public void Compress(string bases, TwoBitSequence twoBitSequence)
{
twoBitSequence.Allocate(bases.Length);
byte num1 = 0;
var index1 = 0;
var num2 = 0;
foreach (char index2 in bases)
{
byte num3 = _convertBaseToNumber[index2];
if (num3 == 10)
{
num3 = 0;
}
num1 = (byte)((uint)num1 << 2 | num3);
++num2;
if (num2 != 4)
{
continue;
}
twoBitSequence.Buffer[index1] = num1;
num1 = 0;
num2 = 0;
++index1;
}
if (num2 != 0)
{
twoBitSequence.Buffer[index1] = (byte)((uint)num1 << (4 - num2) * 2);
}
for (var index2 = 0; index2 < bases.Length; ++index2)
{
if (bases[index2] != 'N')
{
continue;
}
int begin = index2;
int end = index2;
for (++index2; index2 < bases.Length && bases[index2] == 'N'; ++index2)
{
end = index2;
}
var maskedEntry = new MaskedEntry(begin, end);
twoBitSequence.MaskedIntervals.Add(maskedEntry);
}
}
public CompressedSequenceWriter(Stream stream, IReadOnlyCollection <ReferenceMetadata> referenceMetadataList,
ISerializable genomeCytobands, GenomeAssembly genomeAssembly)
{
_stream = stream;
_writer = new ExtendedBinaryWriter(_stream);
_refSeqNames = new List <string>();
_refSeqIndex = new List <SequenceIndexEntry>();
_twoBitSequence = new TwoBitSequence();
_sequenceCompressor = new SequenceCompressor();
_refSeqMaskedIntervals = new List <List <MaskedEntry> >();
WriteHeader(referenceMetadataList, genomeCytobands, genomeAssembly);
}
private void Dispose(bool disposing)
{
if (disposing)
{
WriteReferenceSequenceIndex();
WriteMaskedIntervals();
WriteEofTag();
_stream.Dispose();
}
_refSeqIndex = null;
_refSeqMaskedIntervals = null;
_twoBitSequence = null;
_sequenceCompressor = null;
_headerDataOffset = 0L;
_indexOffset = 0L;
_maskedIntervalsOffset = 0L;
}