public RepeatExpansionProvider(GenomeAssembly genomeAssembly, IDictionary <string, IChromosome> refNameToChromosome,
int numRefSeqs, string customTsvPath)
{
using (Stream stream = GetTsvStream(genomeAssembly, customTsvPath))
{
IIntervalForest <RepeatExpansionPhenotype> phenotypeForest = RepeatExpansionReader.Load(stream, genomeAssembly, refNameToChromosome, numRefSeqs);
_matcher = new Matcher(phenotypeForest);
}
}
private static void TryLoadStrFile(Stream stream, GenomeAssembly genomeAssembly, ISequenceProvider refProvider)
{
try
{
RepeatExpansionReader.Load(stream, genomeAssembly, refProvider.RefNameToChromosome,
refProvider.RefIndexToChromosome.Count);
}
catch (Exception exception)
{
throw new UserErrorException(exception.Message);
}
}
public void ComputePercentiles_Nominal()
{
var repeatNumbers = new[] { 10, 15, 20, 100, 200 };
var alleleCounts = new[] { 550, 34, 78, 30, 45 };
double[] expectedPercentiles =
{
0, 550 * 100.0 / 737, (550 + 34) * 100.0 / 737, (550 + 34 + 78) * 100.0 / 737,
(550 + 34 + 78 + 30) * 100.0 / 737
};
double[] observedResults = RepeatExpansionReader.ComputePercentiles(repeatNumbers, alleleCounts);
Assert.Equal(expectedPercentiles, observedResults);
}
