From 9e10779fa77e34564e6050c768636a31f196e05b Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 21 Mar 2012 08:45:42 -0400 Subject: [PATCH] Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. --- .../sting/utils/QualityUtils.java | 34 +++++++--- .../sting/utils/QualityUtilsUnitTest.java | 66 +++++++++++++++++++ 2 files changed, 92 insertions(+), 8 deletions(-) create mode 100644 public/java/test/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java diff --git a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java index 7756ac71b..b5aa2598e 100755 --- a/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/QualityUtils.java @@ -22,6 +22,16 @@ public class QualityUtils { for (int i = 0; i < 256; i++) qualToErrorProbCache[i] = qualToErrorProbRaw(i); } + private static double qualToErrorProbLog10Cache[] = new double[256]; + static { + for (int i = 0; i < 256; i++) qualToErrorProbLog10Cache[i] = qualToErrorProbLog10Raw(i); + } + + private static double qualToProbLog10Cache[] = new double[256]; + static { + for (int i = 0; i < 256; i++) qualToProbLog10Cache[i] = qualToProbLog10Raw(i); + } + /** * Private constructor. No instantiating this class! */ @@ -31,7 +41,7 @@ public class QualityUtils { * Convert a quality score to a probability. This is the Phred-style * conversion, *not* the Illumina-style conversion (though asymptotically, they're the same). * - * @param qual a quality score (0-40) + * @param qual a quality score (0-255) * @return a probability (0.0-1.0) */ static public double qualToProb(byte qual) { @@ -42,6 +52,14 @@ public class QualityUtils { return 1.0 - Math.pow(10.0, qual/(-10.0)); } + static private double qualToProbLog10Raw(int qual) { + return Math.log10(1.0 - qualToErrorProbRaw(qual)); + } + + static public double qualToProbLog10(byte qual) { + return qualToProbLog10Cache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc. + } + /** * Convert a quality score to a probability of error. This is the Phred-style * conversion, *not* the Illumina-style conversion (though asymptotically, they're the same). @@ -57,14 +75,14 @@ public class QualityUtils { return qualToErrorProbCache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc. } - static public double[] qualArrayToLog10ErrorProb(byte[] quals) { - double[] returnArray = new double[quals.length]; - for( int iii = 0; iii < quals.length; iii++ ) { - returnArray[iii] = ((double) quals[iii])/-10.0; - } - return returnArray; + static private double qualToErrorProbLog10Raw(int qual) { + return ((double) qual)/-10.0; } - + + static public double qualToErrorProbLog10(byte qual) { + return qualToErrorProbLog10Cache[(int)qual & 0xff]; // Map: 127 -> 127; -128 -> 128; -1 -> 255; etc. + } + /** * Convert a probability to a quality score. Note, this is capped at Q40. * diff --git a/public/java/test/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java new file mode 100644 index 000000000..18a214950 --- /dev/null +++ b/public/java/test/org/broadinstitute/sting/utils/QualityUtilsUnitTest.java @@ -0,0 +1,66 @@ +/* + * 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.Test; + +import java.util.*; + +/** + * Basic unit test for QualityUtils class + */ +public class QualityUtilsUnitTest extends BaseTest { + @BeforeClass + public void init() { + } + + @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); + } +} \ No newline at end of file