//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
if (vc.NAlleles > BCF2Utils.MAX_ALLELES_IN_GENOTYPES)
{
throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.NAlleles + " at " + vc.Chr + ":" + vc.Start);
}
encodingType = BCF2Type.INT8;
buildAlleleMap(vc);
nValuesPerGenotype = vc.getMaxPloidy(2);
base.start(encoder, vc);
}
/// <summary>
/// add the genotype data
/// </summary>
/// <param name="vc"> the variant context </param>
/// <param name="genotypeFormatKeys"> Genotype formatting string </param>
/// <param name="alleleMap"> alleles for this context </param>
/// <exception cref="IOException"> for writer </exception>
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private void addGenotypeData(VariantContext vc, Map<Allele, String> alleleMap, List<String> genotypeFormatKeys) throws IOException
private void addGenotypeData(VariantContext vc, IDictionary <Allele, string> alleleMap, IList <string> genotypeFormatKeys)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int ploidy = vc.getMaxPloidy(2);
int ploidy = vc.getMaxPloidy(2);
foreach (string sample in mHeader.GenotypeSampleNames)
{
write(VCFConstants.FIELD_SEPARATOR);
Genotype g = vc.getGenotype(sample);
if (g == null)
{
g = GenotypeBuilder.createMissing(sample, ploidy);
}
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final List<String> attrs = new ArrayList<String>(genotypeFormatKeys.size());
IList <string> attrs = new List <string>(genotypeFormatKeys.Count);
foreach (string field in genotypeFormatKeys)
{
if (field.Equals(VCFConstants.GENOTYPE_KEY))
{
if (!g.Available)
{
throw new IllegalStateException("GTs cannot be missing for some samples if they are available for others in the record");
}
writeAllele(g.getAllele(0), alleleMap);
for (int i = 1; i < g.Ploidy; i++)
{
write(g.Phased ? VCFConstants.PHASED : VCFConstants.UNPHASED);
writeAllele(g.getAllele(i), alleleMap);
}
continue;
}
else
{
string outputValue;
if (field.Equals(VCFConstants.GENOTYPE_FILTER_KEY))
{
outputValue = g.Filtered ? g.Filters : VCFConstants.PASSES_FILTERS_v4;
}
else
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.getAccessor(field);
IntGenotypeFieldAccessors.Accessor accessor = intGenotypeFieldAccessors.getAccessor(field);
if (accessor != null)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int[] intValues = accessor.getValues(g);
int[] intValues = accessor.getValues(g);
if (intValues == null)
{
outputValue = VCFConstants.MISSING_VALUE_v4;
}
else if (intValues.Length == 1) // fast path
{
outputValue = Convert.ToString(intValues[0]);
}
else
{
StringBuilder sb = new StringBuilder();
sb.Append(intValues[0]);
for (int i = 1; i < intValues.Length; i++)
{
sb.Append(",");
sb.Append(intValues[i]);
}
outputValue = sb.ToString();
}
}
else
{
object val = g.hasExtendedAttribute(field) ? g.getExtendedAttribute(field) : VCFConstants.MISSING_VALUE_v4;
VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(field);
if (metaData != null)
{
int numInFormatField = metaData.getCount(vc);
if (numInFormatField > 1 && val.Equals(VCFConstants.MISSING_VALUE_v4))
{
// If we have a missing field but multiple values are expected, we need to construct a new string with all fields.
// For example, if Number=2, the string has to be ".,."
StringBuilder sb = new StringBuilder(VCFConstants.MISSING_VALUE_v4);
for (int i = 1; i < numInFormatField; i++)
{
sb.Append(",");
sb.Append(VCFConstants.MISSING_VALUE_v4);
}
val = sb.ToString();
}
}
// assume that if key is absent, then the given string encoding suffices
outputValue = formatVCFField(val);
}
}
if (outputValue != null)
{
attrs.Add(outputValue);
}
}
}
// strip off trailing missing values
for (int i = attrs.Count - 1; i >= 0; i--)
{
if (isMissingValue(attrs[i]))
{
attrs.RemoveAt(i);
}
else
{
break;
}
}
for (int i = 0; i < attrs.Count; i++)
{
if (i > 0 || genotypeFormatKeys.Contains(VCFConstants.GENOTYPE_KEY))
{
write(VCFConstants.GENOTYPE_FIELD_SEPARATOR);
}
write(attrs[i]);
}
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
if (vc.NAlleles > BCF2Utils.MAX_ALLELES_IN_GENOTYPES)
{
throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.NAlleles + " at " + vc.Chr + ":" + vc.Start);
}
encodingType = BCF2Type.INT8;
buildAlleleMap(vc);
nValuesPerGenotype = vc.getMaxPloidy(2);
base.start(encoder, vc);
}
