TempReadAlignment::TempReadAlignment(AlignmentPtr alignment,
char* path)
: _path(path)
{
alignment->close();
alignment->open(_path, true);
_alignment = alignment;
}
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);
}
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();
}