/// <summary>
/// create a VCF format header line
/// </summary>
/// <param name="line"> the header line </param>
/// <param name="version"> the VCF header version </param>
/// <param name="lineType"> the header line type
/// </param>
protected internal VCFCompoundHeaderLine(string line, VCFHeaderVersion version, SupportedHeaderLineType lineType) : base(lineType.ToString(), "")
{
IDictionary <string, string> mapping = VCFHeaderLineTranslator.parseLine(version, line, "ID", "Number", "Type", "Description");
name = mapping["ID"];
count = -1;
string numberStr = mapping["Number"];
if (numberStr.Equals(VCFConstants.PER_ALTERNATE_ALLELE_COUNT))
{
countType = VCFHeaderLineCount.A;
}
else if (numberStr.Equals(VCFConstants.PER_ALLELE_COUNT))
{
countType = VCFHeaderLineCount.R;
}
else if (numberStr.Equals(VCFConstants.PER_GENOTYPE_COUNT))
{
countType = VCFHeaderLineCount.G;
}
else if (((version == VCFHeaderVersion.VCF4_0 || version == VCFHeaderVersion.VCF4_1 || version == VCFHeaderVersion.VCF4_2) && numberStr.Equals(VCFConstants.UNBOUNDED_ENCODING_v4)) || ((version == VCFHeaderVersion.VCF3_2 || version == VCFHeaderVersion.VCF3_3) && numberStr.Equals(VCFConstants.UNBOUNDED_ENCODING_v3)))
{
countType = VCFHeaderLineCount.UNBOUNDED;
}
else
{
countType = VCFHeaderLineCount.INTEGER;
count = Convert.ToInt32(numberStr);
}
if (count < 0 && countType == VCFHeaderLineCount.INTEGER)
{
throw new VCFParsingError("Count < 0 for fixed size VCF header field " + name);
}
try
{
type = (VCFHeaderLineType)Enum.Parse(typeof(VCFHeaderLineType), mapping["Type"]);
}
#pragma warning disable 0168
catch (Exception e)
#pragma warning restore 0168
{
throw new VCFParsingError(mapping["Type"] + " is not a valid type in the VCF specification (note that types are case-sensitive)");
}
if (type == VCFHeaderLineType.Flag && !allowFlagValues())
{
throw new ArgumentException("Flag is an unsupported type for this kind of field");
}
description = mapping["Description"];
if (description == null && ALLOW_UNBOUND_DESCRIPTIONS) // handle the case where there's no description provided
{
description = UNBOUND_DESCRIPTION;
}
this.lineType = lineType;
validate();
}
/// <summary>
/// create a VCF info header line
/// </summary>
/// <param name="line"> the header line </param>
/// <param name="version"> the vcf header version </param>
/// <param name="key"> the key for this header line </param>
/// <param name="expectedTagOrdering"> the tag ordering expected for this header line </param>
public VCFSimpleHeaderLine(string line, VCFHeaderVersion version, string key, params string[] expectedTagOrdering)
: this(key, VCFHeaderLineTranslator.parseLine(version, line, expectedTagOrdering), expectedTagOrdering)
{
}
