/// <summary>
/// make a string representation of this header line </summary>
/// <returns> a string representation </returns>
protected internal override string toStringEncoding()
{
IDictionary <string, object> map = new OrderedGenericDictionary <string, object>();
map["ID"] = name;
object number;
switch (countType)
{
case Bio.VCF.VCFHeaderLineCount.A:
number = VCFConstants.PER_ALTERNATE_ALLELE_COUNT;
break;
case Bio.VCF.VCFHeaderLineCount.R:
number = VCFConstants.PER_ALLELE_COUNT;
break;
case Bio.VCF.VCFHeaderLineCount.G:
number = VCFConstants.PER_GENOTYPE_COUNT;
break;
case Bio.VCF.VCFHeaderLineCount.UNBOUNDED:
number = VCFConstants.UNBOUNDED_ENCODING_v4;
break;
case Bio.VCF.VCFHeaderLineCount.INTEGER:
default:
number = count;
break;
}
map["Number"] = number;
map["Type"] = type;
map["Description"] = description;
return(lineType.ToString() + "=" + VCFHeaderLine.toStringEncoding(map));
}
protected internal override string toStringEncoding()
{
OrderedGenericDictionary <string, string> map = new OrderedGenericDictionary <string, string>();
map["ID"] = name;
map.putAll(genericFields);
return(Key + "=" + VCFHeaderLine.toStringEncoding(map));
}
/// <summary>
/// Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
/// allocated VCFHeader with standard VCF header lines repaired as necessary
/// </summary>
/// <param name="header">
/// @return </param>
public static VCFHeader repairStandardHeaderLines(VCFHeader header)
{
ISet <VCFHeaderLine> newLines = new LinkedHashSet <VCFHeaderLine>();
foreach (VCFHeaderLine line in header.MetaDataInInputOrder)
{
VCFHeaderLine cur = line;
if (line is VCFFormatHeaderLine)
{
cur = formatStandards.repair((VCFFormatHeaderLine)line);
}
else if (line is VCFInfoHeaderLine)
{
cur = infoStandards.repair((VCFInfoHeaderLine)line);
}
newLines.Add(cur);
}
return(new VCFHeader(newLines, header.GenotypeSampleNames));
}
/// <summary>
/// Adds a header line to the header metadata.
/// </summary>
/// <param name="headerLine"> Line to add to the existing metadata component. </param>
private void addMetaDataLine(VCFHeaderLine headerLine)
{
mMetaData.Add(headerLine);
loadMetaDataMaps();
}