@Test
public void testTrueProbWithVerySmallValue() {
final byte actual = QualityUtils.trueProbToQual(1.7857786272673852E-19);
Assert.assertEquals(
actual,
1,
"Failed to convert true prob of very small value 1.7857786272673852E-19 to 1 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);
}
}
@Test
public void testTrueProbWithMinDouble() {
final byte actual = QualityUtils.trueProbToQual(Double.MIN_VALUE);
Assert.assertEquals(actual, 1, "Failed to convert true prob of min double to 1 qual");
}