public static SimplePosition GetSimplePosition(string[] vcfFields, IVcfFilter vcfFilter, IDictionary <string, IChromosome> refNameToChromosome, bool isRecomposed = false)
{
var simplePosition = new SimplePosition(
ReferenceNameUtilities.GetChromosome(refNameToChromosome, vcfFields[VcfCommon.ChromIndex]),
int.Parse(vcfFields[VcfCommon.PosIndex]),
vcfFields[VcfCommon.RefIndex],
vcfFields[VcfCommon.AltIndex].OptimizedSplit(','));
if (vcfFilter.PassedTheEnd(simplePosition.Chromosome, simplePosition.Start))
{
return(null);
}
simplePosition.End = vcfFields[VcfCommon.AltIndex].OptimizedStartsWith('<') || vcfFields[VcfCommon.AltIndex] == "*" ? -1 : simplePosition.Start + simplePosition.RefAllele.Length - 1;
simplePosition.VcfFields = vcfFields;
simplePosition.IsRecomposed = isRecomposed;
simplePosition.IsDecomposed = new bool[simplePosition.AltAlleles.Length]; // false by default
simplePosition.Vids = new string[simplePosition.AltAlleles.Length];
simplePosition.LinkedVids = new List <string> [simplePosition.AltAlleles.Length];
return(simplePosition);
}
public static SimplePosition GetSimplePosition(IChromosome chromosome, int position, string[] vcfFields, IVcfFilter vcfFilter, bool isRecomposed = false)
{
if (vcfFilter.PassedTheEnd(chromosome, position))
{
return(null);
}
string refAllele = vcfFields[VcfCommon.RefIndex];
string altAlleleField = vcfFields[VcfCommon.AltIndex];
string[] altAlleles = altAlleleField.OptimizedSplit(',');
int numAltAlleles = altAlleles.Length;
return(new SimplePosition(chromosome, position, refAllele, altAlleles)
{
End = altAlleleField.OptimizedStartsWith('<') || altAlleleField == "*" ? -1 : position + refAllele.Length - 1,
VcfFields = vcfFields,
IsRecomposed = isRecomposed,
IsDecomposed = new bool[numAltAlleles],
Vids = new string[numAltAlleles],
LinkedVids = new List <string> [numAltAlleles]
});
}
