//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final void buildAlleleMap(final org.broadinstitute.variant.variantcontext.VariantContext vc)
private void buildAlleleMap(VariantContext vc)
{
// these are fast path options to determine the offsets for
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nAlleles = vc.getNAlleles();
int nAlleles = vc.NAlleles;
@ref = vc.Reference;
alt1 = nAlleles > 1 ? vc.getAlternateAllele(0) : null;
if (nAlleles > 2)
{
// for multi-allelics we need to clear the map, and add additional looks
alleleMapForTriPlus.Clear();
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final java.util.List<org.broadinstitute.variant.variantcontext.Allele> alleles = vc.getAlleles();
IList <Allele> alleles = vc.Alleles;
for (int i = 2; i < alleles.Count; i++)
{
alleleMapForTriPlus[alleles[i]] = i;
}
}
}
/// <summary>
/// add a record to the file
/// </summary>
/// <param name="vc"> the Variant Context object </param>
public override void add(VariantContext vc)
{
if (mHeader == null)
{
throw new IllegalStateException("The VCF Header must be written before records can be added: " + StreamName);
}
if (doNotWriteGenotypes)
{
vc = (new VariantContextBuilder(vc)).noGenotypes().make();
}
try
{
base.add(vc);
IDictionary <Allele, string> alleleMap = buildAlleleMap(vc);
// CHROM
write(vc.Chr);
write(VCFConstants.FIELD_SEPARATOR);
// POS
write(Convert.ToString(vc.Start));
write(VCFConstants.FIELD_SEPARATOR);
// ID
string ID = vc.ID;
write(ID);
write(VCFConstants.FIELD_SEPARATOR);
// REF
string refString = vc.Reference.DisplayString;
write(refString);
write(VCFConstants.FIELD_SEPARATOR);
// ALT
if (vc.Variant)
{
Allele altAllele = vc.getAlternateAllele(0);
string alt = altAllele.DisplayString;
write(alt);
for (int i = 1; i < vc.AlternateAlleles.Count; i++)
{
altAllele = vc.getAlternateAllele(i);
alt = altAllele.DisplayString;
write(",");
write(alt);
}
}
else
{
write(VCFConstants.EMPTY_ALTERNATE_ALLELE_FIELD);
}
write(VCFConstants.FIELD_SEPARATOR);
// QUAL
if (!vc.hasLog10PError())
{
write(VCFConstants.MISSING_VALUE_v4);
}
else
{
write(formatQualValue(vc.PhredScaledQual));
}
write(VCFConstants.FIELD_SEPARATOR);
// FILTER
string filters = getFilterString(vc);
write(filters);
write(VCFConstants.FIELD_SEPARATOR);
// INFO
IDictionary <string, string> infoFields = new SortedDictionary <string, string>();
foreach (KeyValuePair <string, object> field in vc.Attributes)
{
string key = field.Key;
if (!mHeader.hasInfoLine(key))
{
fieldIsMissingFromHeaderError(vc, key, "INFO");
}
string outputValue = formatVCFField(field.Value);
if (outputValue != null)
{
infoFields[key] = outputValue;
}
}
writeInfoString(infoFields);
// FORMAT
GenotypesContext gc = vc.Genotypes;
if (gc.LazyWithData && ((LazyGenotypesContext)gc).UnparsedGenotypeData is string)
{
write(VCFConstants.FIELD_SEPARATOR);
write(((LazyGenotypesContext)gc).UnparsedGenotypeData.ToString());
}
else
{
IList <string> genotypeAttributeKeys = calcVCFGenotypeKeys(vc, mHeader);
if (genotypeAttributeKeys.Count > 0)
{
foreach (String format in genotypeAttributeKeys)
{
if (!mHeader.hasFormatLine(format))
{
fieldIsMissingFromHeaderError(vc, format, "FORMAT");
}
}
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String genotypeFormatString = org.broad.tribble.util.ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
string genotypeFormatString = ParsingUtils.join(VCFConstants.GENOTYPE_FIELD_SEPARATOR, genotypeAttributeKeys);
write(VCFConstants.FIELD_SEPARATOR);
write(genotypeFormatString);
addGenotypeData(vc, alleleMap, genotypeAttributeKeys);
}
}
write("\n");
// note that we cannot call flush here if we want block gzipping to work properly
// calling flush results in all gzipped blocks for each variant
flushBuffer();
}
catch (IOException e)
{
throw new Exception("Unable to write the VCF object to " + StreamName, e);
}
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final void buildAlleleMap(final org.broadinstitute.variant.variantcontext.VariantContext vc)
private void buildAlleleMap(VariantContext vc)
{
// these are fast path options to determine the offsets for
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nAlleles = vc.getNAlleles();
int nAlleles = vc.NAlleles;
@ref = vc.Reference;
alt1 = nAlleles > 1 ? vc.getAlternateAllele(0) : null;
if (nAlleles > 2)
{
// for multi-allelics we need to clear the map, and add additional looks
alleleMapForTriPlus.Clear();
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final java.util.List<org.broadinstitute.variant.variantcontext.Allele> alleles = vc.getAlleles();
IList<Allele> alleles = vc.Alleles;
for (int i = 2; i < alleles.Count; i++)
{
alleleMapForTriPlus[alleles[i]] = i;
}
}
}
