void LodManager::checkAlignment(hal_size_t minQuery,
const string& path,
AlignmentConstPtr alignment)
{
if (alignment->getNumGenomes() == 0)
{
stringstream ss;
ss << "No genomes found in base alignment specified in " << path;
throw hal_exception(ss.str());
}
#ifndef NDEBUG
if (minQuery == 0)
{
vector<string> leafNames = alignment->getLeafNamesBelow(
alignment->getRootName());
string name = !leafNames.empty() ? leafNames[0] : alignment->getRootName();
const Genome* genome = alignment->openGenome(name);
bool seqFound = genome->containsDNAArray();
alignment->closeGenome(genome);
if (seqFound == false)
{
stringstream ss;
ss << "HAL file for highest level of detail (0) in " << path
<< "must contain DNA sequence information.";
throw hal_exception(ss.str());
}
}
#endif
}
void MafExport::convertEntireAlignment(ostream& mafStream,
AlignmentConstPtr alignment)
{
hal_size_t appendCount = 0;
size_t numBlocks = 0;
_mafStream = &mafStream;
_alignment = alignment;
writeHeader();
// Load in all leaves from alignment
vector<string> leafNames = alignment->getLeafNamesBelow(alignment->getRootName());
vector<const Genome *> leafGenomes;
for (hal_size_t i = 0; i < leafNames.size(); i++) {
const Genome *genome = alignment->openGenome(leafNames[i]);
assert(genome != NULL);
leafGenomes.push_back(genome);
}
ColumnIterator::VisitCache visitCache;
// Go through all the genomes one by one, and spit out any columns
// they participate in that we haven't seen.
for (hal_size_t i = 0; i < leafGenomes.size(); i++) {
const Genome *genome = leafGenomes[i];
ColumnIteratorConstPtr colIt = genome->getColumnIterator(NULL,
0,
0,
NULL_INDEX,
_noDupes,
_noAncestors);
colIt->setVisitCache(&visitCache);
for (;;) {
if (appendCount == 0) {
_mafBlock.initBlock(colIt, _ucscNames, _printTree);
assert(_mafBlock.canAppendColumn(colIt) == true);
}
if (_mafBlock.canAppendColumn(colIt) == false)
{
// erase empty entries from the column. helps when there are
// millions of sequences (ie from fastas with lots of scaffolds)
if (numBlocks++ % 1000 == 0)
{
colIt->defragment();
}
if (appendCount > 0)
{
mafStream << _mafBlock << '\n';
}
_mafBlock.initBlock(colIt, _ucscNames, _printTree);
assert(_mafBlock.canAppendColumn(colIt) == true);
}
_mafBlock.appendColumn(colIt);
appendCount++;
if (colIt->lastColumn()) {
// Have to break here because otherwise
// colIt->toRight() will crash.
break;
}
colIt->toRight();
}
// Copy over the updated visit cache information. This is a
// deep copy, so it's slow, but necessary to preserve the
// column iterator ownership of the visit cache
visitCache.clear();
ColumnIterator::VisitCache *newVisitCache = colIt->getVisitCache();
for(ColumnIterator::VisitCache::iterator it = newVisitCache->begin();
it != newVisitCache->end(); it++) {
visitCache[it->first] = new PositionCache(*it->second);
}
}
// if nothing was ever added (seems to happen in corner case where
// all columns violate unique), mafBlock ostream operator will crash
// so we do following check
if (appendCount > 0)
{
mafStream << _mafBlock << endl;
}
}