176 lines
7.6 KiB
Java
176 lines
7.6 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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/**
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: 3/21/12
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*/
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import org.broadinstitute.sting.BaseTest;
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import org.testng.Assert;
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import org.testng.annotations.BeforeClass;
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import org.testng.annotations.DataProvider;
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import org.testng.annotations.Test;
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import java.util.*;
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/**
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* Basic unit test for QualityUtils class
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*/
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public class QualityUtilsUnitTest extends BaseTest {
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final private static double TOLERANCE = 1e-9;
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@BeforeClass
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public void init() {
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}
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@DataProvider(name = "QualTest")
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public Object[][] makeMyDataProvider() {
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List<Object[]> tests = new ArrayList<Object[]>();
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for ( int qual = 0; qual < 255; qual++ ) {
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tests.add(new Object[]{(byte)(qual & 0xFF), Math.pow(10.0, ((double)qual)/-10.0)});
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}
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return tests.toArray(new Object[][]{});
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}
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/**
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* Example testng test using MyDataProvider
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*/
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@Test(dataProvider = "QualTest")
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public void testMyData(final byte qual, final double errorRate) {
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final double trueRate = 1 - errorRate;
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final double actualErrorRate = QualityUtils.qualToErrorProb(qual);
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Assert.assertEquals(actualErrorRate, errorRate, TOLERANCE);
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final double actualTrueRate = QualityUtils.qualToProb(qual);
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Assert.assertEquals(actualTrueRate, trueRate, TOLERANCE);
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// log10 tests
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final double actualLog10ErrorRate = QualityUtils.qualToErrorProbLog10(qual);
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Assert.assertEquals(actualLog10ErrorRate, Math.log10(errorRate), TOLERANCE);
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final double actualLog10TrueRate = QualityUtils.qualToProbLog10(qual);
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Assert.assertEquals(actualLog10TrueRate, Math.log10(trueRate), TOLERANCE);
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// test that we can convert our error rates to quals, accounting for boundaries
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final int expectedQual = Math.max(Math.min(qual & 0xFF, QualityUtils.MAX_SAM_QUAL_SCORE), 1);
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final byte actualQual = QualityUtils.trueProbToQual(trueRate);
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Assert.assertEquals(actualQual, expectedQual & 0xFF);
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final byte actualQualFromErrorRate = QualityUtils.errorProbToQual(errorRate);
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Assert.assertEquals(actualQualFromErrorRate, expectedQual & 0xFF);
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for ( int maxQual = 10; maxQual < QualityUtils.MAX_SAM_QUAL_SCORE; maxQual++ ) {
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final byte maxAsByte = (byte)(maxQual & 0xFF);
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final byte expectedQual2 = (byte)(Math.max(Math.min(qual & 0xFF, maxQual), 1) & 0xFF);
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final byte actualQual2 = QualityUtils.trueProbToQual(trueRate, maxAsByte);
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Assert.assertEquals(actualQual2, expectedQual2, "Failed with max " + maxQual);
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final byte actualQualFromErrorRate2 = QualityUtils.errorProbToQual(errorRate, maxAsByte);
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Assert.assertEquals(actualQualFromErrorRate2, expectedQual2, "Failed with max " + maxQual);
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// test the integer routines
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final byte actualQualInt2 = QualityUtils.trueProbToQual(trueRate, maxQual);
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Assert.assertEquals(actualQualInt2, expectedQual2, "Failed with max " + maxQual);
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final byte actualQualFromErrorRateInt2 = QualityUtils.errorProbToQual(errorRate, maxQual);
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Assert.assertEquals(actualQualFromErrorRateInt2, expectedQual2, "Failed with max " + maxQual);
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}
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}
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@Test
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public void testQualCaches() {
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Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 20), 0.01, 1e-6);
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Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 20), -2.0, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProb((byte) 20), 0.99, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 20), -0.0043648054, 1e-6);
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Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 30), 0.001, 1e-6);
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Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 30), -3.0, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProb((byte) 30), 0.999, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 30), -0.000434511774, 1e-6);
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Assert.assertEquals(QualityUtils.qualToErrorProb((byte) 40), 0.0001, 1e-6);
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Assert.assertEquals(QualityUtils.qualToErrorProbLog10((byte) 40), -4.0, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProb((byte) 40), 0.9999, 1e-6);
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Assert.assertEquals(QualityUtils.qualToProbLog10((byte) 40), -4.34316198e-5, 1e-6);
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}
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@Test()
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public void testBoundingDefault() {
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for ( int qual = 0; qual < 1000; qual++ ) {
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final byte expected = (byte)Math.max(Math.min(qual, QualityUtils.MAX_SAM_QUAL_SCORE), 1);
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Assert.assertEquals(QualityUtils.boundQual(qual), expected);
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}
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}
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@Test()
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public void testBoundingWithMax() {
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for ( int max = 10; max < 255; max += 50 ) {
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for ( int qual = 0; qual < 1000; qual++ ) {
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final int expected = Math.max(Math.min(qual, max), 1);
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Assert.assertEquals(QualityUtils.boundQual(qual, (byte)(max & 0xFF)) & 0xFF, expected & 0xFF, "qual " + qual + " max " + max);
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}
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}
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}
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@DataProvider(name = "PhredScaleDoubleOps")
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public Object[][] makePhredDoubleTest() {
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List<Object[]> tests = new ArrayList<Object[]>();
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tests.add(new Object[]{0.0, -10 * Math.log10(Double.MIN_VALUE)});
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tests.add(new Object[]{1.0, 0.0});
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for ( int pow = 1; pow < 20; pow++ ) {
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tests.add(new Object[]{Math.pow(10.0, -1.0 * pow), pow * 10});
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tests.add(new Object[]{Math.pow(10.0, -1.5 * pow), pow * 15});
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}
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return tests.toArray(new Object[][]{});
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}
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@Test()
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public void testQualToErrorProbDouble() {
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for ( double qual = 3.0; qual < 255.0; qual += 0.1 ) {
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final double expected = Math.pow(10.0, qual / -10.0);
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Assert.assertEquals(QualityUtils.qualToErrorProb(qual), expected, TOLERANCE, "failed qual->error prob for double qual " + qual);
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}
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}
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@Test(dataProvider = "PhredScaleDoubleOps")
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public void testPhredScaleDoubleOps(final double errorRate, final double expectedPhredScaled) {
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final double actualError = QualityUtils.phredScaleErrorRate(errorRate);
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Assert.assertEquals(actualError, expectedPhredScaled, TOLERANCE);
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final double trueRate = 1 - errorRate;
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final double actualTrue = QualityUtils.phredScaleCorrectRate(trueRate);
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if ( trueRate == 1.0 ) {
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Assert.assertEquals(actualTrue, QualityUtils.MIN_PHRED_SCALED_QUAL);
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} else {
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final double tol = errorRate < 1e-10 ? 10.0 : 1e-3;
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Assert.assertEquals(actualTrue, expectedPhredScaled, tol);
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}
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}
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} |