private IVariant GetVariant(IChromosome chromosome, int start, int end, string refAllele, string altAllele,
IInfoData infoData, VariantCategory category, bool isDecomposed, bool isRecomposed, string[] linkedVids)
{
string vid = _vidCreator.Create(_sequence, category, infoData.SvType, chromosome, start, end, refAllele, altAllele, infoData.RepeatUnit);
int svEnd = infoData.End ?? start;
// ReSharper disable once SwitchStatementMissingSomeCases
switch (category)
{
case VariantCategory.SmallVariant:
return(SmallVariantCreator.Create(chromosome, start, end, refAllele, altAllele, isDecomposed, isRecomposed, linkedVids, vid,
false));
case VariantCategory.ROH:
return(RohVariantCreator.Create(chromosome, start, svEnd, refAllele, altAllele, vid));
case VariantCategory.SV:
return(StructuralVariantCreator.Create(chromosome, start, svEnd, refAllele, altAllele, infoData.SvType, vid));
case VariantCategory.CNV:
return(CnvCreator.Create(chromosome, start, svEnd, refAllele, altAllele, vid));
case VariantCategory.RepeatExpansion:
return(RepeatExpansionCreator.Create(chromosome, start, svEnd, refAllele, altAllele, infoData.RefRepeatCount, vid));
default:
throw new NotImplementedException($"Unrecognized variant category: {category}");
}
}
private IVariant GetVariant(IChromosome chromosome, int start, int end, string refAllele, string altAllele,
IInfoData infoData, VariantCategory category, bool isDecomposedVar, bool isRecomposed, string[] linkedVids, string globalMajorAllele)
{
switch (category)
{
case VariantCategory.Reference:
return(ReferenceVariantCreator.Create(chromosome, start, end, refAllele, altAllele, globalMajorAllele));
case VariantCategory.SmallVariant:
return(SmallVariantCreator.Create(chromosome, start, refAllele, altAllele, isDecomposedVar, isRecomposed, linkedVids));
case VariantCategory.ROH:
return(RohVariantCreator.Create(chromosome, start, refAllele, altAllele, infoData));
case VariantCategory.SV:
var svBreakEnds = infoData.SvType == VariantType.translocation_breakend ?
GetTranslocationBreakends(chromosome, refAllele, altAllele, start)
: GetSvBreakEnds(chromosome.EnsemblName, start, infoData.SvType, infoData.End);
return(StructuralVariantCreator.Create(chromosome, start, refAllele, altAllele, svBreakEnds, infoData));
case VariantCategory.CNV:
return(CnvCreator.Create(chromosome, start, refAllele, altAllele, infoData));
case VariantCategory.RepeatExpansion:
return(RepeatExpansionCreator.Create(chromosome, start, refAllele, altAllele, infoData));
default:
throw new NotImplementedException("Unrecognized variant category.");
}
}
public void Create_StructuralVariants_ReturnVid(int start, int end, string altAllele, string repeatUnit,
string svType, VariantCategory category, string expectedVid)
{
string observedVid = _vidCreator.Create(null, category, svType, ChromosomeUtilities.Chr1, start, end, "", altAllele, repeatUnit);
Assert.Equal(expectedVid, observedVid);
}
public string Create(ISequence sequence, VariantCategory category, string svType, IChromosome chromosome, int start, int end,
string refAllele, string altAllele, string repeatUnit)
{
if (altAllele == ".")
{
altAllele = refAllele;
}
// fix N reference
if (refAllele == "N")
{
refAllele = sequence.Substring(start - 1, 1);
}
// add padding bases
if (string.IsNullOrEmpty(refAllele) || string.IsNullOrEmpty(altAllele))
{
start--;
string paddingBase = sequence.Substring(start - 1, 1);
refAllele = paddingBase + refAllele;
altAllele = paddingBase + altAllele;
}
if (category == VariantCategory.SmallVariant ||
category == VariantCategory.Reference ||
svType == "BND")
{
return(GetVid(chromosome.EnsemblName, start, refAllele, altAllele));
}
if (category == VariantCategory.RepeatExpansion)
{
svType = "STR";
}
return(GetLongVid(chromosome.EnsemblName, start, end, refAllele, altAllele, svType));
}
public void Create_StructuralVariants_RecoverRefAllele_ReturnLongVid(int position, int endPosition,
string refAllele, string altAllele, string svType, VariantCategory category, string expectedVid)
{
string observedVid = _vidCreator.Create(_sequence, category, svType, ChromosomeUtilities.Chr1, position, endPosition, refAllele, altAllele, null);
Assert.Equal(expectedVid, observedVid);
}
private IVariant GetVariant(IChromosome chromosome, string id, int start, int end, string refAllele, string altAllele, IInfoData infoData, VariantCategory category, bool isDecomposedVar, bool isRecomposed)
{
switch (category)
{
case VariantCategory.Reference:
var refMinorGlobalMajorAllele = _refMinorProvider?.GetGlobalMajorAlleleForRefMinor(chromosome, start);
return(ReferenceVariantCreator.Create(chromosome, start, end, refAllele, altAllele, refMinorGlobalMajorAllele));
case VariantCategory.SmallVariant:
return(SmallVariantCreator.Create(chromosome, start, refAllele, altAllele, isDecomposedVar, isRecomposed));
case VariantCategory.SV:
var svBreakEnds = infoData.SvType == VariantType.translocation_breakend ?
GetTranslocationBreakends(chromosome, refAllele, altAllele, start)
: GetSvBreakEnds(chromosome.EnsemblName, start, infoData.SvType, infoData.End, infoData.IsInv3, infoData.IsInv5);
return(StructuralVariantCreator.Create(chromosome, start, refAllele, altAllele, svBreakEnds, infoData, _enableVerboseTranscript));
case VariantCategory.CNV:
return(CnvCreator.Create(chromosome, id, start, refAllele, altAllele, infoData, _enableVerboseTranscript));
case VariantCategory.RepeatExpansion:
return(RepeatExpansionCreator.Create(chromosome, start, refAllele, altAllele, infoData));
default:
throw new NotImplementedException("Unrecognized variant category.");
}
}
