void SequenceIteratorTest::checkCallBack(const Alignment *alignment) {
const Genome *ancGenome = alignment->openGenome("AncGenome");
hal_size_t numSequences = ancGenome->getNumSequences();
CuAssertTrue(_testCase, numSequences = 1000);
for (SequenceIteratorPtr seqIt = ancGenome->getSequenceIterator(); not seqIt->atEnd(); seqIt->toNext()) {
const Sequence *seq = seqIt->getSequence();
hal_size_t i = seq->getArrayIndex();
TopSegmentIteratorPtr tsIt = seq->getTopSegmentIterator();
hal_size_t numTopSegments = seq->getNumTopSegments();
for (hal_size_t j = 0; j < numTopSegments; ++j) {
TopSegmentIteratorPtr gtsIt = ancGenome->getTopSegmentIterator((i - 1) * 100 + j);
const TopSegment *gsTopSegment = gtsIt->getTopSegment();
const TopSegment *sqTopSegment = tsIt->getTopSegment();
CuAssertTrue(_testCase, gsTopSegment->getArrayIndex() == sqTopSegment->getArrayIndex());
tsIt->toRight();
}
BottomSegmentIteratorPtr bsIt = seq->getBottomSegmentIterator();
hal_size_t numBottomSegments = seq->getNumBottomSegments();
for (hal_size_t j = 0; j < numBottomSegments; ++j) {
BottomSegmentIteratorPtr gbsIt = ancGenome->getBottomSegmentIterator((i - 1) * 100 + j);
const BottomSegment *gsBottomSegment = gbsIt->getBottomSegment();
const BottomSegment *sqBottomSegment = bsIt->getBottomSegment();
CuAssertTrue(_testCase, gsBottomSegment->getArrayIndex() == sqBottomSegment->getArrayIndex());
bsIt->toRight();
}
}
}
void SequenceUpdateTest::checkCallBack(const Alignment *alignment) {
const Genome *ancGenome = alignment->openGenome("AncGenome");
hal_size_t numSequences = ancGenome->getNumSequences();
CuAssertTrue(_testCase, numSequences = 1000);
hal_size_t numTopSegments = 0;
hal_size_t numBottomSegments = 0;
hal_size_t totalLength = 0;
hal_size_t lastStart = 0;
hal_size_t lastLength = 0;
for (SequenceIteratorPtr seqIt = ancGenome->getSequenceIterator(); not seqIt->atEnd(); seqIt->toNext()) {
const Sequence *sequence = seqIt->getSequence();
hal_size_t i = (hal_size_t)sequence->getArrayIndex();
hal_size_t len = 1 + i * 5 + i;
hal_size_t numTop = i < numSequences / 2 ? i * 7 : i;
hal_size_t numBottom = i < numSequences / 3 ? i * 5 : i * 2;
string name = "sequence" + std::to_string(i);
const Sequence *seq = seqIt->getSequence();
CuAssertTrue(_testCase, seq->getName() == name);
CuAssertTrue(_testCase, seq->getSequenceLength() == len);
CuAssertTrue(_testCase, seq->getNumTopSegments() == numTop);
CuAssertTrue(_testCase, seq->getNumBottomSegments() == numBottom);
const Genome *gen = seq->getGenome();
CuAssertTrue(_testCase, gen->getName() == "AncGenome");
numTopSegments += seq->getNumTopSegments();
numBottomSegments += seq->getNumBottomSegments();
totalLength += seq->getSequenceLength();
if (i == 0) {
CuAssertTrue(_testCase, seq->getStartPosition() == 0);
} else {
CuAssertTrue(_testCase, seq->getStartPosition() - lastStart == lastLength);
}
lastStart = seq->getStartPosition();
lastLength = seq->getSequenceLength();
}
const Sequence *seq = ancGenome->getSequence("sequence555");
CuAssertTrue(_testCase, seq->getName() == "sequence555");
seq = ancGenome->getSequenceBySite(0);
CuAssertTrue(_testCase, seq->getName() == "sequence0");
seq = ancGenome->getSequenceBySite(45);
CuAssertTrue(_testCase, seq->getName() == "sequence4");
CuAssertTrue(_testCase, ancGenome->getSequenceLength() == totalLength);
CuAssertTrue(_testCase, ancGenome->getNumTopSegments() == numTopSegments);
CuAssertTrue(_testCase, ancGenome->getNumBottomSegments() == numBottomSegments);
}
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);
}
}
}
}
