Merge branch 'master' of github.com:broadinstitute/gsa-unstable

protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java

@@ -1,34 +0,0 @@
-package org.broadinstitute.sting.gatk;
-
-/*
- * Copyright (c) 2009 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.
- */
-
-import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
-
-public class DummyProtectedClass implements ProtectedPackageSource {
-
-    // THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK
-    // **** DO NOT REMOVE! ****
-}

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/genotyper/UnifiedGenotyper.java

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
@@ -41,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -230,25 +228,6 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
      **/
     public void initialize() {
 
-        // Check for protected modes
-        if (GATKLiteUtils.isGATKLite()) {
-            // no polyploid/pooled mode in GATK Like
-            if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY ||
-                    UAC.referenceSampleName != null ||
-                    UAC.referenceSampleRod.isBound())  {
-                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
-            }
-
-            if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
-                if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) {
-                    UAC.CONTAMINATION_FRACTION = 0.0;
-                    logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite");
-                } else {
-                    throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
-                }
-            }
-        }
-
         if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) {
             samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
         } else {