/// <summary>
/// Try to get the nGenotypeFields as efficiently as possible.
///
/// If this is a lazy BCF2 object just grab the field count from there,
/// otherwise do the whole counting by types test in the actual data
/// </summary>
/// <param name="vc">
/// @return </param>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final int getNGenotypeFormatFields(final VariantContext vc)
private int getNGenotypeFormatFields(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);
return(lazyData != null ? lazyData.nGenotypeFields : VCFWriter.calcVCFGenotypeKeys(vc, header).Count);
}
/// <summary>
/// Can we safely write on the raw (undecoded) genotypes of an input VC?
///
/// The cache depends on the undecoded lazy data header == lastVCFHeaderOfUnparsedGenotypes, in
/// which case we return the previous result. If it's not cached, we use the BCF2Util to
/// compare the VC header with our header (expensive) and cache it.
/// </summary>
/// <param name="lazyData">
/// @return </param>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private boolean canSafelyWriteRawGenotypesBytes(final org.broadinstitute.variant.bcf2.BCF2Codec.LazyData lazyData)
private bool canSafelyWriteRawGenotypesBytes(BCF2Codec.LazyData lazyData)
{
if (lazyData.header != lastVCFHeaderOfUnparsedGenotypes)
{
// result is already cached
canPassOnUnparsedGenotypeDataForLastVCFHeader = BCF2Utils.headerLinesAreOrderedConsistently(this.header, lazyData.header);
lastVCFHeaderOfUnparsedGenotypes = lazyData.header;
}
return(canPassOnUnparsedGenotypeDataForLastVCFHeader);
}
//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);
}
