/**
* 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());
}
