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());
}