// --------------------------------------------------------------------------------
//
// 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);
}
}
