Collapse the PerReadAlleleLikelihoodMap classes into 1 now that Lite is gone

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java

@@ -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()) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java

@@ -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

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -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) {

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

@@ -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,

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

@@ -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

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java

@@ -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()];

protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java

@@ -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);
-    }
-}

protected/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java

@@ -25,26 +25,23 @@
 package org.broadinstitute.sting.utils.genotyper;
 
 
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
+import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 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 PerReadAlleleLikelihoodMap() {}
-    public abstract ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction, final PrintStream log);
 
     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());
-        }
-    }
 }

public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java

@@ -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; }
-}