public void GetDataSourceVersions_grch37()
{
var grch37SaDir = Resources.SaGRCh37("");
var dataSourceVersions = SaReaderUtils.GetDataSourceVersions(new List <string> {
grch37SaDir
});
Assert.True(dataSourceVersions.Any());
}
public void GetGenomeAssembly_grch37()
{
var grch37SaDir = Resources.SaGRCh37("");
var genomeAssembly = SaReaderUtils.GetGenomeAssembly(new List <string> {
grch37SaDir
});
Assert.Equal(GenomeAssembly.GRCh37, genomeAssembly);
}
public static IGeneAnnotationProvider GetGeneAnnotationProvider(IEnumerable <string> supplementaryAnnotationDirectories)
{
var reader = SaReaderUtils.GetGeneAnnotationDatabaseReader(supplementaryAnnotationDirectories.ToList());
if (reader == null)
{
return(null);
}
var geneAnnotationProvider = new GeneAnnotationProvider(reader);
return(geneAnnotationProvider);
}
private static void AddSaPositon(ISaPosition saPosition, IAnnotatedVariant annotatedVariant)
{
foreach (var dataSource in saPosition.DataSources)
{
var saAltAllele = SaReaderUtils.GetReducedAllele(annotatedVariant.Variant.RefAllele,
annotatedVariant.Variant.AltAllele);
if (dataSource.MatchByAllele && dataSource.AltAllele != saAltAllele)
{
continue;
}
annotatedVariant.SupplementaryAnnotations.Add(new AnnotatedSaDataSource(dataSource, saAltAllele));
}
}
private void LoadChromosome(IChromosome chromosome)
{
var ucscReferenceName = chromosome.UcscName;
if (_saDirs == null || _saDirs.Count == 0 || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
_saReaders = SaReaderUtils.GetReaders(_saDirs, ucscReferenceName);
BuildIntervalForests();
_hasSmallVariantIntervals = !(_smallVariantIntervalArray is NullIntervalSearch <ISupplementaryInterval>);
_hasSvIntervals = !(_svIntervalArray is NullIntervalSearch <ISupplementaryInterval>);
_hasAllVariantIntervals = !(_allVariantIntervalArray is NullIntervalSearch <ISupplementaryInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
public void GetReducedAlleleTest(string refAllele, string altAllele, string expectedOut)
{
var reducedAllele = SaReaderUtils.GetReducedAllele(refAllele, altAllele);
Assert.Equal(expectedOut, reducedAllele);
}
