private static ExitCodes ProgramExecution()
{
var rootDirectory = new FileInfo(MitoMapFileNames[0]).Directory;
if (rootDirectory == null)
{
return(ExitCodes.PathNotFound);
}
var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapSv"));
var sequenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var chrom = sequenceProvider.RefNameToChromosome["chrM"];
sequenceProvider.LoadChromosome(chrom);
var mitoMapSvReaders = MitoMapFileNames.Select(mitoMapFileName => new MitoMapSvReader(new FileInfo(mitoMapFileName), sequenceProvider)).ToList();
var mergedMitoMapVarItems = MitoMapSvReader.MergeAndSort(mitoMapSvReaders);
string outFileName = $"{version.Name}_{version.Version}";
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
{
var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, GenomeAssembly.rCRS, SaCommon.MitoMapTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion);
nsiWriter.Write(mergedMitoMapVarItems);
}
return(ExitCodes.Success);
}
public void Readback_clingen()
{
var version = new DataSourceVersion("source1", "v1", DateTime.Now.Ticks, "description");
using (var saStream = new MemoryStream())
{
using (var siWriter = new NsiWriter(saStream, version, GenomeAssembly.GRCh37, "clingen",
ReportFor.StructuralVariants, SaCommon.SchemaVersion, true))
{
siWriter.Write(GetClinGenItems());
}
saStream.Position = 0;
var siReader = NsiReader.Read(saStream);
var annotations = siReader.GetAnnotation(new Variant(ChromosomeUtilities.Chr1, 100, 14590, "", "<DEL>", VariantType.deletion, "1:100:14590:del", false, false, false, null, null, true)).ToArray();
string[] expected =
{
"\"chromosome\":\"1\",\"begin\":145,\"end\":2743,\"variantType\":\"copy_number_gain\",\"id\":\"cg1\",\"clinicalInterpretation\":\"likely benign\",\"phenotypes\":[\"phenotype1\",\"phenotype2\"],\"phenotypeIds\":[\"pid1\",\"pid2\"],\"observedGains\":3,\"validated\":true,\"reciprocalOverlap\":0.17935,\"annotationOverlap\":1",
"\"chromosome\":\"1\",\"begin\":14585,\"end\":5872743,\"variantType\":\"copy_number_loss\",\"id\":\"cg2\",\"clinicalInterpretation\":\"likely pathogenic\",\"phenotypes\":[\"phenotype3\",\"phenotype5\"],\"phenotypeIds\":[\"pid3\",\"pid5\"],\"observedLosses\":5,\"validated\":true,\"reciprocalOverlap\":0,\"annotationOverlap\":0"
};
Assert.Equal(2, annotations.Length);
Assert.Equal(expected, annotations);
}
}
private static ExitCodes ProgramExecution()
{
var refProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_referenceSequencePath));
var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version");
var outFileName = $"{version.Name}_{version.Version}";
using (var parser = new LcrRegionParser(GZipUtilities.GetAppropriateStreamReader(_inputFile), refProvider))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.LcrFileSuffix)))
using (var writer = new NsiWriter(stream, version, refProvider.Assembly, SaCommon.LowComplexityRegionTag, ReportFor.AllVariants, SaCommon.NsiSchemaVersion))
{
writer.Write(parser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var dosageMapRegionVersion = DataSourceVersionReader.GetSourceVersion(_dosageMapRegionFile + ".version");
string outFileName = $"{dosageMapRegionVersion.Name.Replace(' ', '_')}_{dosageMapRegionVersion.Version}";
var referenceProvider = new ReferenceSequenceProvider(GZipUtilities.GetAppropriateReadStream(_inputReferencePath));
using (var dosageSensitivityParser = new DosageMapRegionParser(GZipUtilities.GetAppropriateReadStream(_dosageMapRegionFile), referenceProvider.RefNameToChromosome))
using (var stream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(stream, dosageMapRegionVersion, referenceProvider.Assembly, SaCommon.DosageSensitivityTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(dosageSensitivityParser.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version");
string outFileName = $"{version.Name}_{version.Version}";
using (var clinGenReader = new ClinGenReader(GZipUtilities.GetAppropriateStreamReader(_inputFileName), referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, referenceProvider.Assembly, SaCommon.ClinGenTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(clinGenReader.GetItems());
}
return(ExitCodes.Success);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version");
string outFileName = $"{version.Name}_{version.Version}".Replace(' ', '_');
using (var reader = GZipUtilities.GetAppropriateStreamReader(_inputFileName))
using (var oneKGenSvReader = new OneKGenSvReader(reader, referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.IntervalFileSuffix)))
using (var nsiWriter = new NsiWriter(nsaStream, version, referenceProvider.Assembly,
SaCommon.OnekSvTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(oneKGenSvReader.GetItems());
}
return(ExitCodes.Success);
}
private Stream GetNsiStream()
{
var stream = new MemoryStream();
var version = new DataSourceVersion("test", "June_2020", DateTime.Now.Ticks, "dummy");
using (var writer = new NsiWriter(stream, version, GenomeAssembly.GRCh37, SaCommon.LowComplexityRegionTag,
ReportFor.AllVariants,
SaCommon.NsiSchemaVersion, true))
{
writer.Write(new []
{
new LcrInterval(ChromosomeUtilities.Chr1, 100, 150),
new LcrInterval(ChromosomeUtilities.Chr1, 300, 450),
new LcrInterval(ChromosomeUtilities.Chr1, 600, 650),
new LcrInterval(ChromosomeUtilities.Chr2, 100, 150),
new LcrInterval(ChromosomeUtilities.Chr2, 300, 450),
new LcrInterval(ChromosomeUtilities.Chr2, 600, 650),
});
}
stream.Position = 0;
return(stream);
}
private static ExitCodes ProgramExecution()
{
var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference));
List <CustomInterval> intervals;
SaJsonSchema intervalJsonSchema;
string jsonTag;
DataSourceVersion version;
string outputPrefix = GetOutputPrefix(_inputFile);
var nsaFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix);
var nsaIndexFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix + SaCommon.IndexSufix);
var nsaSchemaFileName = Path.Combine(_outputDirectory, outputPrefix + SaCommon.SaFileSuffix + SaCommon.JsonSchemaSuffix);
var nsaItemsCount = 0;
using (var customReader = CustomAnnotationsParser.Create(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider))
using (var nsaStream = FileUtilities.GetCreateStream(nsaFileName))
using (var indexStream = FileUtilities.GetCreateStream(nsaIndexFileName))
using (var nsaWriter = new NsaWriter(
new ExtendedBinaryWriter(nsaStream),
new ExtendedBinaryWriter(indexStream),
version = new DataSourceVersion(customReader.JsonTag, GetInputFileName(_inputFile), DateTime.Now.Ticks),
referenceProvider,
customReader.JsonTag,
customReader.MatchByAllele, // match by allele
customReader.IsArray, // is array
SaCommon.SchemaVersion,
false, // is positional
false, // skip incorrect ref base
true // throw error on conflicting entries
))
using (var saJsonSchemaStream = FileUtilities.GetCreateStream(nsaSchemaFileName))
using (var schemaWriter = new StreamWriter(saJsonSchemaStream))
{
jsonTag = customReader.JsonTag;
nsaItemsCount = nsaWriter.Write(customReader.GetItems());
schemaWriter.Write(customReader.JsonSchema);
intervalJsonSchema = customReader.IntervalJsonSchema;
intervals = customReader.GetCustomIntervals();
}
if (nsaItemsCount == 0)
{
if (File.Exists(nsaFileName))
{
File.Delete(nsaFileName);
}
if (File.Exists(nsaIndexFileName))
{
File.Delete(nsaIndexFileName);
}
if (File.Exists(nsaSchemaFileName))
{
File.Delete(nsaSchemaFileName);
}
}
if (nsaItemsCount == 0 && intervals == null)
{
throw new UserErrorException("The provided TSV has no valid custom annotation entries.");
}
if (intervals == null)
{
return(ExitCodes.Success);
}
using (var nsiStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.SiFileSuffix)))
using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsiStream), version, referenceProvider.Assembly, jsonTag, ReportFor.AllVariants, SaCommon.SchemaVersion))
using (var siJsonSchemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outputPrefix + SaCommon.SiFileSuffix + SaCommon.JsonSchemaSuffix)))
using (var schemaWriter = new StreamWriter(siJsonSchemaStream))
{
nsiWriter.Write(intervals);
schemaWriter.Write(intervalJsonSchema);
}
return(ExitCodes.Success);
}
