public RepeatExpansionPhenotypeTests()
{
var repeatNumbers = new[] { 7, 8, 9, 10, 11, 12, 13, 15 };
double[] percentiles = { 0, 1, 1.5, 3.5, 75.5, 86.5, 98.5, 99.5 };
_phenotype = new RepeatExpansionPhenotype(null, null, null, repeatNumbers, percentiles, null, null);
}
private static (ushort RefIndex, Interval <RepeatExpansionPhenotype> Interval) GetPhenotype(string line, IDictionary <string, IChromosome> refNameToChromosome)
{
string[] cols = line.OptimizedSplit('\t');
if (cols.Length < MinNumberOfColumns)
{
throw new InvalidDataException($"Expected at least {MinNumberOfColumns} columns in the STR data file, but found only {cols.Length}.");
}
string chromosomeString = cols[ChromIndex];
int start = int.Parse(cols[StartIndex]);
int end = int.Parse(cols[EndIndex]);
string phenotype = cols[PhenotypeIndex];
string omimId = cols[OmimIndex];
int[] repeatNumbers = cols[RepeatNumbersIndex].Split(',').Select(int.Parse).ToArray();
int[] alleleCounts = cols[AlleleCountsIndex].Split(',').Select(int.Parse).ToArray();
string[] classifications = cols[CategoriesIndex].Split(',').ToArray();
Interval[] classificationRanges = cols[CategoryRangesIndex].Split(',').Select(GetInterval).ToArray();
if (repeatNumbers.Length != alleleCounts.Length)
{
throw new InvalidDataException($"Inconsistent number of repeat numbers ({repeatNumbers.Length}) vs. allele counts ({alleleCounts.Length})");
}
if (classifications.Length != classificationRanges.Length)
{
throw new InvalidDataException($"Inconsistent number of values of classifications ({classifications.Length}) vs. classification ranges ({classificationRanges.Length})");
}
var chromosome = ReferenceNameUtilities.GetChromosome(refNameToChromosome, chromosomeString);
var chromosomeInterval = new ChromosomeInterval(chromosome, start, end);
double[] percentiles = PercentileUtilities.ComputePercentiles(repeatNumbers.Length, alleleCounts);
var rePhenotype = new RepeatExpansionPhenotype(chromosomeInterval, phenotype, omimId, repeatNumbers, percentiles, classifications, classificationRanges);
return(chromosome.Index, new Interval <RepeatExpansionPhenotype>(start, end, rePhenotype));
}
public MatcherTests()
{
var repeatNumbers = new[] { 7, 8, 9 };
double[] percentiles = { 0, 1, 1.5 };
var classificationRanges = new[] { new Interval(0, 27) };
var classifications = new[] { "Normal" };
var aInterval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 100, 200);
var aPhenotype = new RepeatExpansionPhenotype(aInterval, "A", null, repeatNumbers, percentiles, classifications, classificationRanges);
var chr1Phenotypes = new Interval <RepeatExpansionPhenotype> [1];
chr1Phenotypes[0] = new Interval <RepeatExpansionPhenotype>(aInterval.Start, aInterval.End, aPhenotype);
var intervalArrays = new IntervalArray <RepeatExpansionPhenotype> [1];
intervalArrays[ChromosomeUtilities.Chr1.Index] = new IntervalArray <RepeatExpansionPhenotype>(chr1Phenotypes);
var phenotypeForest = new IntervalForest <RepeatExpansionPhenotype>(intervalArrays);
_matcher = new Matcher(phenotypeForest);
}