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 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, 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(); }