void GenomeStringTest::createCallBack(Alignment *alignment) {
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
hal_size_t seqLength = 28889943;
Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
vector<Sequence::Info> seqVec(1);
seqVec[0] = Sequence::Info("Sequence", seqLength, 5000, 700000);
ancGenome->setDimensions(seqVec);
_string = randomString(seqLength);
ancGenome->setString(_string);
}
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);
}
// Test copying when the sequences aren't in the same order.
//
// Create an alignment with "Sequence1" positions aligned to
// "Sequence1" positions, and "Sequence2" to "Sequence2", but try
// copying the segments to an alignment with "Sequence2" before
// "Sequence1" in the ordering.
void GenomeCopySegmentsWhenSequencesOutOfOrderTest::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, CREATE_ACCESS));
Genome *rootGenome = alignment->addRootGenome("root", 0);
Genome *internalGenome = alignment->addLeafGenome("internal", "root", 0);
Genome *leaf1Genome = alignment->addLeafGenome("leaf1", "root", 0);
Genome *leaf2Genome = alignment->addLeafGenome("leaf2", "internal", 0);
Genome *copyRootGenome = _secondAlignment->addRootGenome("root", 0);
Genome *copyInternalGenome = _secondAlignment->addLeafGenome("internal", "root", 0);
Genome *copyLeaf1Genome = _secondAlignment->addLeafGenome("leaf1", "root", 0);
Genome *copyLeaf2Genome = _secondAlignment->addLeafGenome("leaf2", "internal", 0);
vector<Sequence::Info> seqVec(2);
seqVec[0] = Sequence::Info("Sequence1", 130, 0, 13);
seqVec[1] = Sequence::Info("Sequence2", 170, 0, 17);
rootGenome->setDimensions(seqVec);
rootGenome->setString(randomString(rootGenome->getSequenceLength()));
seqVec[0] = Sequence::Info("Sequence1", 130, 13, 13);
seqVec[1] = Sequence::Info("Sequence2", 170, 17, 17);
internalGenome->setDimensions(seqVec);
internalGenome->setString(randomString(internalGenome->getSequenceLength()));
seqVec[0] = Sequence::Info("Sequence1", 130, 13, 0);
seqVec[1] = Sequence::Info("Sequence2", 170, 17, 0);
leaf1Genome->setDimensions(seqVec);
leaf1Genome->setString(randomString(leaf1Genome->getSequenceLength()));
leaf2Genome->setDimensions(seqVec);
leaf2Genome->setString(randomString(leaf2Genome->getSequenceLength()));
setTopSegments(internalGenome, 10);
setTopSegments(leaf1Genome, 10);
setTopSegments(leaf2Genome, 10);
setBottomSegments(rootGenome, 10);
setBottomSegments(internalGenome, 10);
rootGenome->fixParseInfo();
internalGenome->fixParseInfo();
leaf1Genome->fixParseInfo();
leaf2Genome->fixParseInfo();
seqVec[0] = Sequence::Info("Sequence1", 130, 0, 13);
seqVec[1] = Sequence::Info("Sequence2", 170, 0, 17);
copyRootGenome->setDimensions(seqVec);
copyRootGenome->setString(randomString(copyRootGenome->getSequenceLength()));
seqVec[0] = Sequence::Info("Sequence1", 130, 13, 0);
seqVec[1] = Sequence::Info("Sequence2", 170, 17, 0);
copyLeaf1Genome->setDimensions(seqVec);
copyLeaf2Genome->setDimensions(seqVec);
copyLeaf1Genome->setString(randomString(copyLeaf1Genome->getSequenceLength()));
copyLeaf2Genome->setString(randomString(copyLeaf2Genome->getSequenceLength()));
seqVec[0] = Sequence::Info("Sequence2", 170, 17, 17);
seqVec[1] = Sequence::Info("Sequence1", 130, 13, 13);
copyInternalGenome->setDimensions(seqVec);
copyInternalGenome->setString(randomString(copyInternalGenome->getSequenceLength()));
rootGenome->copyBottomDimensions(copyRootGenome);
rootGenome->copyBottomSegments(copyRootGenome);
copyRootGenome->fixParseInfo();
internalGenome->copyBottomDimensions(copyInternalGenome);
internalGenome->copyBottomSegments(copyInternalGenome);
internalGenome->copyTopDimensions(copyInternalGenome);
internalGenome->copyTopSegments(copyInternalGenome);
copyInternalGenome->fixParseInfo();
leaf1Genome->copyTopDimensions(copyLeaf1Genome);
leaf1Genome->copyTopSegments(copyLeaf1Genome);
copyLeaf1Genome->fixParseInfo();
leaf2Genome->copyTopDimensions(copyLeaf2Genome);
leaf2Genome->copyTopSegments(copyLeaf2Genome);
copyLeaf2Genome->fixParseInfo();
_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);
}
}
}
