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.");
}
}
public IVariant[] CreateVariants(IChromosome chromosome, int start, int end, string refAllele,
string[] altAlleles, IInfoData infoData, bool[] isDecomposedByAllele, bool isRecomposed, List <string>[] linkedVids, string globalMajorAllele)
{
bool isReference = globalMajorAllele != null;
if (isReference)
{
return(ReferenceVariantCreator.Create(_vidCreator, _sequence, chromosome, start, end, refAllele, altAlleles[0], globalMajorAllele));
}
var variantCategory = GetVariantCategory(altAlleles[0], infoData.SvType);
var variants = new List <IVariant>(altAlleles.Length);
for (var i = 0; i < altAlleles.Length; i++)
{
#if (!NI_ALLELE)
if (VcfCommon.IsNonInformativeAltAllele(altAlleles[i]))
{
continue;
}
#endif
string altAllele = altAlleles[i];
bool isDecomposed = isDecomposedByAllele[i];
if (isDecomposed && isRecomposed)
{
throw new InvalidDataException("A variant can't be both decomposed and recomposed");
}
(int shiftedStart, string shiftedRef, string shiftedAlt) =
VariantUtils.TrimAndLeftAlign(start, refAllele, altAllele, _sequence);
if (variantCategory == VariantCategory.SmallVariant || variantCategory == VariantCategory.Reference)
{
end = shiftedStart + shiftedRef.Length - 1;
}
variants.Add(GetVariant(chromosome, shiftedStart, end, shiftedRef, shiftedAlt, infoData, variantCategory,
isDecomposed, isRecomposed, linkedVids?[i]?.ToArray()));
}
return(variants.Count == 0 ? null : variants.ToArray());
}
