public void CosmicAltAllele()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(6928019, "C", 'A', ChromosomeUtilities.RefNameToChromosome);
var cosmicReader = new MergedCosmicReader(Resources.TopPath("COSM983708.vcf"), Resources.TopPath("COSM983708.tsv"), seqProvider);
var items = cosmicReader.GetItems().ToList();
Assert.Single((IEnumerable)items);
Assert.Contains("\"refAllele\":\"-\"", items[0].GetJsonString());
}
public void CosmicAlleleSpecificIndel()
{
//10188320
var seqProvider = ParserTestUtils.GetSequenceProvider(10188320, "G", 'A', ChromosomeUtilities.RefNameToChromosome);
var cosmicReader = new MergedCosmicReader(Resources.TopPath("COSM18152.vcf"), Resources.TopPath("COSM18152.tsv"), seqProvider);
var items = cosmicReader.GetItems();
Assert.Single(items);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var cosmicReader = new MergedCosmicReader(_vcfFile, _tsvFile, referenceProvider);
var version = DataSourceVersionReader.GetSourceVersion(_vcfFile + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix)))
using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix)))
using (var nsaWriter = new NsaWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.CosmicTag, false, true, SaCommon.SchemaVersion, false))
{
nsaWriter.Write(cosmicReader.GetItems());
}
return(ExitCodes.Success);
}
public void TwoStudyCosmicCoding()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(35416, "A", 'C', ChromosomeUtilities.RefNameToChromosome);
var cosmicReader = new MergedCosmicReader(Resources.TopPath("cosm5428243.vcf"), Resources.TopPath("cosm5428243.tsv"), seqProvider);
var cosmicItem = cosmicReader.GetItems().ToList()[0];
var studies = cosmicItem.Studies.ToList();
Assert.Equal("544", studies[0].Id);
Assert.Equal(new[] { "haematopoietic and lymphoid tissue" }, studies[0].Sites);
Assert.Equal(new[] { "haematopoietic neoplasm" }, studies[0].Histologies);
//Assert.Equal(new [] { "haematopoietic neoplasm", "acute myeloid leukaemia" }, study.Histologies);
Assert.Equal("544", studies[1].Id);
Assert.Equal(new[] { "haematopoietic;lymphoid tissue" }, studies[1].Sites);
Assert.Equal(new[] { "haematopoietic neoplasm" }, studies[1].Histologies);
//Assert.Equal(new[] { "haematopoietic_neoplasm", "acute_myeloid_leukaemia" }, study.Histologies);
}
