public void SetAlleles(IList <string> alleleStrings)
{
IList <Allele> alleles = new List <Allele> (alleleStrings.Count);
for (int i = 0; i < alleleStrings.Count; i++)
{
alleles.Add(Allele.Create(alleleStrings [i], i == 0));
}
SetAlleles(alleles);
}
/// <summary>
/// parse a single allele, given the allele list </summary>
/// <param name="alleles"> the alleles available </param>
/// <param name="alt"> the allele to parse </param>
/// <param name="lineNo"> the line number for this record </param>
private static void parseSingleAltAllele(IList <Allele> alleles, string alt, int lineNo)
{
checkAllele(alt, false, lineNo);
Allele allele = Allele.Create(alt, false);
if (!allele.NoCall)
{
alleles.Add(allele);
}
}
/// <summary>
/// parse out the alleles </summary>
/// <param name="reference"> the reference base </param>
/// <param name="alts"> a string of alternates to break into alleles </param>
/// <param name="lineNo"> the line number for this record </param>
/// <returns> a list of alleles, and a pair of the shortest and longest sequence </returns>
protected internal static IList <Allele> parseAlleles(string reference, string alts, int lineNo)
{
IList <Allele> alleles = new List <Allele> (2); // we are almost always biallelic
// ref
checkAllele(reference, true, lineNo);
Allele refAllele = Allele.Create(reference, true);
alleles.Add(refAllele);
if (alts.IndexOf(",") == -1) // only 1 alternatives, don't call string split
{
parseSingleAltAllele(alleles, alts, lineNo);
}
else
{
foreach (string alt in alts.Split(VCFConstants.COMMA_AS_CHAR_ARRAY, StringSplitOptions.RemoveEmptyEntries))
{
parseSingleAltAllele(alleles, alt, lineNo);
}
}
return(alleles);
}
