public void LoopbackTest()
{
var wigFixFile = Resources.TopPath("mini.WigFix");
var version = new DataSourceVersion("phylop", "0", DateTime.Now.Ticks, "unit test");
using (var reader = new PhylopParser(FileUtilities.GetReadStream(wigFixFile), GenomeAssembly.GRCh37, ChromosomeUtilities.RefNameToChromosome))
using (var npdStream = new MemoryStream())
using (var indexStream = new MemoryStream())
using (var npdWriter = new NpdWriter(npdStream, indexStream, version, GenomeAssembly.GRCh37, SaCommon.PhylopTag, SaCommon.SchemaVersion))
{
npdWriter.Write(reader.GetItems());
npdStream.Position = 0;
indexStream.Position = 0;
using (var phylopReader = new NpdReader(npdStream, indexStream))
{
Assert.Equal(0.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 100)); //first position of first block
Assert.Equal(0.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 101)); // second position
Assert.Equal(0.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 120)); // some internal position
Assert.Equal(0.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 130)); //last position of first block
//moving on to the next block: should cause reloading from file
Assert.Equal(0.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 175)); //first position of second block
Assert.Equal(-2.1, phylopReader.GetAnnotation(ChromosomeUtilities.Chr1, 182)); // some negative value
//chrom 2
Assert.Null(phylopReader.GetAnnotation(ChromosomeUtilities.Chr2, 400));//values past the last phylop positions should return null
}
}
}
public void Annotate(IAnnotatedPosition annotatedPosition)
{
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
if (annotatedVariant.Variant.Type != VariantType.SNV)
{
continue;
}
annotatedVariant.PhylopScore = _phylopReader.GetAnnotation(annotatedPosition.Position.Chromosome, annotatedVariant.Variant.Start);
}
}