/// <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);
}
//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);
}
// --------------------------------------------------------------------------------
//
// Interface functions
//
// --------------------------------------------------------------------------------
public override void writeHeader(VCFHeader header)
{
// make sure the header is sorted correctly
header = new VCFHeader(header.MetaDataInSortedOrder, header.GenotypeSampleNames);
// create the config offsets map
if (header.ContigLines.Count == 0)
{
if (ALLOW_MISSING_CONTIG_LINES)
{
if (GeneralUtils.DEBUG_MODE_ENABLED)
{
Console.Error.WriteLine("No contig dictionary found in header, falling back to reference sequence dictionary");
}
createContigDictionary(VCFUtils.makeContigHeaderLines(RefDict, null));
}
else
{
throw new IllegalStateException("Cannot write BCF2 file with missing contig lines");
}
}
else
{
createContigDictionary(header.ContigLines);
}
// set up the map from dictionary string values -> offset
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final ArrayList<String> dict = org.broadinstitute.variant.bcf2.BCF2Utils.makeDictionary(header);
List <string> dict = BCF2Utils.makeDictionary(header);
for (int i = 0; i < dict.Count; i++)
{
stringDictionaryMap[dict[i]] = i;
}
sampleNames = header.GenotypeSampleNames.ToArray();
// setup the field encodings
fieldManager.setup(header, encoder, stringDictionaryMap);
try
{
// write out the header into a byte stream, get it's length, and write everything to the file
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final ByteArrayOutputStream capture = new ByteArrayOutputStream();
ByteArrayOutputStream capture = new ByteArrayOutputStream();
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final OutputStreamWriter writer = new OutputStreamWriter(capture);
OutputStreamWriter writer = new OutputStreamWriter(capture);
this.header = VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.VersionLine, "BCF2 stream");
writer.append('\0'); // the header is null terminated by a byte
writer.close();
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final byte[] headerBytes = capture.toByteArray();
sbyte[] headerBytes = capture.toByteArray();
(new BCFVersion(MAJOR_VERSION, MINOR_VERSION)).write(outputStream);
BCF2Type.INT32.write(headerBytes.Length, outputStream);
outputStream.write(headerBytes);
}
catch (IOException e)
{
throw new Exception("BCF2 stream: Got IOException while trying to write BCF2 header", e);
}
}
