public void ReaderAndWriterTests()
{
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");
var ms = new MemoryStream();
var writer = new ExtendedBinaryWriter(ms);
saPos.Write(writer);
ms.Position = 0;
var reader = new ExtendedBinaryReader(ms);
var observedSa = SaPosition.Read(reader);
Assert.Equal(saPos.GlobalMajorAllele, observedSa.GlobalMajorAllele);
Assert.Equal(saPos.DataSources.Length, observedSa.DataSources.Length);
Assert.Equal(saPos.DataSources[3].KeyName, observedSa.DataSources[3].KeyName);
Assert.Equal(saPos.DataSources[2].JsonStrings, observedSa.DataSources[2].JsonStrings);
ms.Dispose();
}
public void GetJsonStrings_NullJsonStrings()
{
var dataSource = new SaDataSource("bob", "bobVcf", "A", false, false, null, null);
var annotatedSaDataSource = new AnnotatedSaDataSource(dataSource, "A");
var jsonStrings = annotatedSaDataSource.GetJsonStrings();
Assert.Null(jsonStrings);
}
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);
}
private static void AddSupplementaryAnnotation(IAnnotatedVariant annotatedVariant)
{
var dataSource = new SaDataSource("clinVar", "clinVar", "C", true, false, null,
new[] { "\"good\":\"result\"" });
var annotatedSaDataSource = new AnnotatedSaDataSource(dataSource, "C");
var dataSource2 = new SaDataSource("exac", "exac", "G", true, true, null,
new[] { "\"bad\":\"temper\"", "\"brutal\":\"kangaroo\"" });
var annotatedSaDataSource2 = new AnnotatedSaDataSource(dataSource2, "G");
annotatedVariant.SupplementaryAnnotations.Add(annotatedSaDataSource);
annotatedVariant.SupplementaryAnnotations.Add(annotatedSaDataSource2);
}
public void GetJsonStrings_Positional_AlleleSpecific()
{
string[] expectedJsonStrings = { "test1", "test2" };
var dataSource = new SaDataSource("bob", "bobVcf", "A", false, false, null, expectedJsonStrings);
var annotatedSaDataSource = new AnnotatedSaDataSource(dataSource, "A");
var jsonStrings = annotatedSaDataSource.GetJsonStrings();
Assert.NotNull(jsonStrings);
Assert.Equal(2, jsonStrings.Count);
Assert.Contains(expectedJsonStrings[0], jsonStrings[0]);
Assert.Contains(expectedJsonStrings[1], jsonStrings[1]);
}
