//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: public static VCFHeader writeHeader(VCFHeader header, final Writer writer, final boolean doNotWriteGenotypes, final String versionLine, final String streamNameForError)
public static VCFHeader writeHeader(VCFHeader header, Writer writer, bool doNotWriteGenotypes, string versionLine, string streamNameForError)
{
header = doNotWriteGenotypes ? new VCFHeader(header.MetaDataInSortedOrder) : header;
try
{
// the file format field needs to be written first
writer.write(versionLine + "\n");
foreach (VCFHeaderLine line in header.MetaDataInSortedOrder)
{
if (VCFHeaderVersion.isFormatString(line.Key))
{
continue;
}
writer.write(VCFHeader.METADATA_INDICATOR);
writer.write(line.ToString());
writer.write("\n");
}
// write out the column line
writer.write(VCFHeader.HEADER_INDICATOR);
bool isFirst = true;
foreach (string field in VCFHeader.HEADER_FIELDS)
{
if (isFirst)
{
isFirst = false; // don't write out a field separator
}
else
{
writer.write(VCFConstants.FIELD_SEPARATOR);
}
writer.write(field.ToString());
}
if (header.hasGenotypingData())
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write("FORMAT");
foreach (string sample in header.GenotypeSampleNames)
{
writer.write(VCFConstants.FIELD_SEPARATOR);
writer.write(sample);
}
}
writer.write("\n");
writer.flush(); // necessary so that writing to an output stream will work
}
catch (IOException e)
{
throw new Exception("IOException writing the VCF header to " + streamNameForError, e);
}
return(header);
}
public VCFInfoHeaderLine(string line, VCFHeaderVersion version) : base(line, version, SupportedHeaderLineType.INFO)
{
}
/// <summary>
/// create a VCF info header line
/// </summary>
/// <param name="line"> the header line </param>
/// <param name="version"> the vcf header version </param>
public VCFFilterHeaderLine(string line, VCFHeaderVersion version) : base(line, version, "FILTER", "ID", "Description")
{
}
public VCFFormatHeaderLine(string line, VCFHeaderVersion version)
: base(line, version, SupportedHeaderLineType.FORMAT)
{
}
public VCFFormatHeaderLine(string line, VCFHeaderVersion version)
: base(line, version, SupportedHeaderLineType.FORMAT)
{
}
public VCFInfoHeaderLine(string line, VCFHeaderVersion version) : base(line, version, SupportedHeaderLineType.INFO)
{
}
