/// <summary>
/// Create the info string; assumes that no values are null
/// </summary>
/// <param name="infoFields"> a map of info fields </param>
/// <exception cref="IOException"> for writer </exception>
private string getInfoString(IDictionary <string, string> infoFields)
{
if (infoFields.Count == 0)
{
return(VCFConstants.EMPTY_INFO_FIELD);
}
bool isFirst = true;
string toReturn = "";
foreach (KeyValuePair <string, string> entry in infoFields)
{
if (isFirst)
{
isFirst = false;
}
else
{
toReturn += VCFConstants.INFO_FIELD_SEPARATOR;
}
string key = entry.Key;
toReturn += key;
if (!entry.Value.Equals(""))
{
VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
if (metaData == null || metaData.CountType != VCFHeaderLineCount.INTEGER || metaData.Count != 0)
{
toReturn += "=";
toReturn += entry.Value;
}
}
}
return(toReturn);
}
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);
}
/// <summary>
/// parse out the info fields into a dictionary of key/values </summary>
/// <param name="infoField"> the fields </param>
/// <returns> a mapping of keys to objects </returns>
private IDictionary <string, object> parseInfo(string infoField)
{
IDictionary <string, object> attributes = new Dictionary <string, object> ();
if (infoField.Length == 0)
{
generateException("The VCF specification requires a valid info field");
}
if (!infoField.Equals(VCFConstants.EMPTY_INFO_FIELD))
{
if (infoField.IndexOf("\t") != -1 || infoField.IndexOf(" ") != -1)
{
generateException("The VCF specification does not allow for whitespace in the INFO field");
}
string[] infoFieldArray = infoField.Split(VCFConstants.INFO_FIELD_SEPARATOR_CHAR_AS_ARRAY);
//int infoFieldSplitSize = ParsingUtils.Split(infoField, infoFieldArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR, false);
for (int i = 0; i < infoFieldArray.Length; i++)
{
string key;
object value;
int eqI = infoFieldArray [i].IndexOf("=");
if (eqI != -1)
{
key = infoFieldArray [i].Substring(0, eqI);
string valueString = infoFieldArray [i].Substring(eqI + 1);
// split on the INFO field separator
string[] infoValueArray = valueString.Split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR);
//int infoValueSplitSize = ParsingUtils.Split(valueString, infoValueArray, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR, false);
if (infoValueArray.Length == 1) // infoValueSplitSize == 1)
{
value = infoValueArray [0];
VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key);
if (headerLine != null && headerLine.Type == VCFHeaderLineType.Flag && value.Equals("0"))
{
// deal with the case where a flag field has =0, such as DB=0, by skipping the add
continue;
}
}
else
{
//List<string> valueList = new List<string>(infoValueArray);
value = infoValueArray;
}
}
else
{
key = infoFieldArray [i];
VCFInfoHeaderLine headerLine = header.getInfoHeaderLine(key);
if (headerLine != null && headerLine.Type != VCFHeaderLineType.Flag)
{
//Note: This was originally a warning that was only thrown once
throw new VCFParsingError("Found info key " + key + " without a = value, but the header says the field is of type " + headerLine.Type + " but this construct is only value for FLAG type fields");
//Old version just set this value
// value = VCFConstants.MISSING_VALUE_v4;
}
else
{
value = true;
}
}
// this line ensures that key/value pairs that look like key=; are parsed correctly as MISSING
if ("".Equals(value))
{
value = VCFConstants.MISSING_VALUE_v4;
}
//TODO: We should have enough information in the header here to
attributes [key] = value;
}
}
return(attributes);
}
