void Genome::copyTopSegments(Genome *dest) const
{
const Genome *inParent = getParent();
const Genome *outParent = dest->getParent();
TopSegmentIteratorConstPtr inTop = getTopSegmentIterator();
TopSegmentIteratorPtr outTop = dest->getTopSegmentIterator();
hal_size_t n = dest->getNumTopSegments();
assert(n == 0 || n == getNumTopSegments());
if (n == 0) {
// Nothing to do if there are no top segments.
return;
}
BottomSegmentIteratorConstPtr inParentBottomSegIt = inParent->getBottomSegmentIterator();
BottomSegmentIteratorConstPtr outParentBottomSegIt = outParent->getBottomSegmentIterator();
for (; (hal_size_t)inTop->getArrayIndex() < n; inTop->toRight(),
outTop->toRight())
{
hal_index_t genomePos = inTop->getStartPosition();
assert(genomePos != NULL_INDEX);
string inSeqName = getSequenceBySite(genomePos)->getName();
string outSeqName = dest->getSequenceBySite(genomePos)->getName();
// if (inSeqName != outSeqName) {
// stringstream ss;
// ss << "When copying top segments from " << getName() << " to " << dest->getName() << ": sequence " << inSeqName << " != " << outSeqName << " at site " << genomePos;
// throw hal_exception(ss.str());
// }
outTop->setCoordinates(inTop->getStartPosition(), inTop->getLength());
outTop->setParentIndex(inTop->getParentIndex());
outTop->setParentReversed(inTop->getParentReversed());
outTop->setBottomParseIndex(inTop->getBottomParseIndex());
outTop->setNextParalogyIndex(inTop->getNextParalogyIndex());
// Check that the sequences from the bottom segments we point to are the same. If not, correct the indices so that they are.
if (inTop->getParentIndex() != NULL_INDEX) {
inParentBottomSegIt->toParent(inTop);
const Sequence *inParentSequence = inParentBottomSegIt->getSequence();
const Sequence *outParentSequence = outParent->getSequence(inParentSequence->getName());
hal_index_t inParentSegmentOffset = inTop->getParentIndex() - inParentSequence->getBottomSegmentArrayIndex();
hal_index_t outParentSegmentIndex = inParentSegmentOffset + outParentSequence->getBottomSegmentArrayIndex();
outTop->setParentIndex(outParentSegmentIndex);
}
}
}
int main(int argc, char** argv)
{
CLParserPtr optionsParser = hdf5CLParserInstance();
optionsParser->setDescription("Rertrieve chain (pairwise alignment) "
"information from a hal database.\n"
"WARNING: THIS TOOL WAS NEVER FINISHED OR"
" TESTED. USE AT OWN RISK. PLEASE "
"CONSIDER halLiftover --outPSL INSTEAD.");
optionsParser->addArgument("halFile", "path to hal file to analyze");
optionsParser->addArgument("genome", "(query) genome to process");
optionsParser->addOption("sequence", "sequence name in query genome ("
"all sequences if not specified)", "\"\"");
optionsParser->addOption("start", "start position in query genome", 0);
optionsParser->addOption("length", "maximum length of chain to output.", 0);
optionsParser->addOption("chainFile", "path for output file. stdout if not"
" specified", "\"\"");
optionsParser->addOption("maxGap",
"maximum indel length to be considered a gap within"
" a chain.",
20);
string halPath;
string chainPath;
string genomeName;
string sequenceName;
hal_size_t start;
hal_size_t length;
hal_size_t maxGap;
try
{
optionsParser->parseOptions(argc, argv);
halPath = optionsParser->getArgument<string>("halFile");
genomeName = optionsParser->getArgument<string>("genome");
sequenceName = optionsParser->getOption<string>("sequence");
start = optionsParser->getOption<hal_size_t>("start");
length = optionsParser->getOption<hal_size_t>("length");
chainPath = optionsParser->getOption<string>("chainFile");
maxGap = optionsParser->getOption<hal_size_t>("maxGap");
}
catch(exception& e)
{
cerr << e.what() << endl;
optionsParser->printUsage(cerr);
exit(1);
}
try
{
cerr << "WARNING: THIS TOOL WAS NEVER FINISHED OR TESTED. USE AT OWN RISK."
<< " PLEASE CONSIDER halLiftover --outPSL INSTEAD." <<endl;
AlignmentConstPtr alignment = openHalAlignmentReadOnly(halPath,
optionsParser);
const Genome* genome = alignment->openGenome(genomeName);
if (genome == NULL)
{
throw hal_exception(string("Genome not found: ") + genomeName);
}
hal_index_t endPosition =
length > 0 ? start + length : genome->getSequenceLength();
const Sequence* sequence = NULL;
if (sequenceName != "\"\"")
{
sequence = genome->getSequence(sequenceName);
if (sequence == NULL)
{
throw hal_exception(string("Sequence not found: ") + sequenceName);
}
start += sequence->getStartPosition();
endPosition =
length > 0 ? start + length : sequence->getSequenceLength();
}
ofstream ofile;
ostream& outStream = chainPath == "\"\"" ? cout : ofile;
if (chainPath != "\"\"")
{
ofile.open(chainPath.c_str());
if (!ofile)
{
throw hal_exception(string("Error opening output file ") +
chainPath);
}
}
TopSegmentIteratorConstPtr top = genome->getTopSegmentIterator();
top->toSite(start, false);
// do slicing here;
GappedTopSegmentIteratorConstPtr gtop =
genome->getGappedTopSegmentIterator(top->getArrayIndex(), maxGap);
// need to review!
Chain chain;
chain._id = 0;
while (gtop->getRightArrayIndex() <
(hal_index_t)genome->getNumTopSegments() &&
gtop->getLeft()->getStartPosition() < endPosition)
{
if (gtop->hasParent() == true)
{
hal_offset_t leftOffset = 0;
if ((hal_index_t)start > gtop->getStartPosition()
&& (hal_index_t)start < gtop->getEndPosition())
{
leftOffset = start - gtop->getStartPosition() ;
}
hal_offset_t rightOffset = 0;
if (endPosition - 1 > gtop->getStartPosition()
&& endPosition - 1 < gtop->getEndPosition())
{
rightOffset = gtop->getEndPosition() + 1 - endPosition;
}
// need to do offsets for edge cases
gtIteratorToChain(gtop, chain, leftOffset, rightOffset);
outStream << chain;
++chain._id;
}
gtop->toRight();
}
}
catch(hal_exception& e)
{
cerr << "hal exception caught: " << e.what() << endl;
return 1;
}
catch(exception& e)
{
cerr << "Exception caught: " << e.what() << endl;
return 1;
}
return 0;
}
