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.

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.
      *

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);
+    }
+}