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/*=========================================================================
Copyright (C) 2009 by Stephan Aiche
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/>.
==========================================================================
$Id$
==========================================================================*/
#ifndef REPSEP_HEADER_ASSEMBLY_PARSER_H
#define REPSEP_HEADER_ASSEMBLY_PARSER_H
#include <seqan/store.h>
#include <seqan/modifier.h>
#include <map>
//#define REPSEP_DEBUG_ASSEMBLY_COL_PARSER
using namespace seqan2;
template<typename TGapsAnchorArray, typename TUngappedSequence, typename TReadPos, typename TGappedSequence>
inline void
_gap_sequence(TGapsAnchorArray const & gaps,
TUngappedSequence const & ungapped_sequence,
TReadPos beginClr,
TReadPos endClr,
TGappedSequence & seq)
{
clear(seq);
typedef typename Size<TGapsAnchorArray>::Type TSize;
typedef typename Value<TGappedSequence>::Type TGappedValue;
TSize ungapped_position = beginClr;
TSize gapped_position = 0;
for(TSize g = 0; g < length(gaps) ; ++g) {
while (static_cast<TReadPos>(ungapped_position) < gaps[g].seqPos && static_cast<TReadPos>(ungapped_position) < endClr) {
// put
append(seq, TGappedValue(ungapped_sequence[ungapped_position] , ungapped_position));
++ungapped_position;
++gapped_position;
}
while (static_cast<TReadPos>(gapped_position) < gaps[g].gapPos) {
append(seq, TGappedValue('-', endClr + 1));
++gapped_position;
}
}
// fill up the rest
while (static_cast<TReadPos>(ungapped_position) < endClr) {
append(seq, TGappedValue(ungapped_sequence[ungapped_position] , ungapped_position));
++ungapped_position;
}
}
// build alignment matrix based on Amos-Assembly -- the main worker
template<typename TSpec, typename TConfig, typename TId, typename TAnnotatedCandidateColumn, typename TScannerType>
inline void
parseContig(FragmentStore<TSpec, TConfig> const& fragStore,
TId const contigId,
String<TAnnotatedCandidateColumn> & candidates,
TScannerType const algo_spec)
{
clear(candidates);
typedef FragmentStore<TSpec, TConfig> TFragmentStore;
typedef typename Size<TFragmentStore>::Type TSize;
typedef typename TFragmentStore::TContigPos TContigPos;
typedef typename TFragmentStore::TReadPos TReadPos;
typedef typename Value<TAnnotatedCandidateColumn, 2>::Type TCandidateColumn;
// must be triplet
typedef typename Value<TCandidateColumn>::Type TAssignedReadChar;
// All fragment store element types
//typedef typename Value<typename TFragmentStore::TReadStore>::Type TReadStoreElement;
typedef typename Value<typename TFragmentStore::TAlignedReadStore>::Type TAlignedElement;
//
typedef Pair<char, TReadPos> TGappedSequenceChar;
typedef String<TGappedSequenceChar> TGappedSequence;
// Sort by begin position ..
sortAlignedReads(fragStore.alignedReadStore, SortBeginPos());
// Sort aligned reads according to contig id
sortAlignedReads(fragStore.alignedReadStore, SortContigId());
TGappedSequence gapped_consensus;
_gap_sequence(fragStore.contigStore[contigId].gaps, fragStore.contigStore[contigId].seq, (TReadPos) 0 , (TReadPos) length(fragStore.contigStore[contigId].seq), gapped_consensus);
TSize l_gapped_consensus = length(gapped_consensus);
typedef typename Iterator<typename TFragmentStore::TAlignedReadStore const>::Type TAlignIter;
TAlignIter alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
TAlignIter alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
typedef std::multiset< TAlignedElement , _LessAlignedRead< TAlignedElement, SortEndPos > > TAlignedReadSet;
typedef typename TAlignedReadSet::iterator TAlignedReadSetIter;
TAlignedReadSet current_read_set;
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER // debug output of all reads in this contig
TAlignIter debug_alignIt = lowerBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
TAlignIter debug_alignItEnd = upperBoundAlignedReads(fragStore.alignedReadStore, contigId, SortContigId());
while(debug_alignIt != debug_alignItEnd)
{
cout << debug_alignIt->readId << " (" << fragStore.readNameStore[debug_alignIt->readId] << ")" << endl;
goNext(debug_alignIt);
}
#endif
for(TSize p = 0 ; p < l_gapped_consensus ; ++p)
{
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << "Start inspecting column " << p << endl;
#endif
// check if we need to remove some of the reads
TAlignedReadSetIter end_erase = current_read_set.begin();
TAlignedReadSetIter set_end = current_read_set.end();
if(end_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) {
// we need to remove some of our AlignedReads
TAlignedReadSetIter start_erase = end_erase;
while (end_erase != set_end && _max(end_erase->beginPos, end_erase->endPos) == static_cast<TContigPos>(p)) {
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << "-> will remove: " << end_erase->readId << " (" << fragStore.readNameStore[end_erase->readId] << ")" << endl;
#endif
++end_erase;
}
// do we need to go to previous ???
current_read_set.erase(start_erase, end_erase);
}
// add all open reads into set
while(alignIt != alignItEnd && _min(alignIt->beginPos, alignIt->endPos) == static_cast<TContigPos>(p)) {
// add
current_read_set.insert(*alignIt);
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << "added" << endl;
cout << alignIt->readId << " (" << fragStore.readNameStore[alignIt->readId] << ")" << endl;
#endif
goNext(alignIt);
}
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << "after add cycle iterator points to " << endl;
cout << alignIt->readId << " (" << fragStore.readNameStore[alignIt->readId] << ")" << endl;
#endif
// since also a gap can be off interest we also inspect those
TCandidateColumn column;
// inspect consensus
TAlignedReadSetIter iter_cr = current_read_set.begin();
TAlignedReadSetIter iter_cr_end = current_read_set.end();
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << "at position " << p << " following reads are active (" << current_read_set.size() << "):" << endl;
#endif
while(iter_cr != iter_cr_end) {
#ifdef REPSEP_DEBUG_ASSEMBLY_COL_PARSER
cout << iter_cr->readId << " (" << fragStore.readNameStore[iter_cr->readId] << ")" << endl;
#endif
// get position in sequence
TReadPos offset = _min(iter_cr->beginPos, iter_cr->endPos);
TGappedSequence gapped_read;
TReadPos begClr = 0;
TReadPos endClr = 0;
getClrRange(fragStore, *iter_cr, begClr, endClr);
String<Dna5Q> ungapped_seq = fragStore.readSeqStore[iter_cr->readId];
if(iter_cr->beginPos > iter_cr->endPos) {
reverseComplement(ungapped_seq);
// swap the clr's
TReadPos tmp = begClr;
begClr = length(ungapped_seq) - endClr;
endClr = length(ungapped_seq) - tmp;
}
_gap_sequence(iter_cr->gaps, ungapped_seq, begClr, endClr, gapped_read);
// increase vote
append(column, TAssignedReadChar(_sequenceCharacter(gapped_read[p - offset]), iter_cr->readId, _positionInRead(gapped_read[p - offset])));
++iter_cr;
}
// inspect column and mark as candidate ..
if( isCandidate(fragStore, contigId, gapped_consensus[p], column, algo_spec ) )
{
appendValue(candidates, TAnnotatedCandidateColumn(p, column));
}
}
}
#endif
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