// --------------------------------------------------------------------------------
//
// implementation functions
//
// --------------------------------------------------------------------------------
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final String getFilterString(final VariantContext vc)
private string getFilterString(VariantContext vc)
{
if (vc.Filtered)
{
foreach (String filter in vc.Filters)
{
if (!mHeader.hasFilterLine(filter))
{
fieldIsMissingFromHeaderError(vc, filter, "FILTER");
}
}
return(ParsingUtils.join(";", ParsingUtils.sortList(vc.Filters)));
}
else if (vc.filtersWereApplied())
{
return(VCFConstants.PASSES_FILTERS_v4);
}
else
{
return(VCFConstants.UNFILTERED);
}
}
/// <summary>
/// Determine which genotype fields are in use in the genotypes in VC </summary>
/// <param name="vc"> </param>
/// <returns> an ordered list of genotype fields in use in VC. If vc has genotypes this will always include GT first </returns>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static List<String> calcVCFGenotypeKeys(final VariantContext vc, final VCFHeader header)
public static IList <string> calcVCFGenotypeKeys(VariantContext vc, VCFHeader header)
{
Set <string> keys = new HashSet <string>();
bool sawGoodGT = false;
bool sawGoodQual = false;
bool sawGenotypeFilter = false;
bool sawDP = false;
bool sawAD = false;
bool sawPL = false;
foreach (Genotype g in vc.Genotypes)
{
keys.addAll(g.ExtendedAttributes.Keys);
if (g.Available)
{
sawGoodGT = true;
}
if (g.hasGQ())
{
sawGoodQual = true;
}
if (g.hasDP())
{
sawDP = true;
}
if (g.hasAD())
{
sawAD = true;
}
if (g.hasPL())
{
sawPL = true;
}
if (g.Filtered)
{
sawGenotypeFilter = true;
}
}
if (sawGoodQual)
{
keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
}
if (sawDP)
{
keys.add(VCFConstants.DEPTH_KEY);
}
if (sawAD)
{
keys.add(VCFConstants.GENOTYPE_ALLELE_DEPTHS);
}
if (sawPL)
{
keys.add(VCFConstants.GENOTYPE_PL_KEY);
}
if (sawGenotypeFilter)
{
keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
}
IList <string> sortedList = ParsingUtils.sortList(new List <string>(keys));
// make sure the GT is first
if (sawGoodGT)
{
IList <string> newList = new List <string>(sortedList.Count + 1);
newList.Add(VCFConstants.GENOTYPE_KEY);
newList.AddRange(sortedList);
sortedList = newList;
}
if (sortedList.Count == 0 && header.hasGenotypingData())
{
// this needs to be done in case all samples are no-calls
return(Collections.singletonList(VCFConstants.GENOTYPE_KEY));
}
else
{
return(sortedList);
}
}
