void TopSegmentSequenceTest::checkCallBack(AlignmentConstPtr alignment)
{
const Genome* ancGenome = alignment->openGenome("Anc0");
TopSegmentIteratorConstPtr tsIt = ancGenome->getTopSegmentIterator(100);
CuAssertTrue(_testCase, tsIt->getTopSegment()->getStartPosition() == 500);
CuAssertTrue(_testCase, tsIt->getTopSegment()->getLength() == 9);
string seq;
tsIt->getString(seq);
CuAssertTrue(_testCase, seq == "CACACATTC");
tsIt->toReverse();
tsIt->getString(seq);
CuAssertTrue(_testCase, seq == "GAATGTGTG");
}
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;
}
}
}
}
}
// quickly count subsitutions without loading rearrangement machinery.
// used for benchmarks for basic file scanning... and not much else since
// the interface is still a bit wonky.
void SummarizeMutations::substitutionAnalysis(const Genome* genome,
MutationsStats& stats)
{
assert(stats._subs == 0);
if (genome->getNumChildren() == 0 || genome->getNumBottomSegments() == 0 ||
(_targetSet && _targetSet->find(genome->getName()) == _targetSet->end()))
{
return;
}
const Genome* parent = genome->getParent();
string pname = parent != NULL ? parent->getName() : string();
StrPair branchName(genome->getName(), pname);
BottomSegmentIteratorConstPtr bottom = genome->getBottomSegmentIterator();
TopSegmentIteratorConstPtr top = genome->getChild(0)->getTopSegmentIterator();
string gString, cString;
hal_size_t n = genome->getNumBottomSegments();
vector<hal_size_t> children;
hal_size_t m = genome->getNumChildren();
for (hal_size_t i = 0; i < m; ++i)
{
string cName = genome->getChild(i)->getName();
if (!_targetSet ||
(_targetSet && _targetSet->find(cName) != _targetSet->end()))
{
children.push_back(i);
}
}
if (children.empty())
{
return;
}
for (hal_size_t i = 0; i < n; ++i)
{
bool readString = false;
for (size_t j = 0; j < children.size(); ++j)
{
if (bottom->hasChild(children[j]))
{
if (readString == false)
{
bottom->getString(gString);
readString = true;
}
top->toChild(bottom, children[j]);
top->getString(cString);
assert(gString.length() == cString.length());
for (hal_size_t k = 0; k < gString.length(); ++k)
{
if (isSubstitution(gString[k], cString[k]))
{
++stats._subs;
}
}
}
}
bottom->toRight();
}
}
