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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_STORE_ALIGN_INTERVALS_H
#define SEQAN_HEADER_STORE_ALIGN_INTERVALS_H
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
// MatchedIntervals Store
//////////////////////////////////////////////////////////////////////////////
template<typename TValue = int >
struct Interval
{
TValue i1;
TValue i2;
Interval() : i1(0), i2(0) {}
};
template<typename TValue>
inline bool
operator == (Interval<TValue> const & interval1, Interval<TValue> const & interval2)
{
return (interval1.i1 == interval2.i1 && interval1.i2 == interval2.i2);
}
template<typename TValue>
inline bool
operator < (Interval<TValue> const & interval1, Interval<TValue> const & interval2)
{
if (interval1.i1 == interval2.i1)
return (interval1.i2 < interval2.i2);
else
return (interval1.i1 < interval2.i1);
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
template <typename TInterval = Interval<unsigned>, typename TSpec = void>
struct AlignIntervalsStoreElement
{
typedef String<TInterval> TIntervals;
TIntervals intervals;
};
///////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////
template<typename TAlignIntervalsStore, typename TSpec, typename TConfig >
inline void
buildAlignIntervalsStore(TAlignIntervalsStore & alignIntervalsStore,
FragmentStore<TSpec, TConfig> & me, const unsigned & thresholdGaps)
{
typedef typename FragmentStore<TSpec, TConfig>::TAlignedReadStore TAlignedReadStore;
typedef typename Iterator<TAlignedReadStore, Standard>::Type TAlignIter;
typedef typename Iterator<TAlignIntervalsStore>::Type TAlignIntervalsStoreIter;
if (!empty(me.alignedReadStore))
{
resize(alignIntervalsStore, length(me.alignedReadStore));
TAlignIntervalsStoreIter it = begin(alignIntervalsStore);
TAlignIter itAlign = begin(me.alignedReadStore);
TAlignIter itAlignEnd = end(me.alignedReadStore);
// get matched intervals for each aligned read
for ( ; itAlign != itAlignEnd; goNext(itAlign), goNext(it))
{
extractAlignIntervals(value(it).intervals, getValue(itAlign), me, thresholdGaps);
}
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////
/////// extract contig intervals of aligned read
////////////////////////////////////////////////////////////////////////////////////////////////////////
template<typename TIntervals, typename TAlignedReadStoreElement, typename TSpec, typename TConfig>
inline void
extractAlignIntervals(TIntervals & contigIntervals, TAlignedReadStoreElement & align, FragmentStore<TSpec, TConfig> & me, const unsigned & thresholdGaps)
{
////////////////////////////////////////////////////////////////////////////////////////////////////////
///////// get read intervals in gapped contig sequence:
typedef typename FragmentStore<TSpec, TConfig>::TContigPos TContigPos;
typedef typename FragmentStore<TSpec, TConfig>::TReadGapAnchor TReadGapAnchor;
typedef String<TReadGapAnchor> TReadGaps;
typedef typename Position<TReadGaps >::Type TGapPos;
typedef typename Value<TIntervals>::Type TInterval;
typedef typename Iterator<TReadGaps>::Type TReadGapsIter;
clear(contigIntervals);
TIntervals readIntervals;
TContigPos beginPos = align.beginPos;
TContigPos endPos = align.endPos;
if (beginPos > endPos)
{
TContigPos help = beginPos;
beginPos = endPos;
endPos = help;
}
TInterval interval;
if (length(align.gaps) == 0)
{
resize(readIntervals, 1, Generous());
interval.i1 = beginPos;
interval.i2 = endPos -1;
assignValue(readIntervals, 0, interval);
}
else
{
TReadGapsIter itGap = begin(align.gaps);
TReadGapsIter itGapEnd = end(align.gaps);
TContigPos firstSeqPos = getValue(itGap).seqPos + beginPos; // seqPos from Read projected to pos in ungapped contig sequence
TContigPos firstGapPos = getValue(itGap).gapPos + beginPos; // gapPos from Read projected to pos in ungapped contig sequence
TGapPos i = 0;
// without gaps at the beginnig
if (beginPos < firstGapPos) // end != 0 ??
{
resize(readIntervals, length(align.gaps), Generous());
interval.i1 = beginPos;
interval.i2 = firstSeqPos - 1;
assignValue(readIntervals, i, interval);
++i;
}
// with gaps at the beginning
else resize(readIntervals, length(align.gaps) -1, Generous());
TContigPos seqPos1 = 0;
TContigPos gapPos1 = 0;
TContigPos seqPos2 = firstSeqPos;
TContigPos gapPos2 = firstGapPos;
goNext(itGap);
// calculate interval between 2 gaps:
for (; itGap != itGapEnd; goNext(itGap), ++i)
{
seqPos1 = seqPos2;
gapPos1 = gapPos2;
seqPos2 = getValue(itGap).seqPos + beginPos;
gapPos2 = getValue(itGap).gapPos + beginPos;
interval.i1 = gapPos1; // == gapPos of Gap-Anchor1 + beginPos
interval.i2 = seqPos2 + gapPos1 - seqPos1 - 1; // == gapPos2 - ((gapPos2-seqPos2) - (gapPos1-seqPos1)) - 1
assignValue(readIntervals, i, interval);
}
// without gaps at the end
if (endPos != gapPos2)
{
interval.i1 = gapPos2;
interval.i2 = endPos - 1;
appendValue(readIntervals, interval, Generous());
}
// with gaps at the end
else if (endPos == gapPos2)
{
interval.i1 = gapPos1;
interval.i2 = endPos - 1;
assignValue(readIntervals, i - 1, interval);
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////
///////// get contig intervals in ungapped sequence:
typedef typename TAlignedReadStoreElement::TId TId;
typedef typename FragmentStore<TSpec, TConfig>::TContigGapAnchor TContigGapAnchor;
typedef String<TContigGapAnchor> TContigGaps;
typedef typename Iterator<TContigGaps const>::Type TContigGapsIter;
typedef typename Iterator<TIntervals>::Type TReadIntervalIter;
TId contigId = align.contigId;
if (empty(getValue(me.contigStore, contigId).gaps))
{
contigIntervals = readIntervals;
}
else
{
if (front(getValue(me.contigStore, contigId).gaps).seqPos != 0)
{
TContigGapAnchor pseudoGapAnchor;
pseudoGapAnchor.seqPos = 0;
pseudoGapAnchor.gapPos = 0;
insertValue(value(me.contigStore, contigId).gaps, 0, pseudoGapAnchor, Generous());
}
TReadIntervalIter itI = begin(readIntervals);
TReadIntervalIter itIEnd = end(readIntervals);
TContigGapsIter it1Gap = begin(getValue(me.contigStore, contigId).gaps);
TContigGapsIter it2Gap = begin(getValue(me.contigStore, contigId).gaps);
TContigGapsIter it2GapEnd = end(getValue(me.contigStore, contigId).gaps);
goNext(it2Gap);
TInterval contigInterval;
TInterval readInterval;
TContigPos lastGapPosBeforeGap1;
TContigPos lastGapPosBeforeGap2;
for ( ; itI != itIEnd; goNext(itI))
{
readInterval = getValue(itI);
if (static_cast<TContigPos>(readInterval.i2) < getValue(it1Gap).gapPos) continue; // interval-positions are smaller than first-position of contig: read-interval mappt in contig gaps
// interval i1:
while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i1) >= getValue(it2Gap).gapPos) ) // iterate over 2 contig gap-anchors, until gapPos2 is behind start of read-interval
{
goNext(it1Gap);
goNext(it2Gap);
}
if (it2Gap != it2GapEnd)
{
lastGapPosBeforeGap1 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1; // last position in gapped sequence before gap
if (static_cast<TContigPos>(readInterval.i1) < getValue(it1Gap).gapPos) // occurs, if interval.i1 position is smaller than start-postion of contig
{
contigInterval.i1 = getValue(it1Gap).gapPos;
}
else if (static_cast<TContigPos>(readInterval.i1) <= lastGapPosBeforeGap1) // read-interval starts in contig-interval between the 2 gaps
{
contigInterval.i1 = readInterval.i1 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos); // project position onto ungapped sequence
}
else if (static_cast<TContigPos>(readInterval.i2) < getValue(it2Gap).gapPos) // whole read-interval lies in gaps of contig
{
continue;
}
else // read-interval starts in contig gap -> alignment-interval starts in seqPos2
{
contigInterval.i1 = getValue(it2Gap).seqPos;
}
}
else // read-interval lies behind last gap-anchor
{
goPrevious(it1Gap);
goPrevious(it2Gap);
contigInterval.i1 = readInterval.i1 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos); // not goPrev -> it1Gap
}
// interval i2:
while ( (it2Gap != it2GapEnd) && (static_cast<TContigPos>(readInterval.i2) >= getValue(it2Gap).gapPos) ) // iterate over 2 contig gap-anchors, until gapPos2 is behind end of read-interval
{
goNext(it1Gap);
goNext(it2Gap);
}
if (it2Gap != it2GapEnd)
{
lastGapPosBeforeGap2 = getValue(it2Gap).seqPos + getValue(it1Gap).gapPos - getValue(it1Gap).seqPos -1; // last position in gapped sequence before gap
if (static_cast<TContigPos>(readInterval.i2) <= lastGapPosBeforeGap2) // read-interval ends in contig-interval between the 2 gaps
{
contigInterval.i2 = readInterval.i2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos); // project position onto ungapped sequence
}
else // read-interval ends in gap -> end of alignment-interval is last position before gap
{
contigInterval.i2 = lastGapPosBeforeGap2 - (getValue(it1Gap).gapPos - getValue(it1Gap).seqPos);
}
}
else if (it2Gap == it2GapEnd) // read-intervall ends behind the last gap-anchor
{
goPrevious(it1Gap);
goPrevious(it2Gap);
contigInterval.i2 = readInterval.i2 - (getValue(it2Gap).gapPos - getValue(it2Gap).seqPos);
}
appendValue(contigIntervals, contigInterval, Generous());
}
}
mergeIntervals(contigIntervals, thresholdGaps);
}
////////////////////////////////////////////////////////////////////////////////////////////////////////
//// merge intervals (for sortet intervals; i1 <= i2 <= (i+1)1 <= (i+1)2 )
////////////////////////////////////////////////////////////////////////////////////////////////////////
template<typename TIntervals>
inline void
mergeIntervals(TIntervals & intervals, const unsigned & thresholdGaps)
{
typedef typename Position<TIntervals>::Type TPos;
typedef typename Value<TIntervals>::Type TInterval;
TPos j;
TInterval newInterval;
for (TPos i = 0; i < length(intervals) - 1; ++i)
{
j = i;
// merge intervals, if the no. of gaps inbetween is smaller than threshold
while ((j < length(intervals) - 1) &&
(getValue(intervals, j).i2 + thresholdGaps >= getValue(intervals, j + 1).i1 - 1))
{
++j;
}
if (j != i) // means j > i
{
newInterval.i1 = getValue(intervals, i).i1;
newInterval.i2 = getValue(intervals, j).i2;
// replace [i, j+1) in intervals by newInterval
erase(intervals, i + 1, j + 1);
intervals[i] = newInterval;
}
}
}
////////////////////////////////////////////////////////////////////////////////////////////////////////
}// namespace seqan2
#endif //#ifndef SEQAN_HEADER_...
|
