void MappedSegmentMapDownTest::testBottomSegment(
AlignmentConstPtr alignment,
BottomSegmentIteratorConstPtr bottom,
hal_size_t childIndex)
{
const Genome* child = bottom->getGenome()->getChild(childIndex);
set<MappedSegmentConstPtr> results;
bottom->getMappedSegments(results, child, NULL, false);
CuAssertTrue(_testCase, results.size() == 1);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() ==
bottom->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
bottom->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == bottom->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == bottom->getReversed());
TopSegmentIteratorConstPtr top = child->getTopSegmentIterator();
top->toChild(bottom, childIndex);
CuAssertTrue(_testCase, mseg->getGenome() == top->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == top->getReversed());
}
// 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();
}
}
