/// <summary>
/// constructor
/// </summary>
public MergeSaTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
_sequence = fixture.Sequence;
_reader = fixture.Reader;
_oneKGenReader = new OneKGenReader(_renamer);
}
/// <summary>
/// constructor
/// </summary>
public SaReadWriteTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
_sequence = fixture.Sequence;
_reader = fixture.Reader;
// create our expected data source versions
_expectedDataSourceVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
_expectedDataSourceVersions = new List <DataSourceVersion> {
_expectedDataSourceVersion
};
// create our expected supplementary annotations
var dbSnp1 = new DbSnpAnnotation
{
DbSnp = new List <long> {
1
}
};
_expectedAnnotation1 = new SupplementaryAnnotationPosition(100);
new SupplementaryPositionCreator(_expectedAnnotation1).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp1);
var dbSnp2 = new DbSnpAnnotation
{
DbSnp = new List <long> {
2
}
};
_expectedAnnotation2 = new SupplementaryAnnotationPosition(101);
new SupplementaryPositionCreator(_expectedAnnotation2).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp2);
var dbSnp3 = new DbSnpAnnotation
{
DbSnp = new List <long> {
3
}
};
_expectedAnnotation3 = new SupplementaryAnnotationPosition(102);
new SupplementaryPositionCreator(_expectedAnnotation3).AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, AltAllele, dbSnp3);
_expectedInterval = new SupplementaryInterval(1, 1000, "chr1", null, VariantType.copy_number_variation, null, _renamer);
_randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
// write the supplementary annotation file
WriteSupplementaryAnnotationFile(_randomPath);
}
/// <summary>
/// constructor
/// </summary>
public CustomIntervalParserTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public DgvTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public DbSnpReaderTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public SampleFieldExtractorTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public SvVcfParsingTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public ClingenTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public JsonOutputTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public ParseVcfLineTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public MergedCosmicReaderTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public CytogeneticBandTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public CustomIntervalOutput(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public VidTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
_vid = new VID();
}
/// <summary>
/// constructor
/// </summary>
public OneKGenTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
_oneKGenReader = new OneKGenReader(_renamer);
}
/// <summary>
/// constructor
/// </summary>
public ClinVarXmlReaderTests(ChromosomeRenamerFixture fixture)
{
_sequence = fixture.Sequence;
_reader = fixture.Reader;
}
/// <summary>
/// constructor
/// </summary>
public TrimmingTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public JsonAnnotationTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
/// <summary>
/// constructor
/// </summary>
public MultiSampleVcfTests(ChromosomeRenamerFixture fixture)
{
_renamer = fixture.Renamer;
}
