@Test(dataProvider = "PhredScaleDoubleOps")
public void testPhredScaleDoubleOps(final double errorRate, final double expectedPhredScaled) {
final double actualError = QualityUtils.phredScaleErrorRate(errorRate);
Assert.assertEquals(actualError, expectedPhredScaled, TOLERANCE);
final double trueRate = 1 - errorRate;
final double actualTrue = QualityUtils.phredScaleCorrectRate(trueRate);
if (trueRate == 1.0) {
Assert.assertEquals(actualTrue, QualityUtils.MIN_PHRED_SCALED_QUAL);
} else {
final double tol = errorRate < 1e-10 ? 10.0 : 1e-3;
Assert.assertEquals(actualTrue, expectedPhredScaled, tol);
}
}
@Test()
public void testBoundingDefault() {
for (int qual = 0; qual < 1000; qual++) {
final byte expected = (byte) Math.max(Math.min(qual, QualityUtils.MAX_SAM_QUAL_SCORE), 1);
Assert.assertEquals(QualityUtils.boundQual(qual), expected);
}
}
private VariantCallContext estimateReferenceConfidence(
VariantContext vc,
Map<String, AlignmentContext> contexts,
double theta,
boolean ignoreCoveredSamples,
double initialPofRef) {
if (contexts == null) return null;
double P_of_ref = initialPofRef;
// for each sample that we haven't examined yet
for (String sample : samples) {
boolean isCovered = contexts.containsKey(sample);
if (ignoreCoveredSamples && isCovered) continue;
int depth = 0;
if (isCovered) {
depth = contexts.get(sample).getBasePileup().depthOfCoverage();
}
P_of_ref *= 1.0 - (theta / 2.0) * getRefBinomialProb(depth);
}
return new VariantCallContext(
vc,
QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING,
false);
}
@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");
}
@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);
}
}
@Test()
public void testBoundingWithMax() {
for (int max = 10; max < 255; max += 50) {
for (int qual = 0; qual < 1000; qual++) {
final int expected = Math.max(Math.min(qual, max), 1);
Assert.assertEquals(
QualityUtils.boundQual(qual, (byte) (max & 0xFF)) & 0xFF,
expected & 0xFF,
"qual " + qual + " max " + max);
}
}
}
/** 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 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 testTrueProbWithMinDouble() {
final byte actual = QualityUtils.trueProbToQual(Double.MIN_VALUE);
Assert.assertEquals(actual, 1, "Failed to convert true prob of min double to 1 qual");
}
protected boolean confidentlyCalled(double conf, double PofF) {
return conf >= UAC.STANDARD_CONFIDENCE_FOR_CALLING
|| (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
&& QualityUtils.phredScaleErrorRate(PofF) >= UAC.STANDARD_CONFIDENCE_FOR_CALLING);
}