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 void WriteHeader(List <ReferenceMetadata> referenceMetadataList, ICytogeneticBands genomeCytobands, GenomeAssembly genomeAssembly)
{
_writer.Write(CompressedSequenceCommon.HeaderTag);
_writer.Write(CompressedSequenceCommon.HeaderVersion);
_writer.Flush();
_headerDataOffset = _stream.Position;
// grab the index and masked intervals offsets
_writer.Write(_indexOffset);
_writer.Write(_maskedIntervalsOffset);
// grab the creation time
_writer.WriteOpt(DateTime.UtcNow.Ticks);
// write the reference metadata
_writer.WriteOpt(referenceMetadataList.Count);
foreach (var refMetadata in referenceMetadataList)
{
refMetadata.Write(_writer);
}
// write the genome cytobands
genomeCytobands.Write(_writer);
// write the genome assembly
_writer.Write((byte)genomeAssembly);
// write the data start tag
_writer.Write(CompressedSequenceCommon.DataStartTag);
}
/// <summary>
/// constructor
/// </summary>
public CompressedSequenceWriter(string path, List <ReferenceMetadata> referenceMetadataList,
ICytogeneticBands genomeCytobands, GenomeAssembly genomeAssembly)
{
_stream = FileUtilities.GetCreateStream(path);
_writer = new ExtendedBinaryWriter(_stream);
_refSeqIndex = new List <SequenceIndexEntry>();
_twoBitSequence = new TwoBitSequence();
_sequenceCompressor = new SequenceCompressor();
_refSeqMaskedIntervals = new List <List <MaskedEntry> >();
WriteHeader(referenceMetadataList, genomeCytobands, genomeAssembly);
}
public CompressedSequenceWriter(Stream stream, IReadOnlyCollection <ReferenceMetadata> referenceMetadataList,
ICytogeneticBands 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);
}
