/// <summary>
/// Returns the reference ploidy for <paramref name="referenceInterval"/><para/>
/// If <paramref name="referenceInterval"/> spans regions with different ploidy an exception is thrown
/// </summary>
public static int GetSingleReferencePloidy(this ReferencePloidy referencePloidy, ReferenceInterval referenceInterval)
{
var referencePloidies = referencePloidy.GetReferencePloidyIntervals(referenceInterval).ToList();
if (referencePloidies.Count != 1)
{
var differentPloidyIntervals = referencePloidies.Select(ploidy => ploidy.Interval);
throw new ArgumentException(
$"Reference interval '{referenceInterval}' overlaps regions with different ploidy: '{string.Join(", ", differentPloidyIntervals)}'");
}
return(referencePloidies.Single().ReferencePloidy);
}
private static ReferencePloidy LoadReferencePloidy(IEnumerable <ReferencePloidyInterval> ploidyVcfIntervals,
bool useSymbolicAltAlleleInPloidyVcf = true)
{
var sampleId = new SampleId("sampleId");
var vcf = GetVcfAsString(sampleId, ploidyVcfIntervals, useSymbolicAltAlleleInPloidyVcf);
using (var textReader = new StringReader(vcf))
using (var reader = new GzipOrTextReader(textReader))
using (var vcfReader = new VcfReader(reader))
{
return(ReferencePloidy.Load(vcfReader, sampleId));
}
}
private static IEnumerable <CNInterval> GetKnownCopyNumberWithReferencePloidy(List <CNInterval> knownCnIntervals, ReferencePloidy referencePloidy)
{
foreach (var knownCnInterval in knownCnIntervals)
{
var interval = new ReferenceInterval(knownCnInterval.Chromosome, new Interval(knownCnInterval.Start + 1, knownCnInterval.End));
var refPloidy = referencePloidy.GetSingleReferencePloidy(interval);
yield return(new CNInterval(knownCnInterval.Chromosome,
knownCnInterval.Start, knownCnInterval.End, knownCnInterval.Cn)
{
ReferenceCopyNumber = refPloidy
});
}
}
private static Dictionary <string, List <CNInterval> > GetKnownCopyNumberWithReferencePloidy(ReferencePloidy referencePloidy, Dictionary <string, List <CNInterval> > knownCn)
{
return(knownCn.SelectValues(knownCnIntervals =>
GetKnownCopyNumberWithReferencePloidy(knownCnIntervals, referencePloidy).ToList()));
}
