/**
* Walks over the VCF header and repairs the standard VCF header lines in it, returning a freshly
* allocated {@link VCFHeader} with standard VCF header lines repaired as necessary.
*/
public static VCFHeader repairStandardHeaderLines(final VCFHeader header) {
final Set<VCFHeaderLine> newLines =
new LinkedHashSet<VCFHeaderLine>(header.getMetaDataInInputOrder().size());
for (VCFHeaderLine line : header.getMetaDataInInputOrder()) {
if (line instanceof VCFFormatHeaderLine) {
line = formatStandards.repair((VCFFormatHeaderLine) line);
} else if (line instanceof VCFInfoHeaderLine) {
line = infoStandards.repair((VCFInfoHeaderLine) line);
}
newLines.add(line);
}
return new VCFHeader(newLines, header.getGenotypeSamples());
}
/**
* Adds header lines for each of the format fields in IDs to header, returning the set of {@code
* IDs} without standard descriptions, unless {@code throwErrorForMissing} is true, in which case
* this situation results in a {@link TribbleException}
*/
public static Set<String> addStandardFormatLines(
final Set<VCFHeaderLine> headerLines,
final boolean throwErrorForMissing,
final Collection<String> IDs) {
return formatStandards.addToHeader(headerLines, IDs, throwErrorForMissing);
}
private static void registerStandard(final VCFFormatHeaderLine line) {
formatStandards.add(line);
}
private static void registerStandard(final VCFInfoHeaderLine line) {
infoStandards.add(line);
}
/**
* Returns the standard info line for {@code ID}. If none exists, return {@code null} or throw a
* {@link TribbleException}, depending on {@code throwErrorForMissing}.
*/
public static VCFInfoHeaderLine getInfoLine(final String ID, final boolean throwErrorForMissing) {
return infoStandards.get(ID, throwErrorForMissing);
}
/**
* Returns the standard format line for {@code ID}. If none exists, throw an {@link
* TribbleException}
*/
public static VCFFormatHeaderLine getFormatLine(final String ID) {
return formatStandards.get(ID, true);
}
/**
* Returns the standard format line for {@code ID}. If none exists, return null or throw an
* exception, depending on {@code throwErrorForMissing}.
*/
public static VCFFormatHeaderLine getFormatLine(
final String ID, final boolean throwErrorForMissing) {
return formatStandards.get(ID, throwErrorForMissing);
}