/**
* Add a "key=value" tuple the info field
*
* @param key : INFO key name
* @param value : Can be null if it is a boolean field.
*/
public void addInfo(String key, String value) {
if (!isValidInfoKey(key))
throw new RuntimeException(
"Illegal INFO key / name. Key: \""
+ key
+ "\" does not match regular expression ^[A-Za-z_][0-9A-Za-z_.]*$");
if (!isValidInfoValue(value))
throw new RuntimeException(
"No white-space, semi-colons, or equals-signs are permitted in INFO field values. Name:\""
+ key
+ "\" Value:\""
+ value
+ "\"");
// Remove previous 'key' for INFO field?
removeInfo(key);
// Is this a 'flag'?
boolean isFlag = false;
VcfHeader vcfHeader = vcfFileIterator.getVcfHeader();
if (vcfHeader != null) {
VcfHeaderInfo vcfHeaderInfo = vcfFileIterator.getVcfHeader().getVcfInfo(key);
isFlag = (vcfHeaderInfo != null) && (vcfHeaderInfo.getVcfInfoType() == VcfInfoType.Flag);
}
// Add to info hash (if available)
if (info != null) info.put(key, value);
// Append value to infoStr
String addInfoStr = key + (value != null && !isFlag ? "=" + value : ""); // String to append
if ((infoStr == null) || infoStr.isEmpty()) infoStr = addInfoStr;
else {
if (!infoStr.endsWith(SUB_FIELD_SEP))
infoStr += SUB_FIELD_SEP; // Do we need to add a semicolon?
infoStr += addInfoStr; // Add info string
}
}
