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 MappedSegmentMapDupeTest::createCallBack(AlignmentPtr alignment) { vector<Sequence::Info> seqVec(1); BottomSegmentIteratorPtr bi; BottomSegmentStruct bs; TopSegmentIteratorPtr ti; TopSegmentStruct ts; // setup simple case were there is an edge from a parent to // child and it is reversed Genome* parent = alignment->addRootGenome("parent"); Genome* child1 = alignment->addLeafGenome("child1", "parent", 1); Genome* child2 = alignment->addLeafGenome("child2", "parent", 1); seqVec[0] = Sequence::Info("Sequence", 3, 0, 1); parent->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 9, 3, 0); child1->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 9, 3, 0); child2->setDimensions(seqVec); parent->setString("CCC"); child1->setString("CCCTACGTG"); child2->setString("CCCTACGTG"); bi = parent->getBottomSegmentIterator(); bs.set(0, 3); bs._children.push_back(pair<hal_size_t, bool>(0, true)); bs._children.push_back(pair<hal_size_t, bool>(0, false)); bs.applyTo(bi); ti = child1->getTopSegmentIterator(); ts.set(0, 3, 0, true, NULL_INDEX, 1); ts.applyTo(ti); ti->toRight(); ts.set(3, 3, 0, true, NULL_INDEX, 2); ts.applyTo(ti); ti->toRight(); ts.set(6, 3, 0, true, NULL_INDEX, 0); ts.applyTo(ti); ti = child2->getTopSegmentIterator(); ts.set(0, 3, 0, false); ts.applyTo(ti); ti->toRight(); ts.set(3, 3, NULL_INDEX, true); ts.applyTo(ti); ti->toRight(); ts.set(6, 3, NULL_INDEX, false); ts.applyTo(ti); }
void LodExtract::writeHomologies(const Genome* inParent, const vector<const Genome*>& inChildren) { vector<const Genome*> inGenomes = inChildren; inGenomes.push_back(inParent); Genome* outParent = _outAlignment->openGenome(inParent->getName()); assert(outParent != NULL && outParent->getNumBottomSegments() > 0); assert(inChildren.size() > 0); Genome* outChild = _outAlignment->openGenome(inChildren[0]->getName()); BottomSegmentIteratorPtr bottom = outParent->getBottomSegmentIterator(); TopSegmentIteratorPtr top = outChild->getTopSegmentIterator(); // FOR EVERY BLOCK for (hal_size_t blockIdx = 0; blockIdx < _graph.getNumBlocks(); ++blockIdx) { SegmentMap segMap; const LodBlock* block = _graph.getBlock(blockIdx); for (hal_size_t segIdx = 0; segIdx < block->getNumSegments(); ++segIdx) { const LodSegment* segment = block->getSegment(segIdx); const Genome* genome = segment->getSequence()->getGenome(); // ADD TO MAP pair<SegmentMap::iterator, bool> res = segMap.insert( pair<const Genome*, SegmentSet*>(genome, NULL)); if (res.second == true) { assert(res.first->second == NULL); res.first->second = new SegmentSet(); } res.first->second->insert(segment); } updateBlockEdges(inParent, segMap, block, bottom, top); // free the temporary sets! for (SegmentMap::iterator mapIt = segMap.begin(); mapIt != segMap.end(); ++mapIt) { delete mapIt->second; } } }
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(); } }
void GenomeCopyTest::createCallBack(Alignment *alignment) { hal_size_t alignmentSize = alignment->getNumGenomes(); CuAssertTrue(_testCase, alignmentSize == 0); // Hacky: Need a different alignment to test copying the bottom // segments correctly. (the names of a node's children are used // when copying bottom segments, and two genomes can't have the same // name in the same alignment) _path = getTempFile(); _secondAlignment = AlignmentPtr(getTestAlignmentInstances(alignment->getStorageFormat(), _path, WRITE_ACCESS | CREATE_ACCESS)); Genome *ancGenome = alignment->addRootGenome("AncGenome", 0); Genome *leafGenome = alignment->addLeafGenome("LeafGenome1", "AncGenome", 0); // This genome will test copyDimensions, copyTopSegments, // copyBottomSegments, copySequence, copyMetadata Genome *copyRootGenome = _secondAlignment->addRootGenome("copyRootGenome", 0); Genome *copyLeafGenome = _secondAlignment->addLeafGenome("LeafGenome1", "copyRootGenome", 0); MetaData *ancMeta = ancGenome->getMetaData(); ancMeta->set("Young", "Jeezy"); vector<Sequence::Info> seqVec(1); seqVec[0] = Sequence::Info("Sequence", 1000000, 0, 700000); ancGenome->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 0); leafGenome->setDimensions(seqVec); string ancSeq = "CAT"; hal_index_t n = ancGenome->getSequenceLength(); DnaIteratorPtr dnaIt = ancGenome->getDnaIterator(); for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) { size_t i = dnaIt->getArrayIndex() % ancSeq.size(); dnaIt->setBase(ancSeq[i]); } dnaIt->flush(); n = leafGenome->getSequenceLength(); dnaIt = leafGenome->getDnaIterator(); for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) { size_t i = dnaIt->getArrayIndex() % ancSeq.size(); dnaIt->setBase(ancSeq[i]); } dnaIt->flush(); TopSegmentIteratorPtr topIt = leafGenome->getTopSegmentIterator(); n = leafGenome->getNumTopSegments(); for (; topIt->getArrayIndex() < n; topIt->toRight()) { topIt->setCoordinates(topIt->getArrayIndex(), 1); topIt->tseg()->setParentIndex(3); topIt->tseg()->setParentReversed(true); topIt->tseg()->setBottomParseIndex(5); if (topIt->getArrayIndex() != 6) { topIt->tseg()->setNextParalogyIndex(6); } else { topIt->tseg()->setNextParalogyIndex(7); } } BottomSegmentIteratorPtr botIt = ancGenome->getBottomSegmentIterator(); n = ancGenome->getNumBottomSegments(); for (; botIt->getArrayIndex() < n; botIt->toRight()) { botIt->setCoordinates(botIt->getArrayIndex(), 1); botIt->bseg()->setChildIndex(0, 3); botIt->bseg()->setChildReversed(0, true); botIt->bseg()->setTopParseIndex(5); } seqVec[0] = Sequence::Info("Sequence", 3300, 0, 1100); copyRootGenome->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 3300, 2200, 0); copyLeafGenome->setDimensions(seqVec); string copySeq = "TAG"; dnaIt = copyRootGenome->getDnaIterator(); n = copyRootGenome->getSequenceLength(); for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) { size_t i = dnaIt->getArrayIndex() % copySeq.size(); dnaIt->setBase(copySeq[i]); } dnaIt->flush(); dnaIt = copyLeafGenome->getDnaIterator(); n = copyLeafGenome->getSequenceLength(); for (; dnaIt->getArrayIndex() < n; dnaIt->toRight()) { size_t i = dnaIt->getArrayIndex() % copySeq.size(); dnaIt->setBase(copySeq[i]); } dnaIt->flush(); topIt = copyLeafGenome->getTopSegmentIterator(); n = copyLeafGenome->getNumTopSegments(); for (; topIt->getArrayIndex() < n; topIt->toRight()) { topIt->setCoordinates(7, 8); topIt->tseg()->setParentIndex(9); topIt->tseg()->setParentReversed(false); topIt->tseg()->setBottomParseIndex(11); if (topIt->getArrayIndex() != 12) { topIt->tseg()->setNextParalogyIndex(12); } else { topIt->tseg()->setNextParalogyIndex(7); } } botIt = copyRootGenome->getBottomSegmentIterator(); n = copyRootGenome->getNumBottomSegments(); for (; botIt->getArrayIndex() < n; botIt->toRight()) { botIt->setCoordinates(6, 7); botIt->bseg()->setChildIndex(0, 8); botIt->bseg()->setChildReversed(0, false); botIt->bseg()->setTopParseIndex(10); } ancGenome->copy(copyRootGenome); leafGenome->copy(copyLeafGenome); _secondAlignment->close(); }
void MappedSegmentMapExtraParalogsTest::createCallBack(AlignmentPtr alignment) { vector<Sequence::Info> seqVec(1); BottomSegmentIteratorPtr bi; BottomSegmentStruct bs; TopSegmentIteratorPtr ti; TopSegmentStruct ts; // Set up a case where all the segments of grandChild1 coalesce with // the first segment of grandChild2, but only if using the root as // the coalescence limit. Otherwise only the first segments map to // each other. Genome* root = alignment->addRootGenome("root"); Genome* parent = alignment->addLeafGenome("parent", "root", 1); Genome* grandChild1 = alignment->addLeafGenome("grandChild1", "parent", 1); Genome* grandChild2 = alignment->addLeafGenome("grandChild2", "parent", 1); seqVec[0] = Sequence::Info("Sequence", 3, 0, 1); root->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 9, 3, 3); parent->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 9, 3, 0); grandChild1->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 9, 3, 0); grandChild2->setDimensions(seqVec); root->setString("CCC"); parent->setString("CCCTACGTG"); grandChild1->setString("CCCTACGTG"); grandChild2->setString("CCCTACGTG"); bi = root->getBottomSegmentIterator(); bs.set(0, 3); bs._children.push_back(pair<hal_size_t, bool>(0, false)); bs.applyTo(bi); ti = parent->getTopSegmentIterator(); ts.set(0, 3, 0, false, NULL_INDEX, 1); ts.applyTo(ti); ti->toRight(); ts.set(3, 3, 0, false, NULL_INDEX, 2); ts.applyTo(ti); ti->toRight(); ts.set(6, 3, 0, false, NULL_INDEX, 0); ts.applyTo(ti); bi = parent->getBottomSegmentIterator(); bs.set(0, 3); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(0, true)); bs._children.push_back(pair<hal_size_t, bool>(0, false)); bs.applyTo(bi); bi->toRight(); bs.set(3, 3); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(1, true)); bs._children.push_back(pair<hal_size_t, bool>(NULL_INDEX, true)); bs.applyTo(bi); bi->toRight(); bs.set(6, 3); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(2, true)); bs._children.push_back(pair<hal_size_t, bool>(NULL_INDEX, false)); bs.applyTo(bi); ti = grandChild1->getTopSegmentIterator(); ts.set(0, 3, 0, true); ts.applyTo(ti); ti->toRight(); ts.set(3, 3, 1, true); ts.applyTo(ti); ti->toRight(); ts.set(6, 3, 2, true); ts.applyTo(ti); ti = grandChild2->getTopSegmentIterator(); ts.set(0, 3, 0, false); ts.applyTo(ti); ti->toRight(); ts.set(3, 3, NULL_INDEX, true); ts.applyTo(ti); ti->toRight(); ts.set(6, 3, NULL_INDEX, false); ts.applyTo(ti); parent->fixParseInfo(); }
void MappedSegmentMapUpTest::createCallBack(AlignmentPtr alignment) { vector<Sequence::Info> seqVec(1); BottomSegmentIteratorPtr bi; BottomSegmentStruct bs; TopSegmentIteratorPtr ti; TopSegmentStruct ts; // setup simple case were there is an edge from a parent to // child1 and it is reversed and nonreversed to child2 Genome* parent = alignment->addRootGenome("parent"); Genome* child1 = alignment->addLeafGenome("child1", "parent", 1); Genome* child2 = alignment->addLeafGenome("child2", "parent", 1); // add a bunch of grandchildren with no rearrangemnts to test // simple parsing Genome* g1 = alignment->addLeafGenome("g1", "child2", 1); Genome* g2 = alignment->addLeafGenome("g2", "g1", 1); Genome* g3 = alignment->addLeafGenome("g3", "g2", 1); Genome* g4 = alignment->addLeafGenome("g4", "g3", 1); Genome* g5 = alignment->addLeafGenome("g5", "g4", 1); // add some with random inversions Genome* gi1 = alignment->addLeafGenome("gi1", "child1", 1); Genome* gi2 = alignment->addLeafGenome("gi2", "gi1", 1); Genome* gi3 = alignment->addLeafGenome("gi3", "gi2", 1); Genome* gi4 = alignment->addLeafGenome("gi4", "gi3", 1); Genome* gi5 = alignment->addLeafGenome("gi5", "gi4", 1); Genome* gs[] = {g1, g2, g3, g4, g5}; Genome* gis[] = {gi1, gi2, gi3, gi4, gi5}; seqVec[0] = Sequence::Info("Sequence", 12, 0, 1); parent->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 1, 6); child1->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 1, 6); child2->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 6, 4); g1->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 4, 3); g2->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 3, 2); g3->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 2, 12); g4->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 12, 0); g5->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 6, 4); gi1->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 4, 3); gi2->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 3, 2); gi3->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 2, 12); gi4->setDimensions(seqVec); seqVec[0] = Sequence::Info("Sequence", 12, 12, 0); gi5->setDimensions(seqVec); parent->setString("CCCTACTTGTGC"); child1->setString("CCCTACTTGTGC"); child2->setString("CCCTACTTGTGC"); for (size_t i = 0; i < 5; ++i) { gs[i]->setString("TCCTACTTGTGC"); gis[i]->setString("TCCTACTTGTGC"); } bi = parent->getBottomSegmentIterator(); bs.set(0, 12); bs._children.push_back(pair<hal_size_t, bool>(0, true)); bs._children.push_back(pair<hal_size_t, bool>(0, false)); bs.applyTo(bi); ti = child1->getTopSegmentIterator(); ts.set(0, 12, 0, true, 0); ts.applyTo(ti); ti = child2->getTopSegmentIterator(); ts.set(0, 12, 0, false, 0); ts.applyTo(ti); for (size_t i = 0; i < 6; ++i) { bi = child2->getBottomSegmentIterator(i); bs.set(i * 2, 2, 0); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(i, false)); bs.applyTo(bi); ti = g1->getTopSegmentIterator(i); ts.set(i * 2, 2, i, false); ts.applyTo(ti); } for (size_t i = 0; i < 6; ++i) { bi = child1->getBottomSegmentIterator(i); bs.set(i * 2, 2, 0); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(i, false)); bs.applyTo(bi); ti = gi1->getTopSegmentIterator(i); ts.set(i * 2, 2, i, false); ts.applyTo(ti); } for (size_t i = 0; i < 5; ++i) { const Genome* g = gs[i]; const Genome* parent = g->getParent(); const Genome* child = i == 4 ? NULL : g->getChild(0); hal_size_t segLen = g->getSequenceLength() / g->getNumTopSegments(); hal_size_t psegLen = parent->getSequenceLength() / parent->getNumTopSegments(); hal_size_t csegLen = 0; if (child) { csegLen = child->getSequenceLength() / child->getNumTopSegments(); } for (size_t j = 0; j < g->getNumTopSegments(); ++j) { bool inv = false; bi = parent->getBottomSegmentIterator(j); bs.set(j * segLen, segLen, (j * segLen) / psegLen); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(j, inv)); bs.applyTo(bi); hal_index_t bparse = NULL_INDEX; if (child != NULL) { bparse = (j * segLen) / csegLen; } ti = g->getTopSegmentIterator(j); ts.set(j * segLen, segLen, j, inv, bparse); ts.applyTo(ti); } } for (size_t i = 0; i < 5; ++i) { const Genome* g = gis[i]; const Genome* parent = g->getParent(); const Genome* child = i == 4 ? NULL : g->getChild(0); hal_size_t segLen = g->getSequenceLength() / g->getNumTopSegments(); hal_size_t psegLen = parent->getSequenceLength() / parent->getNumTopSegments(); hal_size_t csegLen = 0; if (child) { csegLen = child->getSequenceLength() / child->getNumTopSegments(); } for (size_t j = 0; j < g->getNumTopSegments(); ++j) { bool inv = rand() % 4 == 0; bi = parent->getBottomSegmentIterator(j); bs.set(j * segLen, segLen, (j * segLen) / psegLen); bs._children.clear(); bs._children.push_back(pair<hal_size_t, bool>(j, inv)); bs.applyTo(bi); hal_index_t bparse = NULL_INDEX; if (child != NULL) { bparse = (j * segLen) / csegLen; } ti = g->getTopSegmentIterator(j); ts.set(j * segLen, segLen, j, inv, bparse); ts.applyTo(ti); } } }