public void check(String gt, String ad, String aq, Double expQad) {
final VcfRecord rec = new VcfRecord("seq", 0, "A");
rec.addFormatAndSample("GT", gt);
rec.addFormatAndSample("AD", ad);
rec.addFormatAndSample("AQ", aq);
assertEquals(expQad, new MeanQualityDifferenceAnnotation().getValue(rec, 0));
}
public void testAnnotate() {
final NullModelBuilder amb =
getModelBuilder(new String[] {"GQ"}, new String[] {}, new String[] {});
assertNotNull(amb);
amb.setModelParameters(new Properties());
amb.build();
final AbstractPredictModel apm = amb.getModel();
assertNotNull(apm);
final VcfRecord record =
VcfReader.vcfLineToRecord(
"chr5\t12041\trs55926606\tA\tT\t100\tPASS\tXRX\tGT:GQ\t0|1:12.3\t.\t1|1:99.9");
final String s = record.toString();
apm.annotate(record);
assertEquals(s, record.toString());
}
@Override
public void annotateSample(VcfRecord record, int sampleNo) {
record.setFormatAndSample(getField(), mData, sampleNo);
}
@Override
public void annotate(VcfRecord record) {
for (int s = 0; s < record.getNumberOfSamples(); s++) {
annotateSample(record, s);
}
}