Arrays.fill(insQuals, (byte)PairHMMLikelihoodCalculationEngine.INITIAL_QSCORE);
Arrays.fill(delQuals, (byte)PairHMMLikelihoodCalculationEngine.INITIAL_QSCORE);
engine.applyPCRErrorModel(readString.getBytes(), insQuals, delQuals);
final RepeatCovariate repeatCovariate = new RepeatLengthCovariate();
repeatCovariate.initialize(PairHMMLikelihoodCalculationEngine.MAX_STR_UNIT_LENGTH, PairHMMLikelihoodCalculationEngine.MAX_REPEAT_LENGTH);
for ( int i = 1; i < insQuals.length; i++ ) {
final int repeatLengthFromCovariate = repeatCovariate.findTandemRepeatUnits(readString.getBytes(), i-1).getSecond();
final byte adjustedScore = PairHMMLikelihoodCalculationEngine.getErrorModelAdjustedQual(repeatLengthFromCovariate, 3.0);
Assert.assertEquals(insQuals[i-1], adjustedScore);
Assert.assertEquals(delQuals[i-1], adjustedScore);
}