/* * Copyright (c) 2012 The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.utils; /** * Created by IntelliJ IDEA. * User: rpoplin * Date: 3/21/12 */ import org.broadinstitute.sting.BaseTest; import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.util.*; /** * Basic unit test for QualityUtils class */ public class QualityUtilsUnitTest extends BaseTest { final private static double TOLERANCE = 1e-9; @BeforeClass public void init() { } @DataProvider(name = "QualTest") public Object[][] makeMyDataProvider() { List tests = new ArrayList(); for ( int qual = 0; qual < 255; qual++ ) { tests.add(new Object[]{(byte)(qual & 0xFF), Math.pow(10.0, ((double)qual)/-10.0)}); } return tests.toArray(new Object[][]{}); } /** * 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 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); } } @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); } } } @DataProvider(name = "PhredScaleDoubleOps") public Object[][] makePhredDoubleTest() { List tests = new ArrayList(); tests.add(new Object[]{0.0, -10 * Math.log10(Double.MIN_VALUE)}); tests.add(new Object[]{1.0, 0.0}); for ( int pow = 1; pow < 20; pow++ ) { tests.add(new Object[]{Math.pow(10.0, -1.0 * pow), pow * 10}); tests.add(new Object[]{Math.pow(10.0, -1.5 * pow), pow * 15}); } return tests.toArray(new Object[][]{}); } @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(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); } } }