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
This commit is contained in:
Mark DePristo
parent
0670316288
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191294eedc
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@ -1,109 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.bqsr;
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import org.broadinstitute.sting.utils.QualityUtils;
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/*
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* Copyright (c) 2010 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Jan 6, 2010
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*
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* An individual piece of recalibration data. Optimized for CountCovariates. Extras added to make TableRecalibration fast have been removed.
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* Each bin counts up the number of observations and the number of reference mismatches seen for that combination of covariates.
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*/
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public class Datum {
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long numObservations; // number of bases seen in total
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long numMismatches; // number of bases seen that didn't match the reference
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private static final int SMOOTHING_CONSTANT = 1; // used when calculating empirical qualities to avoid division by zero
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//---------------------------------------------------------------------------------------------------------------
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//
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// constructors
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//
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//---------------------------------------------------------------------------------------------------------------
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public Datum() {
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numObservations = 0L;
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numMismatches = 0L;
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}
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public Datum(long numObservations, long numMismatches) {
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this.numObservations = numObservations;
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this.numMismatches = numMismatches;
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}
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//---------------------------------------------------------------------------------------------------------------
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//
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// increment methods
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//
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//---------------------------------------------------------------------------------------------------------------
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synchronized void increment(final long incObservations, final long incMismatches) {
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numObservations += incObservations;
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numMismatches += incMismatches;
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}
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synchronized void increment(final boolean isError) {
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numObservations++;
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numMismatches += isError ? 1:0;
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}
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//---------------------------------------------------------------------------------------------------------------
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//
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// methods to derive empirical quality score
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//
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//---------------------------------------------------------------------------------------------------------------
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double empiricalQualDouble() {
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final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
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final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT + SMOOTHING_CONSTANT); // smoothing is one error and one non-error observation, for example
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final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
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return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
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}
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byte empiricalQualByte() {
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final double doubleMismatches = (double) (numMismatches);
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final double doubleObservations = (double) (numObservations);
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return QualityUtils.probToQual(1.0 - doubleMismatches / doubleObservations); // This is capped at Q40
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}
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@Override
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public String toString() {
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return String.format("%d,%d,%d", numObservations, numMismatches, (int) empiricalQualByte());
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}
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@Override
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public boolean equals(Object o) {
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if (!(o instanceof Datum))
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return false;
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Datum other = (Datum) o;
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return numMismatches == other.numMismatches && numObservations == other.numObservations;
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}
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}
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@ -33,20 +33,40 @@ import org.broadinstitute.sting.utils.QualityUtils;
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import java.util.Random;
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/**
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* An individual piece of recalibration data. Each bin counts up the number of observations and the number
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* of reference mismatches seen for that combination of covariates.
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*
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Nov 3, 2009
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*
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* 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.
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*/
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public class RecalDatum extends Datum {
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public class RecalDatum {
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private static final double UNINITIALIZED = -1.0;
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private double estimatedQReported; // estimated reported quality score based on combined data's individual q-reporteds and number of observations
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private double empiricalQuality; // the empirical quality for datums that have been collapsed together (by read group and reported quality, for example)
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/**
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* estimated reported quality score based on combined data's individual q-reporteds and number of observations
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*/
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private double estimatedQReported;
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/**
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* the empirical quality for datums that have been collapsed together (by read group and reported quality, for example)
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*/
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private double empiricalQuality;
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/**
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* number of bases seen in total
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*/
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long numObservations;
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/**
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* number of bases seen that didn't match the reference
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*/
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long numMismatches;
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/**
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* used when calculating empirical qualities to avoid division by zero
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*/
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private static final int SMOOTHING_CONSTANT = 1;
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//---------------------------------------------------------------------------------------------------------------
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//
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@ -68,26 +88,24 @@ public class RecalDatum extends Datum {
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this.empiricalQuality = copy.empiricalQuality;
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}
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public void combine(final RecalDatum other) {
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public synchronized void combine(final RecalDatum other) {
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final double sumErrors = this.calcExpectedErrors() + other.calcExpectedErrors();
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increment(other.numObservations, other.numMismatches);
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estimatedQReported = -10 * Math.log10(sumErrors / this.numObservations);
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empiricalQuality = UNINITIALIZED;
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}
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@Override
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public void increment(final boolean isError) {
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super.increment(isError);
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empiricalQuality = UNINITIALIZED;
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}
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@Requires("empiricalQuality == UNINITIALIZED")
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@Ensures("empiricalQuality != UNINITIALIZED")
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protected final void calcEmpiricalQuality() {
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empiricalQuality = empiricalQualDouble(); // cache the value so we don't call log over and over again
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private synchronized final void calcEmpiricalQuality() {
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// cache the value so we don't call log over and over again
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final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
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final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT);
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final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
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empiricalQuality = Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
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}
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public void setEstimatedQReported(final double estimatedQReported) {
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public synchronized void setEstimatedQReported(final double estimatedQReported) {
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this.estimatedQReported = estimatedQReported;
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}
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@ -95,7 +113,7 @@ public class RecalDatum extends Datum {
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return estimatedQReported;
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}
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public void setEmpiricalQuality(final double empiricalQuality) {
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public synchronized void setEmpiricalQuality(final double empiricalQuality) {
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this.empiricalQuality = empiricalQuality;
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}
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@ -145,4 +163,22 @@ public class RecalDatum extends Datum {
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return super.equals(o) &&
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MathUtils.compareDoubles(this.empiricalQuality, other.empiricalQuality, 0.001) == 0;
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}
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//---------------------------------------------------------------------------------------------------------------
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//
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// increment methods
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//
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//---------------------------------------------------------------------------------------------------------------
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synchronized void increment(final long incObservations, final long incMismatches) {
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numObservations += incObservations;
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numMismatches += incMismatches;
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empiricalQuality = UNINITIALIZED;
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}
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synchronized void increment(final boolean isError) {
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numObservations++;
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numMismatches += isError ? 1:0;
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empiricalQuality = UNINITIALIZED;
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}
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}
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