/// <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 format header line
/// </summary>
/// <param name="name"> the name for this header line </param>
/// <param name="count"> the count type for this header line </param>
/// <param name="type"> the type for this header line </param>
/// <param name="description"> the description for this header line </param>
/// <param name="lineType"> the header line type </param>
protected internal VCFCompoundHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description, SupportedHeaderLineType lineType) : base(lineType.ToString(), "")
{
this.name = name;
this.countType = count;
this.type = type;
this.description = description;
this.lineType = lineType;
validate();
}
public VCFInfoHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description) : base(name, count, type, description, SupportedHeaderLineType.INFO)
{
}
/// <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_ALLELE_COUNT))
{
countType = VCFHeaderLineCount.A;
}
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"]);
}
catch (Exception e)
{
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 System.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 format header line
/// </summary>
/// <param name="name"> the name for this header line </param>
/// <param name="count"> the count type for this header line </param>
/// <param name="type"> the type for this header line </param>
/// <param name="description"> the description for this header line </param>
/// <param name="lineType"> the header line type </param>
protected internal VCFCompoundHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description, SupportedHeaderLineType lineType) : base(lineType.ToString(), "")
{
this.name = name;
this.countType = count;
this.type = type;
this.description = description;
this.lineType = lineType;
validate();
}
public virtual void setNumberToUnbounded()
{
countType = VCFHeaderLineCount.UNBOUNDED;
count = -1;
}
public VCFFormatHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description)
: base(name, count, type, description, SupportedHeaderLineType.FORMAT)
{
}
public VCFFormatHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description)
: base(name, count, type, description, SupportedHeaderLineType.FORMAT)
{
}
public virtual void setNumberToUnbounded()
{
countType = VCFHeaderLineCount.UNBOUNDED;
count = -1;
}
public VCFInfoHeaderLine(string name, VCFHeaderLineCount count, VCFHeaderLineType type, string description) : base(name, count, type, description, SupportedHeaderLineType.INFO)
{
}