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 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();
}
}
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();
}