void Liftover::liftInterval()
{
PositionMap posCacheMap;
_colIt = _srcSequence->getColumnIterator(&_tgtSet, 0, _inStart, _inEnd - 1);
while (true)
{
const ColumnMap* cMap = _colIt->getColumnMap();
for (ColumnMap::const_iterator i = cMap->begin(); i != cMap->end(); ++i)
{
if (i->first->getGenome() == _tgtGenome)
{
const DNASet* dSet = i->second;
const Sequence* seq = i->first;
// if we're not adding the column, don't bother keeping track
hal_size_t paralogyFactor = _addDupeColumn ? dSet->size() : 0;
SeqIndex seqIdx(seq, paralogyFactor);
for (DNASet::const_iterator j = dSet->begin(); j != dSet->end(); ++j)
{
pair<PositionMap::iterator, bool> res =
posCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
if (res.second == true)
{
res.first->second = new PositionCache();
}
res.first->second->insert((*j)->getArrayIndex());
}
}
}
if (_colIt->lastColumn() == true)
{
break;
}
_colIt->toRight();
}
PositionMap::iterator pcmIt;
for (pcmIt = posCacheMap.begin(); pcmIt != posCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
_outName = seq->getName();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
_outStart = k->second - seqStart;
_outEnd = k->first + 1 - seqStart;
writeBedLine();
}
delete posCache;
}
}
void ColumnLiftover::liftInterval(BedList& mappedBedLines)
{
PositionMap posCacheMap;
PositionMap revCacheMap;
_colIt = _srcSequence->getColumnIterator(&_tgtSet, 0, _bedLine._start,
_bedLine._end - 1,
!_traverseDupes,
false,
_bedLine._strand == '-');
while (true)
{
const ColumnMap* cMap = _colIt->getColumnMap();
for (ColumnMap::const_iterator i = cMap->begin(); i != cMap->end(); ++i)
{
if (i->first->getGenome() == _tgtGenome)
{
const DNASet* dSet = i->second;
const Sequence* seq = i->first;
// if we're not adding the column, don't bother keeping track
SeqIndex seqIdx(seq, 0);
for (DNASet::const_iterator j = dSet->begin(); j != dSet->end(); ++j)
{
pair<PositionMap::iterator, bool> res;
if ((*j)->getReversed() == false)
{
res =
posCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
}
else
{
res =
revCacheMap.insert(pair<SeqIndex, PositionCache*>(seqIdx, NULL));
}
if (res.second == true)
{
res.first->second = new PositionCache();
}
res.first->second->insert((*j)->getArrayIndex());
}
}
}
if (_colIt->lastColumn() == true)
{
break;
}
_colIt->toRight();
}
PositionMap::iterator pcmIt;
for (pcmIt = posCacheMap.begin(); pcmIt != posCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
mappedBedLines.push_back(_bedLine);
BedLine& outBedLine = mappedBedLines.back();
outBedLine._blocks.clear();
outBedLine._chrName = seq->getName();
outBedLine._start = k->second - seqStart;
outBedLine._end = k->first + 1 - seqStart;
outBedLine._strand = _bedLine._strand == '.' ? '.' : '+';
outBedLine._srcStart = NULL_INDEX; // not available from posMap
}
delete posCache;
}
for (pcmIt = revCacheMap.begin(); pcmIt != revCacheMap.end(); ++pcmIt)
{
const Sequence* seq = pcmIt->first.first;
_outParalogy = pcmIt->first.second;
hal_size_t seqStart = seq->getStartPosition();
PositionCache* posCache = pcmIt->second;
const IntervalSet* iSet = posCache->getIntervalSet();
for (IntervalSet::const_iterator k = iSet->begin(); k != iSet->end(); ++k)
{
mappedBedLines.push_back(_bedLine);
BedLine& outBedLine = mappedBedLines.back();
outBedLine._blocks.clear();
outBedLine._chrName = seq->getName();
outBedLine._start = k->second - seqStart;
outBedLine._end = k->first + 1 - seqStart;
outBedLine._strand = _bedLine._strand == '.' ? '.' : '-';
outBedLine._srcStart = NULL_INDEX; // not available from posMap
}
delete posCache;
}
}