void copyFromTopAlignment(AlignmentConstPtr topAlignment, AlignmentPtr mainAlignment, const string &genomeName) { Genome *mainReplacedGenome = mainAlignment->openGenome(genomeName); const Genome *topReplacedGenome = topAlignment->openGenome(genomeName); topReplacedGenome->copyTopDimensions(mainReplacedGenome); topReplacedGenome->copyTopSegments(mainReplacedGenome); mainReplacedGenome->fixParseInfo(); // Copy bot segments for the parent and top segments for the // siblings of the genome that's being replaced Genome *mainParent = mainReplacedGenome->getParent(); const Genome *topParent = topReplacedGenome->getParent(); topParent->copyBottomDimensions(mainParent); topParent->copyBottomSegments(mainParent); mainParent->fixParseInfo(); vector<string> siblings = mainAlignment->getChildNames(mainParent->getName()); for (size_t i = 0; i < siblings.size(); i++) { if (siblings[i] != genomeName) { Genome *mainChild = mainAlignment->openGenome(siblings[i]); const Genome *topChild = topAlignment->openGenome(siblings[i]); topChild->copyTopDimensions(mainChild); topChild->copyTopSegments(mainChild); mainChild->fixParseInfo(); } } }
void GappedSegmentIteratorIndelTest::createCallBack(AlignmentPtr alignment) { addIdenticalParentChild(alignment, 1, 20, 5); Genome* parent = alignment->openGenome(alignment->getRootName()); Genome* child = parent->getChild(0); TopSegmentIteratorPtr ti = child->getTopSegmentIterator(); BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator(); // int i = 0; // bool reversed = true; bi = parent->getBottomSegmentIterator(0); makeDelGap(bi); bi = parent->getBottomSegmentIterator(3); makeDelGap(bi); /* ti = child->getTopSegmentIterator(1); makeInsGap(ti); ti = child->getTopSegmentIterator(21); makeInsGap(ti); ti = child->getTopSegmentIterator(28); makeInsGap(ti); */ /* for (size_t i = 0; i < 20; ++i) { cout << i << ": "; bi = parent->getBottomSegmentIterator(i); ti = child->getTopSegmentIterator(i); cout << "ci=" << bi->getBottomSegment()->getChildIndex(0) << " pi=" << ti->getTopSegment()->getParentIndex() << endl; }*/ }
void GappedSegmentSimpleIteratorTest2::createCallBack(AlignmentPtr alignment) { addIdenticalParentChild(alignment, 2, 100, 5); Genome* parent = alignment->openGenome(alignment->getRootName()); Genome* child = parent->getChild(0); TopSegmentIteratorPtr ti = child->getTopSegmentIterator(); BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator(); hal_index_t i = 0; bool reversed = true; while (ti != child->getTopSegmentEndIterator()) { if (i % 5 == 0) { reversed = !reversed; if (reversed && i < (hal_index_t)(parent->getNumBottomSegments() - 1)) { makeInversion(ti, 5); } } ti->toRight(); bi->toRight(); ++i; } }
void copyFromBottomAlignment(AlignmentConstPtr bottomAlignment, AlignmentPtr mainAlignment, const string &genomeName) { // Copy genome & bottom segments for the genome that's being replaced Genome *mainReplacedGenome = mainAlignment->openGenome(genomeName); const Genome *botReplacedGenome = bottomAlignment->openGenome(genomeName); botReplacedGenome->copyDimensions(mainReplacedGenome); botReplacedGenome->copySequence(mainReplacedGenome); botReplacedGenome->copyBottomDimensions(mainReplacedGenome); botReplacedGenome->copyBottomSegments(mainReplacedGenome); mainReplacedGenome->fixParseInfo(); // Copy top segments for the children vector<string> children = mainAlignment->getChildNames(genomeName); for (size_t i = 0; i < children.size(); i++) { Genome *mainChild = mainAlignment->openGenome(children[i]); const Genome *botChild = bottomAlignment->openGenome(children[i]); botChild->copyTopDimensions(mainChild); botChild->copyTopSegments(mainChild); mainChild->fixParseInfo(); } }
void GenomeUpdateTest::createCallBack(AlignmentPtr alignment) { hal_size_t alignmentSize = alignment->getNumGenomes(); CuAssertTrue(_testCase, alignmentSize == 0); Genome* ancGenome = alignment->addRootGenome("AncGenome", 0); vector<Sequence::Info> seqVec(1); seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 700000); ancGenome->setDimensions(seqVec); alignment->close(); alignment->open(_createPath, false); ancGenome = alignment->openGenome("AncGenome"); seqVec[0] = Sequence::Info("Sequence", 10000005, 14000, 2000001); ancGenome->setDimensions(seqVec); }
void GappedSegmentSimpleIteratorTest::createCallBack(AlignmentPtr alignment) { addIdenticalParentChild(alignment, 2, 100, 5); Genome* parent = alignment->openGenome(alignment->getRootName()); Genome* child = parent->getChild(0); TopSegmentIteratorPtr ti = child->getTopSegmentIterator(); BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator(); int i = 0; while (ti != child->getTopSegmentEndIterator()) { if (i++ % 2) { ti->getTopSegment()->setParentReversed(true); bi->getBottomSegment()->setChildReversed(0, true); } ti->toRight(); bi->toRight(); } }
int main(int argc, char *argv[]) { CLParserPtr optParser = initParser(); string inPath, botAlignmentPath, topAlignmentPath, parentName, insertName, childName, leafName; double upperBranchLength, leafBranchLength; bool noMarkAncestors; try { optParser->parseOptions(argc, argv); inPath = optParser->getArgument<string>("inFile"); botAlignmentPath = optParser->getArgument<string>("botAlignmentFile"); topAlignmentPath = optParser->getArgument<string>("topAlignmentFile"); parentName = optParser->getArgument<string>("parentName"); insertName = optParser->getArgument<string>("insertName"); childName = optParser->getArgument<string>("childName"); leafName = optParser->getArgument<string>("leafName"); upperBranchLength = optParser->getArgument<double>("upperBranchLength"); leafBranchLength = optParser->getArgument<double>("leafBranchLength"); noMarkAncestors = optParser->getFlag("noMarkAncestors"); } catch (exception &e) { optParser->printUsage(cerr); return 1; } AlignmentPtr mainAlignment = openHalAlignment(inPath, optParser); AlignmentConstPtr botAlignment = openHalAlignment(botAlignmentPath, optParser); AlignmentConstPtr topAlignment = openHalAlignment(topAlignmentPath, optParser); mainAlignment->insertGenome(insertName, parentName, childName, upperBranchLength); mainAlignment->addLeafGenome(leafName, insertName, leafBranchLength); // Insert the new intermediate node. Genome *insertGenome = mainAlignment->openGenome(insertName); const Genome *topInsertGenome = topAlignment->openGenome(insertName); const Genome *botInsertGenome = botAlignment->openGenome(insertName); topInsertGenome->copyDimensions(insertGenome); topInsertGenome->copyTopDimensions(insertGenome); botInsertGenome->copyBottomDimensions(insertGenome); topInsertGenome->copySequence(insertGenome); topInsertGenome->copyTopSegments(insertGenome); topInsertGenome->copyMetadata(insertGenome); botInsertGenome->copyBottomSegments(insertGenome); insertGenome->fixParseInfo(); // Copy the bottom segments for the parent genome from the top alignment. Genome *parentGenome = mainAlignment->openGenome(parentName); const Genome *botParentGenome = topAlignment->openGenome(parentName); botParentGenome->copyBottomDimensions(parentGenome); botParentGenome->copyBottomSegments(parentGenome); parentGenome->fixParseInfo(); // Fix the parent's other children as well. vector<string> allChildren = mainAlignment->getChildNames(parentName); for (size_t i = 0; i < allChildren.size(); i++) { if (allChildren[i] != insertName) { Genome *outGenome = mainAlignment->openGenome(allChildren[i]); const Genome *topSegmentsGenome = topAlignment->openGenome(allChildren[i]); topSegmentsGenome->copyTopDimensions(outGenome); topSegmentsGenome->copyTopSegments(outGenome); outGenome->fixParseInfo(); } } // Copy the top segments for the child genome from the bottom alignment. Genome *childGenome = mainAlignment->openGenome(childName); const Genome *topChildGenome = botAlignment->openGenome(childName); topChildGenome->copyTopDimensions(childGenome); topChildGenome->copyTopSegments(childGenome); childGenome->fixParseInfo(); // Copy the entire genome for the leaf from the bottom alignment. Genome *outLeafGenome = mainAlignment->openGenome(leafName); const Genome *inLeafGenome = botAlignment->openGenome(leafName); inLeafGenome->copy(outLeafGenome); if (!noMarkAncestors) { markAncestorsForUpdate(mainAlignment, insertName); } mainAlignment->close(); botAlignment->close(); topAlignment->close(); }
int main(int argc, char *argv[]) { CLParserPtr optParser = initParser(); string inPath, bottomAlignmentFile, topAlignmentFile, genomeName; bool noMarkAncestors; try { optParser->parseOptions(argc, argv); inPath = optParser->getArgument<string>("inFile"); bottomAlignmentFile = optParser->getOption<string>("bottomAlignmentFile"); topAlignmentFile = optParser->getOption<string>("topAlignmentFile"); genomeName = optParser->getArgument<string>("genomeName"); noMarkAncestors = optParser->getFlag("noMarkAncestors"); } catch (exception &e) { optParser->printUsage(cerr); return 1; } AlignmentPtr mainAlignment = openHalAlignment(inPath, optParser); AlignmentConstPtr bottomAlignment; AlignmentConstPtr topAlignment; bool useTopAlignment = mainAlignment->getRootName() != genomeName; bool useBottomAlignment = mainAlignment->getChildNames(genomeName).size() != 0; Genome *mainReplacedGenome = mainAlignment->openGenome(genomeName); if (useTopAlignment) { // Not a root genome. Can update using a top alignment. if (topAlignmentFile == "\"\"") { throw hal_exception("Cannot replace non-root genome without a top " "alignment file."); } topAlignment = openHalAlignment(topAlignmentFile, optParser); const Genome *topReplacedGenome = topAlignment->openGenome(genomeName); topReplacedGenome->copyDimensions(mainReplacedGenome); topReplacedGenome->copySequence(mainReplacedGenome); } if (useBottomAlignment) { // Not a leaf genome. Can update using a bottom alignment. if (bottomAlignmentFile == "\"\"") { throw hal_exception("Cannot replace non-leaf genome without a bottom " "alignment file."); } bottomAlignment = openHalAlignment(bottomAlignmentFile, optParser); const Genome *botReplacedGenome = bottomAlignment->openGenome(genomeName); botReplacedGenome->copyDimensions(mainReplacedGenome); botReplacedGenome->copySequence(mainReplacedGenome); } if (!useTopAlignment && !useBottomAlignment) { throw hal_exception("Root genome is also a leaf genome."); } if (useBottomAlignment) { copyFromBottomAlignment(bottomAlignment, mainAlignment, genomeName); } if (useTopAlignment) { copyFromTopAlignment(topAlignment, mainAlignment, genomeName); } // Clear update flag if present, since the genome has just been updated. MetaData *metaData = mainReplacedGenome->getMetaData(); if (metaData->has("needsUpdate")) { metaData->set("needsUpdate", "false"); } if (!noMarkAncestors) { markAncestorsForUpdate(mainAlignment, genomeName); } if (useTopAlignment) { topAlignment->close(); } if (useBottomAlignment) { bottomAlignment->close(); } mainAlignment->close(); }