void HDF5Genome::setGenomeBottomDimensions(
const vector<Sequence::UpdateInfo>& bottomDimensions)
{
hal_size_t numBottomSegments = 0;
for (vector<Sequence::UpdateInfo>::const_iterator i
= bottomDimensions.begin(); i != bottomDimensions.end();
++i)
{
numBottomSegments += i->_numSegments;
}
H5::Exception::dontPrint();
try
{
DataSet d = _group.openDataSet(bottomArrayName);
_group.unlink(bottomArrayName);
}
catch (H5::Exception){}
hal_size_t numChildren = _alignment->getChildNames(_name).size();
// scale down the chunk size in order to keep chunks proportional to
// the size of a bottom segment with two children.
hsize_t chunk;
_dcprops.getChunk(1, &chunk);
double scale = numChildren < 10 ? 1. : 10. / numChildren;
chunk *= scale;
DSetCreatPropList botDC;
botDC.copy(_dcprops);
botDC.setChunk(1, &chunk);
_bottomArray.create(&_group, bottomArrayName,
HDF5BottomSegment::dataType(numChildren),
numBottomSegments + 1, &botDC, _numChunksInArrayBuffer);
_numChildrenInBottomArray = numChildren;
_childCache.clear();
}
void HDF5Genome::setDimensions(
const vector<Sequence::Info>& sequenceDimensions,
bool storeDNAArrays)
{
_totalSequenceLength = 0;
hal_size_t totalSeq = sequenceDimensions.size();
hal_size_t maxName = 0;
// Copy segment dimensions to use the external interface
vector<Sequence::UpdateInfo> topDimensions;
topDimensions.reserve(sequenceDimensions.size());
vector<Sequence::UpdateInfo> bottomDimensions;
bottomDimensions.reserve(sequenceDimensions.size());
// Compute summary info from the list of sequence Dimensions
for (vector<Sequence::Info>::const_iterator i = sequenceDimensions.begin();
i != sequenceDimensions.end();
++i)
{
_totalSequenceLength += i->_length;
maxName = max(static_cast<hal_size_t>(i->_name.length()), maxName);
topDimensions.push_back(
Sequence::UpdateInfo(i->_name, i->_numTopSegments));
bottomDimensions.push_back(
Sequence::UpdateInfo(i->_name, i->_numBottomSegments));
}
// Unlink the DNA and segment arrays if they exist (using
// exceptions is the only way I know how right now). Note that
// the file needs to be refactored to take advantage of the new
// space.
H5::Exception::dontPrint();
try
{
DataSet d = _group.openDataSet(dnaArrayName);
_group.unlink(dnaArrayName);
}
catch (H5::Exception){}
try
{
DataSet d = _group.openDataSet(sequenceIdxArrayName);
_group.unlink(sequenceIdxArrayName);
}
catch (H5::Exception){}
try
{
DataSet d = _group.openDataSet(sequenceNameArrayName);
_group.unlink(sequenceNameArrayName);
}
catch (H5::Exception){}
if (_totalSequenceLength > 0 && storeDNAArrays == true)
{
hal_size_t arrayLength = _totalSequenceLength / 2;
if (_totalSequenceLength % 2)
{
++arrayLength;
_rup->set(rupGroupName, "1");
}
else
{
_rup->set(rupGroupName, "0");
}
hsize_t chunk;
_dcprops.getChunk(1, &chunk);
// enalarge chunk size because dna bases are so much smaller
// than segments. (about 30x). we default to 10x enlargement
// since the seem to compress about 3x worse.
chunk *= dnaChunkScale;
DSetCreatPropList dnaDC;
dnaDC.copy(_dcprops);
dnaDC.setChunk(1, &chunk);
_dnaArray.create(&_group, dnaArrayName, HDF5DNA::dataType(),
arrayLength, &dnaDC, _numChunksInArrayBuffer);
}
if (totalSeq > 0)
{
_sequenceIdxArray.create(&_group, sequenceIdxArrayName,
HDF5Sequence::idxDataType(),
totalSeq + 1, &_dcprops, _numChunksInArrayBuffer);
_sequenceNameArray.create(&_group, sequenceNameArrayName,
HDF5Sequence::nameDataType(maxName + 1),
totalSeq, &_dcprops, _numChunksInArrayBuffer);
writeSequences(sequenceDimensions);
}
// Do the same as above for the segments.
setGenomeTopDimensions(topDimensions);
setGenomeBottomDimensions(bottomDimensions);
_parentCache = NULL;
_childCache.clear();
}
