void MappedSegmentMapUpTest::testTopSegment(AlignmentConstPtr alignment,
TopSegmentIteratorConstPtr top,
const string& ancName)
{
const Genome* parent = alignment->openGenome(ancName);
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, parent, NULL, false);
CuAssertTrue(_testCase, results.size() == 1);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == top->getReversed());
BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
bottom->toParent(top);
// extra hop for when top is in grand child
if (bottom->getGenome() != parent)
{
TopSegmentIteratorConstPtr temp =
bottom->getGenome()->getTopSegmentIterator();
temp->toParseUp(bottom);
bottom->toParent(temp);
}
CuAssertTrue(_testCase, mseg->getGenome() == bottom->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == bottom->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == bottom->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == bottom->getReversed());
}
void MappedSegmentMapAcrossTest::testTopSegment(AlignmentConstPtr alignment,
TopSegmentIteratorConstPtr top)
{
const Genome* parent = top->getGenome()->getParent();
const Genome* other = top->getGenome()->getName() == "child1" ?
alignment->openGenome("child2") : alignment->openGenome("child1");
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, other, NULL, false);
CuAssertTrue(_testCase, results.size() == 1);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == top->getReversed());
BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
bottom->toParent(top);
TopSegmentIteratorConstPtr sister = other->getTopSegmentIterator();
sister->toChildG(bottom, other);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == sister->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == sister->getReversed());
}
void Genome::copyTopSegments(Genome *dest) const
{
const Genome *inParent = getParent();
const Genome *outParent = dest->getParent();
TopSegmentIteratorConstPtr inTop = getTopSegmentIterator();
TopSegmentIteratorPtr outTop = dest->getTopSegmentIterator();
hal_size_t n = dest->getNumTopSegments();
assert(n == 0 || n == getNumTopSegments());
if (n == 0) {
// Nothing to do if there are no top segments.
return;
}
BottomSegmentIteratorConstPtr inParentBottomSegIt = inParent->getBottomSegmentIterator();
BottomSegmentIteratorConstPtr outParentBottomSegIt = outParent->getBottomSegmentIterator();
for (; (hal_size_t)inTop->getArrayIndex() < n; inTop->toRight(),
outTop->toRight())
{
hal_index_t genomePos = inTop->getStartPosition();
assert(genomePos != NULL_INDEX);
string inSeqName = getSequenceBySite(genomePos)->getName();
string outSeqName = dest->getSequenceBySite(genomePos)->getName();
// if (inSeqName != outSeqName) {
// stringstream ss;
// ss << "When copying top segments from " << getName() << " to " << dest->getName() << ": sequence " << inSeqName << " != " << outSeqName << " at site " << genomePos;
// throw hal_exception(ss.str());
// }
outTop->setCoordinates(inTop->getStartPosition(), inTop->getLength());
outTop->setParentIndex(inTop->getParentIndex());
outTop->setParentReversed(inTop->getParentReversed());
outTop->setBottomParseIndex(inTop->getBottomParseIndex());
outTop->setNextParalogyIndex(inTop->getNextParalogyIndex());
// Check that the sequences from the bottom segments we point to are the same. If not, correct the indices so that they are.
if (inTop->getParentIndex() != NULL_INDEX) {
inParentBottomSegIt->toParent(inTop);
const Sequence *inParentSequence = inParentBottomSegIt->getSequence();
const Sequence *outParentSequence = outParent->getSequence(inParentSequence->getName());
hal_index_t inParentSegmentOffset = inTop->getParentIndex() - inParentSequence->getBottomSegmentArrayIndex();
hal_index_t outParentSegmentIndex = inParentSegmentOffset + outParentSequence->getBottomSegmentArrayIndex();
outTop->setParentIndex(outParentSegmentIndex);
}
}
}
void SummarizeMutations::subsAndGapInserts(
GappedTopSegmentIteratorConstPtr gappedTop, MutationsStats& stats)
{
assert(gappedTop->getReversed() == false);
hal_size_t numGaps = gappedTop->getNumGaps();
if (numGaps > 0)
{
stats._gapInsertionLength.add(gappedTop->getNumGapBases(), numGaps);
}
string parent, child;
TopSegmentIteratorConstPtr l = gappedTop->getLeft();
TopSegmentIteratorConstPtr r = gappedTop->getRight();
BottomSegmentIteratorConstPtr p =
l->getTopSegment()->getGenome()->getParent()->getBottomSegmentIterator();
for (TopSegmentIteratorConstPtr i = l->copy();
i->getTopSegment()->getArrayIndex() <=
r->getTopSegment()->getArrayIndex();
i->toRight())
{
if (i->hasParent())
{
p->toParent(i);
i->getString(child);
p->getString(parent);
assert(child.length() == parent.length());
for (size_t j = 0; j < child.length(); ++j)
{
if (isTransition(child[j], parent[j]))
{
++stats._transitions;
++stats._subs;
}
else if (isTransversion(child[j], parent[j]))
{
++stats._transversions;
++stats._subs;
}
else if (isSubstitution(child[j], parent[j]))
{
++stats._subs;
}
else if (!isMissingData(child[j]) && !isMissingData(parent[j]))
{
++stats._matches;
}
}
}
}
}
void MappedSegmentMapDupeTest::checkCallBack(AlignmentConstPtr alignment)
{
validateAlignment(alignment);
const Genome* parent = alignment->openGenome("parent");
const Genome* child1 = alignment->openGenome("child1");
const Genome* child2 = alignment->openGenome("child2");
TopSegmentIteratorConstPtr top = child1->getTopSegmentIterator();
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, child2, NULL, true);
// CuAssertTrue(_testCase, results.size() == 3);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == top->getReversed());
BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
bottom->toParent(top);
TopSegmentIteratorConstPtr sister = child2->getTopSegmentIterator();
sister->toChildG(bottom, child2);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == sister->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == sister->getReversed());
top = child2->getTopSegmentIterator();
results.clear();
sister = child1->getTopSegmentIterator();
top->getMappedSegments(results, child1, NULL, true);
CuAssertTrue(_testCase, results.size() == 3);
bool found[3] = {false};
set<MappedSegmentConstPtr>::iterator i = results.begin();
for (; i != results.end(); ++i)
{
MappedSegmentConstPtr mseg = *i;
CuAssertTrue(_testCase, mseg->getSource()->getGenome() ==
top->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == top->getReversed());
BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
bottom->toParent(top);
TopSegmentIteratorConstPtr sister = child2->getTopSegmentIterator();
sister->toChildG(bottom, child1);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
found[mseg->getArrayIndex()] = true;
}
CuAssertTrue(_testCase, found[0] == true);
CuAssertTrue(_testCase, found[1] == true);
CuAssertTrue(_testCase, found[2] == true);
}
