//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) { }