//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private byte[] buildSamplesData(final VariantContext vc) throws IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private sbyte[] buildSamplesData(VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Codec.LazyData lazyData = getLazyData(vc);
BCF2Codec.LazyData lazyData = getLazyData(vc); // has critical side effects
if (lazyData != null)
{
// we never decoded any data from this BCF file, so just pass it back
return(lazyData.bytes);
}
// we have to do work to convert the VC into a BCF2 byte stream
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
IList <string> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
foreach (String field in genotypeFields)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldWriter.GenotypesWriter writer = fieldManager.getGenotypeFieldWriter(field);
BCF2FieldWriter.GenotypesWriter writer = fieldManager.getGenotypeFieldWriter(field);
if (writer == null)
{
errorUnexpectedFieldToWrite(vc, field, "FORMAT");
}
Debug.Assert(writer != null);
writer.start(encoder, vc);
foreach (String name in sampleNames)
{
Genotype g = vc.getGenotype(name);
if (g == null)
{
g = GenotypeBuilder.createMissing(name, writer.nValuesPerGenotype);
}
writer.addGenotype(encoder, vc, g);
}
writer.done(encoder, vc);
}
return(encoder.RecordBytes);
}
/// <summary>
/// Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header
///
/// Must be called before any of the getter methods will work
/// </summary>
/// <param name="header"> a VCFHeader containing description for every INFO and FORMAT field we'll attempt to write out to BCF </param>
/// <param name="encoder"> the encoder we are going to use to write out the BCF2 data </param>
/// <param name="stringDictionary"> a map from VCFHeader strings to their offsets for encoding </param>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public void setup(final VCFHeader header, final BCF2Encoder encoder, final java.util.Map<String, Integer> stringDictionary)
public virtual void setup(VCFHeader header, BCF2Encoder encoder, IDictionary <string, int?> stringDictionary)
{
foreach (VCFInfoHeaderLine line in header.InfoHeaderLines)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String field = line.getID();
string field = line.ID;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldWriter.SiteWriter writer = createInfoWriter(header, line, encoder, stringDictionary);
BCF2FieldWriter.SiteWriter writer = createInfoWriter(header, line, encoder, stringDictionary);
add(siteWriters, field, writer);
}
foreach (VCFFormatHeaderLine line in header.FormatHeaderLines)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String field = line.getID();
string field = line.ID;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldWriter.GenotypesWriter writer = createGenotypesWriter(header, line, encoder, stringDictionary);
BCF2FieldWriter.GenotypesWriter writer = createGenotypesWriter(header, line, encoder, stringDictionary);
add(genotypesWriters, field, writer);
}
}
