@Test(dataProvider = "PcrErrorModelTestProvider", enabled = true)
public void createPcrErrorModelTest(final String repeat, final int repeatLength) {
final LikelihoodCalculationEngine engine =
new LikelihoodCalculationEngine(
(byte) 0,
false,
PairHMM.HMM_IMPLEMENTATION.ORIGINAL,
0.0,
true,
LikelihoodCalculationEngine.PCR_ERROR_MODEL.CONSERVATIVE);
final String readString = Utils.dupString(repeat, repeatLength);
final byte[] insQuals = new byte[readString.length()];
final byte[] delQuals = new byte[readString.length()];
Arrays.fill(insQuals, (byte) LikelihoodCalculationEngine.INITIAL_QSCORE);
Arrays.fill(delQuals, (byte) LikelihoodCalculationEngine.INITIAL_QSCORE);
engine.applyPCRErrorModel(readString.getBytes(), insQuals, delQuals);
final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
repeatCovariate.initialize(
LikelihoodCalculationEngine.MAX_STR_UNIT_LENGTH,
LikelihoodCalculationEngine.MAX_REPEAT_LENGTH);
for (int i = 1; i < insQuals.length; i++) {
final int repeatLengthFromCovariate =
repeatCovariate.findTandemRepeatUnits(readString.getBytes(), i - 1).getSecond();
final byte adjustedScore =
LikelihoodCalculationEngine.getErrorModelAdjustedQual(repeatLengthFromCovariate, 3.0);
Assert.assertEquals(insQuals[i - 1], adjustedScore);
Assert.assertEquals(delQuals[i - 1], adjustedScore);
}
}
