StellarMatch<TSource, TId> TMatch;
typedef typename GetSequenceByNo<StringSet<TText, TStringSetSpec> >::Type TPatternSeq;
typedef typename Infix<TText>::Type TInfix;
TSize numSwiftHits = 0;
TSize maxLength = 0;
TSize totalLength = 0;
while (find(finder, pattern, epsilon, minLength)) {
TInfix finderInfix = infix(finder);
TInfix finderInfixSeq = infix(haystack(finder), 0, length(haystack(finder)));
Segment<TInfix, InfixSegment> finderSegment(finderInfixSeq,
beginPosition(finderInfix) - beginPosition(haystack(finder)),
endPosition(finderInfix) - beginPosition(haystack(finder)));
++numSwiftHits;
totalLength += length(finderInfix);
if ((TSize)length(finderInfix) > maxLength) maxLength = length(finderInfix);
if (value(matches, pattern.curSeqNo).disabled) continue;
TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern)));
typename Infix<TPatternSeq>::Type patternInfix = infix(pattern, patternSeq);
typename Infix<TPatternSeq>::Type patternInfixSeq = infix(patternSeq, 0, length(patternSeq));
Segment<typename Infix<TPatternSeq>::Type, InfixSegment> patternSegment(patternInfixSeq,
beginPosition(patternInfix) - beginPosition(patternSeq),
endPosition(patternInfix) - beginPosition(patternSeq));
////Debug stuff:
//typedef typename Infix<TPatternSeq>::Type TPatternSeqInfix;
//bool i = IsSameType<TInfix, TPatternSeqInfix>::VALUE;
//SEQAN_ASSERT(i);
//
//std::cout << beginPosition(finderInfix) << ",";
//std::cout << endPosition(finderInfix) << " ";
//std::cout << beginPosition(patternSegment) << ",";
//std::cout << endPosition(patternSegment) << std::endl;
// verification
verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop,
pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh,
numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag);
}
if (verbose && numSwiftHits > 0) {
std::cout << std::endl << " # SWIFT hits : " << numSwiftHits;
std::cout << std::endl << " Longest hit : " << maxLength;
std::cout << std::endl << " Avg hit length : " << totalLength/numSwiftHits;
}
typedef typename Iterator<StringSet<QueryMatches<TMatch> >, Standard>::Type TIterator;
TIterator it = begin(matches, Standard());
TIterator itEnd = end(matches, Standard());
for(; it < itEnd; ++it) {
QueryMatches<TMatch> &qm = *it;
if (length(qm) > 0 && !qm.disabled) {
maskOverlaps(qm.matches, minLength); // remove overlaps and duplicates
compactMatches(qm.matches, numMatches); // keep only the <numMatches> longest matches
}
}
}
// Wrapper for stellar
template<typename TText, typename TIndex, typename TSize, typename TDrop,
typename TSource, typename TId, typename TTag>
void stellar(Finder<TText, Swift<SwiftLocal> > & finder,
Pattern<TIndex, Swift<SwiftLocal> > & pattern,
double epsilon,
TSize minLength,
TDrop xDrop,
StringSet<QueryMatches<StellarMatch<TSource, TId> > > & matches,
TTag tag) {
unsigned maxValue = (unsigned)-1;
unsigned compactThresh = 1000;
TId id = "db";
stellar(finder, pattern, epsilon, minLength, xDrop,
maxValue, compactThresh, maxValue, 0, id, true,
matches, tag);
}
#endif
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