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.");
}
}
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.");
}
}
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}");
}
}
public static IVariant[] Create(IVariantIdCreator vidCreator, ISequence sequence, IChromosome chromosome, int start, int end,
string refAllele, string altAllele, string globalMajorAllele)
{
bool isRefMinor = end == start && globalMajorAllele != null;
if (!isRefMinor)
{
return(null);
}
string vid = vidCreator.Create(sequence, VariantCategory.SmallVariant, null, chromosome, start, end, refAllele, altAllele, null);
return(new[]
{
SmallVariantCreator.Create(chromosome, start, end, globalMajorAllele, refAllele, false, false, null, vid, true)
});
}