public CosmicTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.CosmicSchemaVersion, InterimSaCommon.CosmicTag, InterimSaCommon.CosmicVcfTag, false, sequenceProvider, true); }
public GnomadTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider, string sequencingDataType) { Console.WriteLine(version.ToString()); _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.SchemaVersion, _jsonKeyDictionary[sequencingDataType], null, true, sequenceProvider); }
public CustomAnnoTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, bool isPositional, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.CustomItemSchemaVersion, version.Name, null, !isPositional, sequenceProvider, true); }
public TopMedTsvWriter(DataSourceVersion version, string outputFileName, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _writer = new SaTsvWriter(outputFileName, version, genomeAssembly.ToString(), SaTsvCommon.SchemaVersion, InterimSaCommon.TopMedTag, null, true, sequenceProvider); }
public ExacTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _writer = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.ExacTag, null, true, sequenceProvider); }
public OnekgTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _onekgWriter = new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.OneKgenTag, "AF1000G", true, sequenceProvider); _refMinorWriter = new SaMiscTsvWriter(outputDirectory, version, genomeAssembly.ToString(), InterimSaCommon.RefMinorTag, sequenceProvider); }
public void Write_clinvar_basic() { var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description"); using (var saStream = new MemoryStream()) using (var indexStream = new MemoryStream()) { using (var saWriter = new NsaWriter(saStream, indexStream, version, GetSequenceProvider(), "clinvar", false, true, SaCommon.SchemaVersion, false, true, false, 1024, GenomeAssembly.GRCh37, true)) { saWriter.Write(GetClinvarItems()); } saStream.Position = 0; indexStream.Position = 0; using (var saReader = new NsaReader(saStream, indexStream, 1024)) { Assert.Equal(GenomeAssembly.GRCh37, saReader.Assembly); Assert.Equal(version.ToString(), saReader.Version.ToString()); saReader.PreLoad(ChromosomeUtilities.Chr1, new List <int> { 100, 101, 106 }); var annotations = saReader.GetAnnotation(100).ToList(); Assert.Equal("T", annotations[0].refAllele); Assert.Equal("A", annotations[0].altAllele); Assert.Equal( "\"id\":\"RCV0001\",\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"T\",\"altAllele\":\"A\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]", annotations[0].annotation); annotations = saReader.GetAnnotation(101).ToList(); Assert.Equal("A", annotations[0].refAllele); Assert.Equal("", annotations[0].altAllele); Assert.Equal( "\"id\":\"RCV00011\",\"variationId\":101,\"reviewStatus\":\"no assertion provided\",\"alleleOrigins\":[\"origin1\"],\"refAllele\":\"A\",\"altAllele\":\"-\",\"phenotypes\":[\"phenotype1\"],\"medGenIds\":[\"medgen1\"],\"omimIds\":[\"omim1\"],\"orphanetIds\":[\"orpha1\"],\"significance\":[\"significance\"],\"lastUpdatedDate\":\"0001-01-01\",\"pubMedIds\":[\"10024875684920\"]", annotations[0].annotation); saReader.PreLoad(ChromosomeUtilities.Chr2, new List <int> { 200, 205 }); var(refAllele, altAllele, annotation) = saReader.GetAnnotation(200).First(); Assert.Equal("G", refAllele); Assert.Equal("A", altAllele); Assert.NotNull(annotation); } } }
public MitoMapVarTsvWriter(DataSourceVersion version, string outputDirectory, string mitoMapDataType, ISequenceProvider sequenceProvider) { Console.WriteLine(version.ToString()); _mitoMapVarWriter = new SaTsvWriter(outputDirectory, version, GenomeAssembly.rCRS.ToString(), SaTsvCommon.MitoMapSchemaVersion, mitoMapDataType, null, false, sequenceProvider, true); }
public ClinvarTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) : this(new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.ClinvarSchemaVersion, InterimSaCommon.ClinvarTag, InterimSaCommon.ClinvarVcfTag, false, sequenceProvider, true)) { Console.WriteLine(version.ToString()); }
public EvsTsvWriter(DataSourceVersion version, string outputDirectory, GenomeAssembly genomeAssembly, ISequenceProvider sequenceProvider) : this(new SaTsvWriter(outputDirectory, version, genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.EvsTag, InterimSaCommon.EvsVcfTag, true, sequenceProvider)) { Console.WriteLine(version.ToString()); }