public void CalculateBndBorderDistanceWorks([NotNull] string chr, uint position, [NotNull] string otherChr, uint otherPos,
int ciStart, int ciEnd, double percentDistance, uint basepairDistance, uint borderStart, uint borderEnd)
{
var thisPos = ContigAndPosition.Create(ContigInfo.Create(chr), position);
var otherPosition = ContigAndPosition.Create(ContigInfo.Create(otherChr), otherPos);
var ci = new InclusiveInterval <int>(ciStart, ciEnd);
var actualCi = thisPos.CalculateBndBorderInterval(otherPosition, ci, percentDistance, basepairDistance);
var expectedCi = ContigAndInterval.Create(ContigInfo.Create(chr), borderStart, borderEnd);
Assert.Equal(expectedCi, actualCi);
}
internal void CheckContigId(string line)
{
var chromAndLengthInfo = GetChromAndLengthInfo(line);
if (chromAndLengthInfo.Length == 0)
{
return;
}
if (!_refNameToChromosome.TryGetValue(chromAndLengthInfo[0], out IChromosome chromosome))
{
return;
}
if (!int.TryParse(chromAndLengthInfo[1], out int length))
{
return;
}
var assemblyThisChrom = ContigInfo.GetGenomeAssembly(chromosome, length);
if (assemblyThisChrom == GenomeAssembly.rCRS)
{
IsRcrsMitochondrion = true;
return;
}
if (!GenomeAssemblyHelper.AutosomeAndAllosomeAssemblies.Contains(assemblyThisChrom))
{
return;
}
if (InferredGenomeAssembly == GenomeAssembly.Unknown)
{
InferredGenomeAssembly = assemblyThisChrom;
}
if (InferredGenomeAssembly != assemblyThisChrom)
{
throw new UserErrorException($"Inconsistent genome assemblies inferred:\ncurrent line \"{line}\" indicates {assemblyThisChrom}, whereas the lines above it indicate {InferredGenomeAssembly}.");
}
}
public static void WittyerBndCreateCorrectly()
{
var vcfSettings =
VcfVariantParserSettings.Create(ImmutableList.Create("proband", "father"), GenomeAssembly.Grch37);
var bnd1 = VcfVariant.TryParse(GenotypedBnd, vcfSettings).GetOrThrowDebug();
var bnd2 = VcfVariant.TryParse(GenotypedBndPair, vcfSettings).GetOrThrowDebug();
var wittyerBnd = WittyerBndInternal
.Create(bnd2, bnd2.Samples["father"], WittyerType.TranslocationBreakend, Bins,
BasepairDistance, PercentDistance, bnd1);
var expectedContig = ContigInfo.Create("1");
var expectedEndInterval = ContigAndInterval.Create(ContigInfo.Create("4"), 191034451, 191035452);
MultiAssert.Equal(expectedContig, wittyerBnd.Contig);
MultiAssert.Equal(expectedEndInterval, wittyerBnd.EndInterval);
MultiAssert.Equal(230675U, wittyerBnd.Start);
MultiAssert.Equal(231676U, wittyerBnd.Stop);
MultiAssert.Equal(WittyerConstants.StartingBin, wittyerBnd.Win.Start);
MultiAssert.Equal(null, wittyerBnd.Win.End);
MultiAssert.AssertAll();
}
