/// <summary>
/// returns true if we're equal to another compounder header line </summary>
/// <param name="o"> a compound header line </param>
/// <returns> true if equal </returns>
public override bool Equals(object o)
{
if (!(o is VCFCompoundHeaderLine))
{
return(false);
}
VCFCompoundHeaderLine other = (VCFCompoundHeaderLine)o;
return(equalsExcludingDescription(other) && description.Equals(other.description));
}
public static VCFCompoundHeaderLine GetMetaDataForField(VCFHeader header, string field)
{
VCFCompoundHeaderLine metaData = header.getFormatHeaderLine(field);
if (metaData == null)
{
metaData = header.getInfoHeaderLine(field);
}
if (metaData == null)
{
throw new VCFParsingError("Fully decoding VariantContext requires header line for all fields, but none was found for " + field);
}
return(metaData);
}
private object decodeOne (string field, string str, VCFCompoundHeaderLine format)
{
try {
if (str.Equals (VCFConstants.MISSING_VALUE_v4)) {
return null;
} else {
switch (format.Type) {
case VCFHeaderLineType.Character:
return str;
case VCFHeaderLineType.Flag:
bool b = Convert.ToBoolean (str) || str.Equals ("1");
if (b == false) {
throw new VCFParsingError ("VariantContext FLAG fields " + field + " cannot contain false values" + " as seen at " + Chr + ":" + Start);
}
return b;
case VCFHeaderLineType.String:
return str;
case VCFHeaderLineType.Integer:
return Convert.ToInt32 (str);
case VCFHeaderLineType.Float:
return Convert.ToDouble (str);
default:
throw new VCFParsingError ("Unexpected type for field" + field);
}
}
} catch (FormatException e) {
throw new VCFParsingError ("Could not decode field " + field + " with value " + str + " of declared type " + format.Type);
}
}
private object decodeValue (string field, object value, VCFCompoundHeaderLine format)
{
if (value is string) {
if (field.Equals (VCFConstants.GENOTYPE_PL_KEY)) {
return GenotypeLikelihoods.fromPLField ((string)value);
}
string str = (string)value;
if (str.IndexOf (',') != -1) {
string[] splits = str.Split (new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries);
IList<object> values = new List<object> (splits.Length);
for (int i = 0; i < splits.Length; i++) {
values.Add (decodeOne (field, splits [i], format));
}
return values;
} else {
return decodeOne (field, str, format);
}
} else if (value is IList && (((IList)value) [0]) is string) {
IList<string> asList = (IList<string>)value;
IList<object> values = new List<object> (asList.Count);
foreach (String s in asList) {
values.Add (decodeOne (field, s, format));
}
return values;
} else {
return value;
}
// allowMissingValuesComparedToHeader
}
public virtual bool sameLineTypeAndName(VCFCompoundHeaderLine other)
{
return lineType == other.lineType && name.Equals(other.name);
}
public virtual bool equalsExcludingDescription(VCFCompoundHeaderLine other)
{
return count == other.count && countType == other.countType && type == other.type && lineType == other.lineType && name.Equals(other.name);
}
public virtual bool sameLineTypeAndName(VCFCompoundHeaderLine other)
{
return(lineType == other.lineType && name.Equals(other.name));
}
public virtual bool equalsExcludingDescription(VCFCompoundHeaderLine other)
{
return(count == other.count && countType == other.countType && type == other.type && lineType == other.lineType && name.Equals(other.name));
}