public void Serialization()
{
ICytogeneticBands expectedCytogeneticBands = GetCytogeneticBands();
ICytogeneticBands observedCytogeneticBands;
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
expectedCytogeneticBands.Write(writer);
}
ms.Seek(0, SeekOrigin.Begin);
using (var reader = new ExtendedBinaryReader(ms))
{
var bands = CytogeneticBands.Read(reader);
observedCytogeneticBands = new CytogeneticBands(bands, _renamer);
}
}
var expectedCytogeneticBand = expectedCytogeneticBands.GetCytogeneticBand(10, 88400000, 92900000);
var observedCytogeneticBand = observedCytogeneticBands.GetCytogeneticBand(10, 88400000, 92900000);
Assert.NotNull(observedCytogeneticBand);
Assert.Equal(expectedCytogeneticBand, observedCytogeneticBand);
}
private static void WriteReference(ILogger logger, string outputPath, CompressedSequenceReader reader,
IChromosome chromosome, string referenceBases, int offset)
{
logger.Write("- writing reference bases... ");
var cytogeneticBands = new CytogeneticBands(reader.CytogeneticBands);
using (var writer = new CompressedSequenceWriter(FileUtilities.GetCreateStream(outputPath),
reader.ReferenceMetadataList, cytogeneticBands, reader.Assembly))
{
writer.Write(chromosome.EnsemblName, referenceBases, offset);
}
logger.WriteLine("finished.");
}
/// <summary>
/// loads the header
/// </summary>
private void LoadHeader()
{
// grab the index and masked intervals offsets
_indexOffset = _reader.ReadInt64();
_maskedIntervalsOffset = _reader.ReadInt64();
// skip the creation time
_reader.ReadOptInt64();
// grab the reference metadata
int numRefSeqs = _reader.ReadOptInt32();
for (int i = 0; i < numRefSeqs; i++)
{
Metadata.Add(ReferenceMetadata.Read(_reader));
}
// update the chromosome renamer
_compressedSequence.Renamer.AddReferenceMetadata(Metadata);
// read the cytogenetic bands
_compressedSequence.CytogeneticBands = new CytogeneticBands(CytogeneticBands.Read(_reader), _compressedSequence.Renamer);
// read the genome assembly
_compressedSequence.GenomeAssembly = (GenomeAssembly)_reader.ReadByte();
// grab the data start tag
ulong dataStartTag = _reader.ReadUInt64();
if (dataStartTag != CompressedSequenceCommon.DataStartTag)
{
throw new UserErrorException($"The data start tag does not match the expected values: Obs: {dataStartTag} vs Exp: {CompressedSequenceCommon.DataStartTag}");
}
_dataStartOffset = _stream.Position;
}
public ReferenceSequenceProvider(Stream stream)
{
_currentChromosome = new EmptyChromosome(string.Empty);
_sequenceReader = new CompressedSequenceReader(stream);
_cytogeneticBands = new CytogeneticBands(_sequenceReader.CytogeneticBands);
}
