public void testCheckHeader() {
final AbstractDerivedAnnotation ann = new DummyDerivedAnnotation();
assertEquals(
"Derived annotation DUMMY missing required fields in VCF header (INFO fields: II) (FORMAT fields: FF)",
ann.checkHeader(null, new String[] {"II"}, new String[] {"FF"}));
final VcfHeader header = new VcfHeader();
header.addInfoField("II", MetaType.INTEGER, VcfNumber.ONE, "Info Field");
header.addFormatField("FF", MetaType.INTEGER, VcfNumber.ONE, "Format Field");
final String res = ann.checkHeader(header, new String[] {"II"}, new String[] {"FF"});
assertNull(res, res);
}
@Override
public void updateHeader(VcfHeader header) {
if (mFormats == null || mFormats.size() == 0) {
return;
}
final Iterator<FormatField> it = header.getFormatLines().iterator();
while (it.hasNext()) {
final FormatField format = it.next();
if (mKeepMode ^ mFormats.contains(format.getId())) {
it.remove();
}
}
}
@Override
public void updateHeader(VcfHeader header) {
header.addFormatField(getField(), MetaType.FLOAT, VcfNumber.ONE, "AVR score");
}
