public void GetCompressedSequence(IChromosome chromosome)
{
var indexEntry = GetIndexEntry(chromosome.EnsemblName);
if (indexEntry == null)
{
return;
}
// jump to that offset
_stream.Position = indexEntry.FileOffset;
// set the data
int numBufferBytes = CompressedSequence.GetNumBufferBytes(indexEntry.NumBases);
Sequence.Set(indexEntry.NumBases, _reader.ReadBytes(numBufferBytes), indexEntry.MaskedEntries, indexEntry.SequenceOffset);
}
public CompressedSequenceReader(Stream stream)
{
_stream = stream;
_reader = new ExtendedBinaryReader(stream);
Sequence = new CompressedSequence();
RefNameToChromosome = new Dictionary <string, IChromosome>();
RefIndexToChromosome = new Dictionary <ushort, IChromosome>();
CheckHeaderVersion();
LoadHeader();
// jump to the index offset
_stream.Position = _indexOffset;
LoadIndex();
LoadMaskedIntervals();
VerifyEofTag();
}
