@Test
public void testQualCaches() {
Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 20), 0.01, 1e-6);
Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 20), -2.0, 1e-6);
Assert.assertEquals(QualityUtils.qualToProb((byte) 20), 0.99, 1e-6);
Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 20), -0.0043648054, 1e-6);
Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 30), 0.001, 1e-6);
Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 30), -3.0, 1e-6);
Assert.assertEquals(QualityUtils.qualToProb((byte) 30), 0.999, 1e-6);
Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 30), -0.000434511774, 1e-6);
Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 40), 0.0001, 1e-6);
Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 40), -4.0, 1e-6);
Assert.assertEquals(QualityUtils.qualToProb((byte) 40), 0.9999, 1e-6);
Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 40), -4.34316198e-5, 1e-6);
}
@Test()
public void testQualToErrorProbDouble() {
for (double qual = 3.0; qual < 255.0; qual += 0.1) {
final double expected = Math.pow(10.0, qual / -10.0);
Assert.assertEquals(
QualityUtils.qualToErrorProb(qual),
expected,
TOLERANCE,
"failed qual->error prob for double qual " + qual);
}
}
/** Example testng test using MyDataProvider */
@Test(dataProvider = "QualTest")
public void testMyData(final byte qual, final double errorRate) {
final double trueRate = 1 - errorRate;
final double actualErrorRate = QualityUtils.qualToErrorProb(qual);
Assert.assertEquals(actualErrorRate, errorRate, TOLERANCE);
final double actualTrueRate = QualityUtils.qualToProb(qual);
Assert.assertEquals(actualTrueRate, trueRate, TOLERANCE);
// log10 tests
final double actualLog10ErrorRate = QualityUtils.qualToErrorProbLog10(qual);
Assert.assertEquals(actualLog10ErrorRate, Math.log10(errorRate), TOLERANCE);
final double actualLog10TrueRate = QualityUtils.qualToProbLog10(qual);
Assert.assertEquals(actualLog10TrueRate, Math.log10(trueRate), TOLERANCE);
// test that we can convert our error rates to quals, accounting for boundaries
final int expectedQual = Math.max(Math.min(qual & 0xFF, QualityUtils.MAX_SAM_QUAL_SCORE), 1);
final byte actualQual = QualityUtils.trueProbToQual(trueRate);
Assert.assertEquals(actualQual, expectedQual & 0xFF);
final byte actualQualFromErrorRate = QualityUtils.errorProbToQual(errorRate);
Assert.assertEquals(actualQualFromErrorRate, expectedQual & 0xFF);
for (int maxQual = 10; maxQual < QualityUtils.MAX_SAM_QUAL_SCORE; maxQual++) {
final byte maxAsByte = (byte) (maxQual & 0xFF);
final byte expectedQual2 = (byte) (Math.max(Math.min(qual & 0xFF, maxQual), 1) & 0xFF);
final byte actualQual2 = QualityUtils.trueProbToQual(trueRate, maxAsByte);
Assert.assertEquals(actualQual2, expectedQual2, "Failed with max " + maxQual);
final byte actualQualFromErrorRate2 = QualityUtils.errorProbToQual(errorRate, maxAsByte);
Assert.assertEquals(actualQualFromErrorRate2, expectedQual2, "Failed with max " + maxQual);
// test the integer routines
final byte actualQualInt2 = QualityUtils.trueProbToQual(trueRate, maxQual);
Assert.assertEquals(actualQualInt2, expectedQual2, "Failed with max " + maxQual);
final byte actualQualFromErrorRateInt2 = QualityUtils.errorProbToQual(errorRate, maxQual);
Assert.assertEquals(actualQualFromErrorRateInt2, expectedQual2, "Failed with max " + maxQual);
}
}