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Collapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone

This commit is contained in:
Eric Banks 2013-01-07 14:55:21 -05:00
parent 35d9bd377c
commit a0219acfaa
9 changed files with 44 additions and 142 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
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@ -60,7 +60,7 @@ public class ErrorModel {
boolean hasCalledAlleles = false;
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
if (refSampleVC != null) {
for (Allele allele : refSampleVC.getAlleles()) {

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
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@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -231,7 +232,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
// no likelihoods have been computed for this sample at this site
perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
}
// create the GenotypeLikelihoods object

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -119,7 +119,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
// no likelihoods have been computed for this sample at this site
perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
}
final ReadBackedPileup pileup = context.getBasePileup();
if (pileup != null) {

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
View File

@ -55,7 +55,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
super(UAC, logger);
useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
}
public VariantContext getLikelihoods(final RefMetaDataTracker tracker,

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -223,7 +223,7 @@ public class GenotypingEngine {
final Map<String, PerReadAlleleLikelihoodMap> returnMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
final GenomeLoc callLoc = parser.createGenomeLoc(call);
for( final Map.Entry<String, PerReadAlleleLikelihoodMap> sample : perSampleReadMap.entrySet() ) {
final PerReadAlleleLikelihoodMap likelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
for( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> mapEntry : sample.getValue().getLikelihoodReadMap().entrySet() ) {
// only count the read if it overlaps the event, otherwise it is not added to the output read list at all
@ -277,7 +277,7 @@ public class GenotypingEngine {
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = new HashMap<String, PerReadAlleleLikelihoodMap>();
for( final Map.Entry<String, PerReadAlleleLikelihoodMap> haplotypeReadMapEntry : haplotypeReadMap.entrySet() ) { // for each sample
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
for( final Map.Entry<Allele, List<Haplotype>> alleleMapperEntry : alleleMapper.entrySet() ) { // for each output allele
final List<Haplotype> mappedHaplotypes = alleleMapperEntry.getValue();
for( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> readEntry : haplotypeReadMapEntry.getValue().getLikelihoodReadMap().entrySet() ) { // for each read

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -104,7 +104,7 @@ public class LikelihoodCalculationEngine {
private PerReadAlleleLikelihoodMap computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final ArrayList<GATKSAMRecord> reads) {
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
final int numHaplotypes = haplotypes.size();
for( final GATKSAMRecord read : reads ) {
final byte[] overallGCP = new byte[read.getReadLength()];

71
protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
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@ -1,71 +0,0 @@
/*
* Copyright (c) 2011 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.genotyper;
import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;
public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLikelihoodMap implements ProtectedPackageSource {
public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log);
}
public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {
// special case removal of all or no reads
if ( downsamplingFraction <= 0.0 )
return;
if ( downsamplingFraction >= 1.0 ) {
likelihoodReadMap.clear();
return;
}
// start by stratifying the reads by the alleles they represent at this position
final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
for ( Allele allele : alleles )
alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
// do not remove reduced reads!
if ( !entry.getKey().isReducedRead() ) {
final Allele bestAllele = getMostLikelyAllele(entry.getValue());
if ( bestAllele != Allele.NO_CALL )
alleleReadMap.get(bestAllele).add(entry.getKey());
}
}
// compute the reads to remove and actually remove them
final List<GATKSAMRecord> readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log);
for ( final GATKSAMRecord read : readsToRemove )
likelihoodReadMap.remove(read);
}
}

54
public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java → protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
View File

@ -25,26 +25,23 @@
package org.broadinstitute.sting.utils.genotyper;
import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.lang.reflect.Constructor;
import java.util.*;
public abstract class PerReadAlleleLikelihoodMap {
public class PerReadAlleleLikelihoodMap {
public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2;
protected List<Allele> alleles;
protected Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap;
public abstract void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log);
public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log);
public PerReadAlleleLikelihoodMap() {}
public void add(GATKSAMRecord read, Allele a, Double likelihood) {
Map<Allele,Double> likelihoodMap;
@ -63,6 +60,39 @@ public abstract class PerReadAlleleLikelihoodMap {
}
public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) {
return AlleleBiasedDownsamplingUtils.createAlleleBiasedBasePileup(pileup, downsamplingFraction, log);
}
public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {
// special case removal of all or no reads
if ( downsamplingFraction <= 0.0 )
return;
if ( downsamplingFraction >= 1.0 ) {
likelihoodReadMap.clear();
return;
}
// start by stratifying the reads by the alleles they represent at this position
final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>(alleles.size());
for ( Allele allele : alleles )
alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
// do not remove reduced reads!
if ( !entry.getKey().isReducedRead() ) {
final Allele bestAllele = getMostLikelyAllele(entry.getValue());
if ( bestAllele != Allele.NO_CALL )
alleleReadMap.get(bestAllele).add(entry.getKey());
}
}
// compute the reads to remove and actually remove them
final List<GATKSAMRecord> readsToRemove = AlleleBiasedDownsamplingUtils.selectAlleleBiasedReads(alleleReadMap, downsamplingFraction, log);
for ( final GATKSAMRecord read : readsToRemove )
likelihoodReadMap.remove(read);
}
public int size() {
return likelihoodReadMap.size();
}
@ -122,16 +152,4 @@ public abstract class PerReadAlleleLikelihoodMap {
}
return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL );
}
public static PerReadAlleleLikelihoodMap getBestAvailablePerReadAlleleLikelihoodMap() {
final Class PerReadAlleleLikelihoodMapClass = GATKLiteUtils.getProtectedClassIfAvailable(PerReadAlleleLikelihoodMap.class);
try {
final Constructor constructor = PerReadAlleleLikelihoodMapClass.getDeclaredConstructor((Class[])null);
constructor.setAccessible(true);
return (PerReadAlleleLikelihoodMap)constructor.newInstance();
}
catch (Exception e) {
throw new ReviewedStingException("Unable to create RecalibrationEngine class instance " + PerReadAlleleLikelihoodMapClass.getSimpleName());
}
}
}

46
public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
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@ -1,46 +0,0 @@
/*
* Copyright (c) 2011 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.genotyper;
import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele;
import java.io.PrintStream;
import java.util.*;
public class StandardPerReadAlleleLikelihoodMap extends PerReadAlleleLikelihoodMap implements PublicPackageSource {
public StandardPerReadAlleleLikelihoodMap() {
likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
alleles = new ArrayList<Allele>();
}
// not implemented in the standard version
public void performPerAlleleDownsampling(final double downsamplingFraction, final PrintStream log) {}
public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log) { return pileup; }
}