public IVariant[] CreateVariants(IChromosome chromosome, int start, int end, string refAllele,
string[] altAlleles, IInfoData infoData, bool[] isDecomposed, bool isRecomposed, List <string>[] linkedVids, string globalMajorAllele)
{
string firstAltAllele = altAlleles[0];
bool isReference = globalMajorAllele != null;
bool isSymbolicAllele = IsSymbolicAllele(firstAltAllele);
var variantCategory = GetVariantCategory(firstAltAllele, isReference, isSymbolicAllele, infoData.SvType);
if (isReference)
{
return new[] { GetVariant(chromosome, start, end, refAllele, firstAltAllele, infoData, variantCategory, isDecomposed[0], isRecomposed, linkedVids?[0]?.ToArray(), globalMajorAllele) }
}
;
_sequenceProvider.LoadChromosome(chromosome);
var variants = new List <IVariant>();
for (var i = 0; i < altAlleles.Length; i++)
{
#if (!NI_ALLELE)
if (VcfCommon.IsNonInformativeAltAllele(altAlleles[i]))
{
continue;
}
#endif
bool isDecomposedVar = isDecomposed[i];
(int shiftedStart, string shiftedRef, string shiftedAlt) =
VariantUtils.TrimAndLeftAlign(start, refAllele, altAlleles[i], _sequenceProvider.Sequence);
variants.Add(GetVariant(chromosome, shiftedStart, end - (start - shiftedStart), shiftedRef, shiftedAlt, infoData, variantCategory, isDecomposedVar, isRecomposed, linkedVids?[i]?.ToArray(), null));
}
return(variants.Count == 0 ? null : variants.ToArray());
}
public static VariantType GetVariantType(string refAllele, string altAllele)
{
if (VcfCommon.IsNonInformativeAltAllele(altAllele))
{
return(VariantType.non_informative_allele);
}
int referenceAlleleLen = refAllele.Length;
int alternateAlleleLen = altAllele.Length;
if (alternateAlleleLen != referenceAlleleLen)
{
if (alternateAlleleLen == 0 && referenceAlleleLen > 0)
{
return(VariantType.deletion);
}
if (alternateAlleleLen > 0 && referenceAlleleLen == 0)
{
return(VariantType.insertion);
}
return(VariantType.indel);
}
var variantType = alternateAlleleLen == 1 ? VariantType.SNV : VariantType.MNV;
return(variantType);
}
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());
}
private static bool IsSymbolicAllele(string altAllele) =>
altAllele.OptimizedStartsWith('<') && altAllele.OptimizedEndsWith('>') && !VcfCommon.IsNonInformativeAltAllele(altAllele);
