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;
}
}
static void printIndels(const Genome *refGenome, const set<const Genome *> targets, hal_size_t adjacentBases) {
hal_size_t refLength = refGenome->getSequenceLength();
hal_size_t numSites = 0;
ColumnIteratorPtr colIt = refGenome->getColumnIterator(&targets);
// good flanking site
PositionCache knownGoodSites;
for (hal_index_t refPos = adjacentBases; refPos < refLength - adjacentBases; refPos++) {
pair<indelType, hal_size_t> indel;
indel = getIndel(refPos, refGenome, &targets);
hal_index_t start = refPos - adjacentBases;
hal_index_t end = refPos + adjacentBases;
if (indel.first == INSERTION) {
end += indel.second;
}
colIt->toSite(start, end, true);
map<const Genome *, hal_index_t> prevPos;
bool failedFiltering = false;
hal_size_t step = 1;
while (1) {
hal_index_t refColPos = colIt->getReferenceSequencePosition() + colIt->getReferenceSequence()->getStartPosition();
if (refColPos == refPos && indel.first == DELETION) {
// jump "step" bases -- i.e. past the deleted region
step = indel.second + 1;
} else if (refColPos == refPos && indel.first == INSERTION) {
// don't enforce adjacency on insertion since we're skipping it
prevPos.erase(refGenome);
if (refGenome->getSequenceBySite(refPos) != refGenome->getSequenceBySite(refPos + indel.second)) {
// Insertion crosses sequence end
failedFiltering = true;
break;
}
colIt->toSite(refPos + indel.second, end);
continue;
} else {
step = 1;
}
const ColumnIterator::ColumnMap *colMap = colIt->getColumnMap();
if (!knownGoodSites.find(refColPos)) {
if (!isStrictSingleCopy(colMap, &targets) || !isContiguous(colMap, &prevPos, step, refGenome) ||
!isNotAmbiguous(colMap) || (step != 1 && !deletionIsNotAmbiguous(colMap, &prevPos, refGenome))) {
failedFiltering = true;
if (indel.first == INSERTION) {
// failed indel means that we don't have to check anywhere
// inside the insertion, it will automatically fail
refPos += indel.second;
}
break;
} else {
knownGoodSites.insert(refColPos);
}
}
updatePrevPos(colMap, &prevPos);
if (colIt->lastColumn()) {
break;
}
colIt->toRight();
}
if (indel.first != NONE && !failedFiltering) {
if (indel.first == DELETION) {
const Sequence *seq = refGenome->getSequenceBySite(refPos);
cout << seq->getName() << "\t" << refPos - seq->getStartPosition() << "\t" << refPos - seq->getStartPosition()
<< "\tD\t" << indel.second << endl;
} else {
const Sequence *seq = refGenome->getSequenceBySite(refPos);
assert(seq == refGenome->getSequenceBySite(refPos + indel.second));
cout << seq->getName() << "\t" << refPos - seq->getStartPosition() << "\t"
<< refPos + indel.second - seq->getStartPosition() << "\tI\t" << endl;
refPos += indel.second;
}
}
if (!failedFiltering) {
numSites++;
}
}
cout << "# num sites possible: " << numSites << endl;
}
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;
}
}