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(); } }