void LodExtract::writeUnsampledSequence(const Sequence* outSequence,
SegmentIteratorPtr outSegment)
{
outSegment->setCoordinates(outSequence->getStartPosition(),
outSequence->getSequenceLength());
if (outSegment->isTop())
{
assert(outSequence->getNumTopSegments() == 1);
TopSegmentIteratorPtr top = outSegment.downCast<TopSegmentIteratorPtr>();
top->setParentIndex(NULL_INDEX);
top->setParentReversed(false);
top->setNextParalogyIndex(NULL_INDEX);
top->setBottomParseIndex(NULL_INDEX);
}
else
{
assert(outSequence->getNumBottomSegments() == 1);
BottomSegmentIteratorPtr bottom =
outSegment.downCast<BottomSegmentIteratorPtr>();
hal_size_t numChildren = bottom->getNumChildren();
for (hal_size_t childNum = 0; childNum < numChildren; ++childNum)
{
bottom->setChildIndex(childNum, NULL_INDEX);
bottom->setChildReversed(childNum, false);
}
bottom->setTopParseIndex(NULL_INDEX);
}
}
void LodExtract::writeSegments(const Genome* inParent,
const vector<const Genome*>& inChildren)
{
vector<const Genome*> inGenomes = inChildren;
inGenomes.push_back(inParent);
const Genome* outParent = _outAlignment->openGenome(inParent->getName());
assert(outParent != NULL && outParent->getNumBottomSegments() > 0);
BottomSegmentIteratorPtr bottom;
TopSegmentIteratorPtr top;
SegmentIteratorPtr outSegment;
// FOR EVERY GENOME
for (hal_size_t i = 0; i < inGenomes.size(); ++i)
{
const Genome* inGenome = inGenomes[i];
Genome* outGenome = _outAlignment->openGenome(inGenome->getName());
SequenceIteratorPtr outSeqIt = outGenome->getSequenceIterator();
SequenceIteratorConstPtr outSeqEnd = outGenome->getSequenceEndIterator();
// FOR EVERY SEQUENCE IN GENOME
for (; outSeqIt != outSeqEnd; outSeqIt->toNext())
{
const Sequence* outSequence = outSeqIt->getSequence();
const Sequence* inSequence =
inGenome->getSequence(outSequence->getName());
if (outGenome != outParent && outSequence->getNumTopSegments() > 0)
{
top = outSequence->getTopSegmentIterator();
outSegment = top;
}
else if (outSequence->getNumBottomSegments() > 0)
{
bottom = outSequence->getBottomSegmentIterator();
outSegment = bottom;
}
const LodGraph::SegmentSet* segSet = _graph.getSegmentSet(inSequence);
assert(segSet != NULL);
LodGraph::SegmentSet::const_iterator segIt = segSet->begin();
if (segSet->size() > 2)
{
//skip left telomere
++segIt;
// use to skip right telomere:
LodGraph::SegmentSet::const_iterator segLast = segSet->end();
--segLast;
// FOR EVERY SEGMENT IN SEQUENCE
for (; segIt != segLast; ++segIt)
{
// write the HAL array index back to the segment to make
// future passes quicker.
(*segIt)->setArrayIndex(outSegment->getArrayIndex());
outSegment->setCoordinates((*segIt)->getLeftPos(),
(*segIt)->getLength());
assert(outSegment->getSequence()->getName() == inSequence->getName());
outSegment->toRight();
}
}
else if (outSequence->getSequenceLength() > 0)
{
assert(segSet->size() == 2);
writeUnsampledSequence(outSequence, outSegment);
}
}
}
}
