Initial cleanup of RecalDatum for move and further refactoring

-- Moved Datum, the now unnecessary superclass, into RecalDatum
-- Fixed some obviously dangerous synchronization errors in RecalDatum, though these may not have caused problems because they may not have been called in parallel mode

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java

@@ -1,109 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.bqsr;
-
-import org.broadinstitute.sting.utils.QualityUtils;
-
-/*
- * Copyright (c) 2010 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.
- */
-
-/**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Jan 6, 2010
- *
- * An individual piece of recalibration data. Optimized for CountCovariates. Extras added to make TableRecalibration fast have been removed.
- * Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates.
- */
-
-public class Datum {
-
-    long numObservations;                                                                                     // number of bases seen in total
-    long numMismatches;                                                                                       // number of bases seen that didn't match the reference
-
-    private static final int SMOOTHING_CONSTANT = 1;                                                                    // used when calculating empirical qualities to avoid division by zero
-
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // constructors
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    public Datum() {
-        numObservations = 0L;
-        numMismatches = 0L;
-    }
-
-    public Datum(long numObservations, long numMismatches) {
-        this.numObservations = numObservations;
-        this.numMismatches = numMismatches;
-    }
-
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // increment methods
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    synchronized void increment(final long incObservations, final long incMismatches) {
-        numObservations += incObservations;
-        numMismatches += incMismatches;
-    }
-
-    synchronized void increment(final boolean isError) {
-        numObservations++;
-        numMismatches += isError ? 1:0;
-    }
-
-    //---------------------------------------------------------------------------------------------------------------
-    //
-    // methods to derive empirical quality score
-    //
-    //---------------------------------------------------------------------------------------------------------------
-
-    double empiricalQualDouble() {
-        final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
-        final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); // smoothing is one error and one non-error observation, for example
-        final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
-        return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
-    }
-
-    byte empiricalQualByte() {
-        final double doubleMismatches = (double) (numMismatches);
-        final double doubleObservations = (double) (numObservations);
-        return QualityUtils.probToQual(1.0 - doubleMismatches / doubleObservations);                                    // This is capped at Q40
-    }
-
-    @Override
-    public String toString() {
-        return String.format("%d,%d,%d", numObservations, numMismatches, (int) empiricalQualByte());
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (!(o instanceof Datum))
-            return false;
-        Datum other = (Datum) o;
-        return numMismatches == other.numMismatches && numObservations == other.numObservations;
-    }
-}

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java

@@ -33,20 +33,40 @@ import org.broadinstitute.sting.utils.QualityUtils;
 import java.util.Random;
 
 /**
+ * An individual piece of recalibration data. Each bin counts up the number of observations and the number
+ * of reference mismatches seen for that combination of covariates.
+ *
  * Created by IntelliJ IDEA.
  * User: rpoplin
  * Date: Nov 3, 2009
- *
- * An individual piece of recalibration data. Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates.
  */
-
+public class RecalDatum {
-public class RecalDatum extends Datum {
-
     private static final double UNINITIALIZED = -1.0;
 
-    private double estimatedQReported;                                                                                  // estimated reported quality score based on combined data's individual q-reporteds and number of observations
+    /**
-    private double empiricalQuality;                                                                                    // the empirical quality for datums that have been collapsed together (by read group and reported quality, for example)
+     * estimated reported quality score based on combined data's individual q-reporteds and number of observations
+     */
+    private double estimatedQReported;
 
+    /**
+     * the empirical quality for datums that have been collapsed together (by read group and reported quality, for example)
+     */
+    private double empiricalQuality;
+
+    /**
+     * number of bases seen in total
+     */
+    long numObservations;
+
+    /**
+     * number of bases seen that didn't match the reference
+     */
+    long numMismatches;
+
+    /**
+     * used when calculating empirical qualities to avoid division by zero
+     */
+    private static final int SMOOTHING_CONSTANT = 1;
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -68,26 +88,24 @@ public class RecalDatum extends Datum {
         this.empiricalQuality = copy.empiricalQuality;
     }
 
-    public void combine(final RecalDatum other) {
+    public synchronized void combine(final RecalDatum other) {
         final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors();
         increment(other.numObservations, other.numMismatches);
         estimatedQReported = -10 * Math.log10(sumErrors / this.numObservations);
         empiricalQuality = UNINITIALIZED;
     }
 
-    @Override
-    public void increment(final boolean isError) {
-        super.increment(isError);
-        empiricalQuality = UNINITIALIZED;
-    }
-
     @Requires("empiricalQuality == UNINITIALIZED")
     @Ensures("empiricalQuality != UNINITIALIZED")
-    protected final void calcEmpiricalQuality() {
+    private synchronized final void calcEmpiricalQuality() {
-        empiricalQuality = empiricalQualDouble();                                                                       // cache the value so we don't call log over and over again
+        // cache the value so we don't call log over and over again
+        final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
+        final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT);
+        final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
+        empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
     }
 
-    public void setEstimatedQReported(final double estimatedQReported) {
+    public synchronized void setEstimatedQReported(final double estimatedQReported) {
         this.estimatedQReported = estimatedQReported;
     }
 
@@ -95,7 +113,7 @@ public class RecalDatum extends Datum {
         return estimatedQReported;
     }
 
-    public void setEmpiricalQuality(final double empiricalQuality) {
+    public synchronized void setEmpiricalQuality(final double empiricalQuality) {
         this.empiricalQuality = empiricalQuality;
     }
 
@@ -145,4 +163,22 @@ public class RecalDatum extends Datum {
         return super.equals(o) &&
                MathUtils.compareDoubles(this.empiricalQuality, other.empiricalQuality, 0.001) == 0;
     }
+
+    //---------------------------------------------------------------------------------------------------------------
+    //
+    // increment methods
+    //
+    //---------------------------------------------------------------------------------------------------------------
+
+    synchronized void increment(final long incObservations, final long incMismatches) {
+        numObservations += incObservations;
+        numMismatches += incMismatches;
+        empiricalQuality = UNINITIALIZED;
+    }
+
+    synchronized void increment(final boolean isError) {
+        numObservations++;
+        numMismatches += isError ? 1:0;
+        empiricalQuality = UNINITIALIZED;
+    }
 }