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);
}
/// <summary>
/// returns true if the specified reference sequence is in the standard reference sequences and in VEP
/// </summary>
public void Annotate(IAnnotatedPosition annotatedPosition)
{
LoadChromosome(annotatedPosition.Position.Chromosome);
if (annotatedPosition.AnnotatedVariants == null)
{
return;
}
annotatedPosition.CytogeneticBand = _cytogeneticBands.GetCytogeneticBand(annotatedPosition.Position.Chromosome, annotatedPosition.Position.Start,
annotatedPosition.Position.End);
if (annotatedPosition.Position.Chromosome.UcscName != "chrM")
{
return;
}
const string assertionNumber = "NC_012920.1";
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
annotatedVariant.HgvsgNotation = HgvsgNotation.GetNotation(assertionNumber, annotatedVariant.Variant, Sequence, new Interval(0, Sequence.Length));
}
}
