private static ISupplementaryAnnotationHeader GetHeader(string saPath)
{
ISupplementaryAnnotationHeader header;
using (var stream = FileUtilities.GetReadStream(saPath))
using (var reader = new ExtendedBinaryReader(stream))
{
header = SaReader.GetHeader(reader);
}
return(header);
}
private static string GetReferenceName(string saPath, IDictionary <string, IChromosome> refChromDict)
{
ISupplementaryAnnotationHeader header;
using (var stream = FileUtilities.GetReadStream(saPath))
using (var reader = new ExtendedBinaryReader(stream))
{
header = SaReader.GetHeader(reader);
}
return(refChromDict[header.ReferenceSequenceName].UcscName);
}
public void SaReader_And_SaWriter_Tests()
{
var saMs = new MemoryStream();
var indexMs = new MemoryStream();
var dataSourceVersions = new[]
{
new DataSourceVersion("clinvar", "20", DateTime.Today.Ticks, "clinvar dataset"),
new DataSourceVersion("dbSnp", "18", DateTime.Parse("12/20/2010").Ticks, "dbSNP")
};
var header = new SupplementaryAnnotationHeader("chr1", DateTime.Now.Ticks, 1, dataSourceVersions, GenomeAssembly.GRCh37);
var smallIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data1", "chr1", 100, 150, "", ReportFor.SmallVariants)
};
var svIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data2", "chr1", 100, 1000, "", ReportFor.StructuralVariants)
};
var allIntervals = new List <ISupplementaryInterval>
{
new SupplementaryInterval("data3", "chr1", 100, 1000, "", ReportFor.AllVariants)
};
var saDataSources = new ISaDataSource[4];
saDataSources[0] = new SaDataSource("data1", "data1", "A", false, true, "acd", new[] { "\"id\":\"123\"" });
saDataSources[1] = new SaDataSource("data2", "data2", "T", false, true, "acd", new[] { "\"id\":\"123\"" });
saDataSources[2] = new SaDataSource("data3", "data3", "A", false, false, "acd", new[] { "\"id\":\"123\"" });
saDataSources[3] = new SaDataSource("data4", "data4", "T", false, false, "acd", new[] { "\"id\":\"123\"" });
var saPos = new SaPosition(saDataSources, "A");
using (var saWriter = new SaWriter(saMs, indexMs, header, smallIntervals, svIntervals, allIntervals, new List <(int, string)>(), true))
{
saWriter.Write(saPos, 150);
}
saMs.Position = 0;
indexMs.Position = 0;
ISaPosition obseveredPosition, obseveredPosition2;
using (var saReader = new SaReader(saMs, indexMs))
{
obseveredPosition = saReader.GetAnnotation(150);
obseveredPosition2 = saReader.GetAnnotation(200);
}
Assert.Equal("A", obseveredPosition.GlobalMajorAllele);
Assert.Equal(4, obseveredPosition.DataSources.Length);
Assert.Null(obseveredPosition2);
}
