void GenomeMetaTest::createCallBack(Alignment *alignment) {
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
MetaData *ancMeta = ancGenome->getMetaData();
ancMeta->set("Young", "Jeezy");
}
void GenomeCreateTest::createCallBack(Alignment *alignment) {
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
Genome *leaf1Genome = alignment->addLeafGenome("Leaf1", "AncGenome", 0.1);
Genome *leaf2Genome = alignment->addLeafGenome("Leaf2", "AncGenome", 0.2);
Genome *leaf3Genome = alignment->addLeafGenome("Leaf3", "AncGenome", 0.3);
MetaData *ancMeta = ancGenome->getMetaData();
ancMeta->set("Young", "Jeezy");
vector<Sequence::Info> seqVec(1);
seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 700000);
ancGenome->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 1000000, 700000, 0);
leaf1Genome->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 2000000, 700000, 0);
leaf2Genome->setDimensions(seqVec);
seqVec[0] = Sequence::Info("Sequence", 3000000, 700000, 0);
leaf3Genome->setDimensions(seqVec);
}
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();
}
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();
}
