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Moving new omniploidy likelihood calculation classes to their final package (as far as this pull-request is concerned) in org.broadinstitute.gatk.tools.walkers.genotyper

This commit is contained in:
Valentin Ruano-Rubio 2014-08-19 10:32:02 -04:00
parent 611b7f25ea
commit 8d9a55ae60
53 changed files with 95 additions and 102 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleLikelihoodMatrixMapper.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
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@ -50,9 +50,6 @@ import htsjdk.samtools.SAMUtils;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.gatk.genotyping.GenotypeAlleleCounts;
import org.broadinstitute.gatk.genotyping.GenotypeLikelihoodCalculator;
import org.broadinstitute.gatk.genotyping.GenotypeLikelihoodCalculators;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACcounts;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.ExactACset;
import org.broadinstitute.gatk.utils.MathUtils;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCounts.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.utils.MathUtils;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculator.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java
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@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculators.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import java.util.Arrays;

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingData.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
@ -78,7 +78,7 @@ public class GenotypingData<A extends Allele> implements SampleList, AlleleList<
throw new IllegalArgumentException("the likelihood object cannot be null");
this.ploidyModel = ploidyModel;
this.likelihoods = likelihoods;
if (!SampleListUtils.equals(ploidyModel,likelihoods))
if (!SampleListUtils.equals(ploidyModel, likelihoods))
throw new IllegalArgumentException("sample list are different between ploidy-model and read-likelihood collection, perhaps just the order");
}

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
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@ -58,7 +58,6 @@ import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalc;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcFactory;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingLikelihoods.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingModel.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModel.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/**
* {@link PloidyModel} implementation tailored to work with a homogeneous constant ploidy

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModel.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
@ -97,7 +97,7 @@ public class InfiniteRandomMatingPopulationModel implements GenotypingModel {
if (data == null)
throw new IllegalArgumentException("the genotyping data cannot be null");
final AlleleListPermutation<A> permutation = AlleleListUtils.permutation(data,genotypingAlleles);
final AlleleListPermutation<A> permutation = AlleleListUtils.permutation(data, genotypingAlleles);
final AlleleLikelihoodMatrixMapper<A> alleleLikelihoodMatrixMapper = AlleleLikelihoodMatrixMapper.newInstance(permutation);
final int sampleCount = data.sampleCount();

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/PloidyModel.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java
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@ -44,7 +44,7 @@
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/**
* Information about the number of chromosome per sample at a given location.

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java
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@ -48,8 +48,6 @@ package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.genotyping.IndexedSampleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java
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@ -54,7 +54,6 @@ import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalcResult;
import org.broadinstitute.gatk.utils.BaseUtils;
import org.broadinstitute.gatk.utils.GenomeLocParser;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
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@ -47,7 +47,7 @@
package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.SeqGraph;
import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
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@ -48,9 +48,9 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import htsjdk.variant.variantcontext.Allele;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.genotyping.AlleleList;
import org.broadinstitute.gatk.genotyping.IndexedAlleleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.MultiSampleEdge;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Path;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.Route;

1
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -65,7 +65,6 @@ import org.broadinstitute.gatk.engine.io.GATKSAMFileWriter;
import org.broadinstitute.gatk.engine.iterators.ReadTransformer;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
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@ -50,11 +50,7 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import htsjdk.variant.variantcontext.*;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode;
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.Utils;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -51,9 +51,9 @@ import com.google.java.contract.Requires;
import htsjdk.samtools.SAMUtils;
import htsjdk.variant.variantcontext.Allele;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.genotyping.AlleleList;
import org.broadinstitute.gatk.genotyping.IndexedAlleleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.exceptions.UserException;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
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@ -48,9 +48,9 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.genotyping.AlleleList;
import org.broadinstitute.gatk.genotyping.IndexedAlleleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;

2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java
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@ -46,7 +46,7 @@
package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java
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@ -51,13 +51,12 @@ import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFSimpleHeaderLine;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.QualityUtils;
import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.locusiterator.LocusIteratorByState;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java
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@ -49,9 +49,9 @@ package org.broadinstitute.gatk.tools.walkers.indels;
import com.google.java.contract.Ensures;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.genotyping.AlleleList;
import org.broadinstitute.gatk.genotyping.IndexedAlleleList;
import org.broadinstitute.gatk.genotyping.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedAlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.clipping.ReadClipper;
import org.broadinstitute.gatk.utils.exceptions.UserException;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
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@ -49,9 +49,9 @@ package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.GenotypeCalculationArgumentCollection;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine;
import org.broadinstitute.gatk.genotyping.IndexedSampleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java
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@ -47,9 +47,9 @@
package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.genotyping.IndexedSampleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.CommandLineGATK;

6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java
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@ -48,9 +48,9 @@ package org.broadinstitute.gatk.utils.haplotype;
import com.google.java.contract.Requires;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.gatk.genotyping.AlleleList;
import org.broadinstitute.gatk.genotyping.AlleleListUtils;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUnitTester.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java
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@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
@ -70,8 +70,8 @@ public class AlleleListUnitTester {
* Test that the contents of an allele-list are the ones expected.
* <p/>
* <p>
* This method perform various consistency check involving all the {@link org.broadinstitute.gatk.genotyping.AlleleList} interface methods.
* Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.genotyping.AlleleList} aspect of
* This method perform various consistency check involving all the {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList} interface methods.
* Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleList} aspect of
* the {@code actual} argument.
* </p>
*

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUtilsUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java
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@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
@ -56,7 +56,7 @@ import org.testng.annotations.Test;
import java.util.*;
/**
* Test {@link org.broadinstitute.gatk.genotyping.AlleleListUtils}.
* Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils}.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

5
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCountsUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java
View File

@ -43,8 +43,9 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@ -52,7 +53,7 @@ import org.testng.annotations.Test;
import java.util.Arrays;
/**
* Test {@link GenotypeAlleleCounts}
* Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeAlleleCounts}
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculatorUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
@ -56,7 +56,7 @@ import org.testng.annotations.Test;
import java.util.Arrays;
/**
* Tests {@link GenotypeLikelihoodCalculators} and {@link GenotypeLikelihoodCalculator}.
* Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators} and {@link org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculator}.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypingDataUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
@ -55,7 +55,7 @@ import java.util.ArrayList;
import java.util.List;
/**
* Test {@link org.broadinstitute.gatk.genotyping.InfiniteRandomMatingPopulationModel}
* Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel}
*/
public class GenotypingDataUnitTest {
@ -65,8 +65,8 @@ public class GenotypingDataUnitTest {
final SampleList sampleList = likelihoods;
final PloidyModel ploidyModel = new HeterogeneousPloidyModel(sampleList,ploidies);
final GenotypingData<Allele> data = new GenotypingData<>(ploidyModel,likelihoods);
Assert.assertTrue(AlleleListUtils.equals(data,likelihoods));
Assert.assertTrue(SampleListUtils.equals(data,likelihoods));
Assert.assertTrue(AlleleListUtils.equals(data, likelihoods));
Assert.assertTrue(SampleListUtils.equals(data, likelihoods));
Assert.assertEquals(data.readLikelihoods(),likelihoods);
Assert.assertEquals(data.ploidyModel(),ploidyModel);
}

5
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HeterogeneousPloidyModel.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java
View File

@ -43,9 +43,12 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.tools.walkers.genotyper.PloidyModel;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
/**
* General heterogeneous ploidy model.
*

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModelUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
@ -53,7 +53,7 @@ import java.util.ArrayList;
import java.util.List;
/**
* Tests {@link HomogeneousPloidyModel}
* Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.HomogeneousPloidyModel}
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedAlleleListUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
@ -52,10 +52,10 @@ import org.testng.annotations.Test;
import java.util.*;
import static org.broadinstitute.gatk.genotyping.AlleleListUnitTester.assertAlleleList;
import static org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUnitTester.assertAlleleList;
/**
* Tests {@link org.broadinstitute.gatk.genotyping.IndexedSampleList}.
* Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList}.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedSampleListUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
@ -52,10 +52,8 @@ import org.testng.annotations.Test;
import java.util.*;
import static org.broadinstitute.gatk.genotyping.SampleListUnitTester.assertSampleList;
/**
* Tests {@link IndexedSampleList}.
* Tests {@link org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList}.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/
@ -64,7 +62,7 @@ public class IndexedSampleListUnitTest {
@Test
public void testEmptyConstructor() {
final IndexedSampleList subject = new IndexedSampleList();
assertSampleList(subject, Collections.EMPTY_LIST);
SampleListUnitTester.assertSampleList(subject, Collections.EMPTY_LIST);
}
@Test(dataProvider="sampleCountMaxSampleIndexData")
@ -73,7 +71,7 @@ public class IndexedSampleListUnitTest {
final LinkedHashSet<String> nonRepeatedNames = new LinkedHashSet<>(Arrays.asList(sampleNames));
final IndexedSampleList subject = new IndexedSampleList(sampleNames);
assertSampleList(subject, Arrays.asList(nonRepeatedNames.toArray(new String[nonRepeatedNames.size()])));
SampleListUnitTester.assertSampleList(subject, Arrays.asList(nonRepeatedNames.toArray(new String[nonRepeatedNames.size()])));
}
@Test(dataProvider="sampleCountMaxSampleIndexData")
@ -83,7 +81,7 @@ public class IndexedSampleListUnitTest {
final List<String> sampleNameList = Arrays.asList(sampleNames);
final LinkedHashSet<String> nonRepeatedNames = new LinkedHashSet<>(Arrays.asList(sampleNames));
final IndexedSampleList subject = new IndexedSampleList(sampleNameList);
assertSampleList(subject, Arrays.asList(nonRepeatedNames.toArray(new String[nonRepeatedNames.size()])));
SampleListUnitTester.assertSampleList(subject, Arrays.asList(nonRepeatedNames.toArray(new String[nonRepeatedNames.size()])));
}
/**

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModelUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
@ -58,7 +58,7 @@ import java.util.List;
import java.util.Random;
/**
* Test {@link InfiniteRandomMatingPopulationModel}
* Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.InfiniteRandomMatingPopulationModel}
*/
public class InfiniteRandomMatingPopulationModelUnitTest {

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/ReadLikelihoodsUnitTester.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java
View File

@ -43,7 +43,7 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.samtools.SAMFileHeader;

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUnitTester.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java
View File

@ -43,8 +43,10 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.testng.Assert;
import java.util.*;
@ -60,8 +62,8 @@ public class SampleListUnitTester {
* Test that the contents of a sample-list are the ones expected.
*
* <p>
* This method perform various consistency check involving all the {@link SampleList} interface methods.
* Therefore calling this method is equivalent to a thorough check of the {@link SampleList} aspect of
* This method perform various consistency check involving all the {@link org.broadinstitute.gatk.tools.walkers.genotyper.SampleList} interface methods.
* Therefore calling this method is equivalent to a thorough check of the {@link org.broadinstitute.gatk.tools.walkers.genotyper.SampleList} aspect of
* the {@code actual} argument.
* </p>
*

8
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUtilsUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java
View File

@ -43,9 +43,11 @@
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
@ -56,7 +58,7 @@ import java.util.Arrays;
import java.util.List;
/**
* Test {@link AlleleListUtils}.
* Test {@link org.broadinstitute.gatk.tools.walkers.genotyper.AlleleListUtils}.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
View File

@ -56,8 +56,6 @@ import htsjdk.variant.variantcontext.VariantContext;
import htsjdk.variant.variantcontext.VariantContextBuilder;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.GATKArgumentCollection;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.Utils;

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
View File

@ -47,7 +47,7 @@ package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet;
import org.broadinstitute.gatk.utils.pairhmm.FastLoglessPairHMM;
import org.broadinstitute.gatk.utils.pairhmm.PairHMM;

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
View File

@ -47,7 +47,7 @@
package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.genotyping.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleListUtils;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.genotyper.PerReadAlleleLikelihoodMap;

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
View File

@ -51,7 +51,7 @@ import htsjdk.variant.variantcontext.Genotype;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import htsjdk.variant.variantcontext.GenotypeType;
import htsjdk.variant.variantcontext.VariantContext;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java
View File

@ -48,7 +48,7 @@ package org.broadinstitute.gatk.utils.genotyper;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.MathUtils;
@ -616,7 +616,7 @@ public class ReadLikelihoodsUnitTest
final Map<String,List<GATKSAMRecord>> sampleToReads = ReadLikelihoodsUnitTester.sampleToReads(sampleList, readCounts);
final ReadLikelihoods<Allele> subject = new ReadLikelihoods<>(sampleList,alleleList,sampleToReads);
AlleleListUnitTester.assertAlleleList(subject,AlleleListUtils.asList(alleleList));
AlleleListUnitTester.assertAlleleList(subject, AlleleListUtils.asList(alleleList));
SampleListUnitTester.assertSampleList(subject,SampleListUtils.asList(sampleList));
if (hasReference) {

4
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java
View File

@ -55,8 +55,8 @@ import org.broadinstitute.gatk.engine.resourcemanagement.ThreadAllocation;
import org.broadinstitute.gatk.engine.samples.SampleDB;
import org.broadinstitute.gatk.engine.samples.SampleDBBuilder;
import org.broadinstitute.gatk.engine.walkers.*;
import org.broadinstitute.gatk.genotyping.IndexedSampleList;
import org.broadinstitute.gatk.genotyping.SampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.IndexedSampleList;
import org.broadinstitute.gatk.tools.walkers.genotyper.SampleList;
import org.broadinstitute.gatk.utils.*;
import org.broadinstitute.gatk.utils.classloader.PluginManager;
import org.broadinstitute.gatk.utils.commandline.*;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java
View File

@ -22,7 +22,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListPermutation.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.utils.collections.Permutation;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import htsjdk.variant.variantcontext.Allele;
import org.broadinstitute.gatk.utils.collections.IndexedSet;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import org.broadinstitute.gatk.utils.collections.IndexedSet;

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java
View File

@ -24,7 +24,7 @@
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
/**
* A indexed set of samples.

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java → public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java
View File

@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.genotyping;
package org.broadinstitute.gatk.tools.walkers.genotyper;
import java.util.*;

4
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java
View File

@ -30,7 +30,7 @@ import it.unimi.dsi.fastutil.ints.IntArrayList;
import it.unimi.dsi.fastutil.objects.Object2IntMap;
import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
import org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtils;
import org.broadinstitute.gatk.genotyping.*;
import org.broadinstitute.gatk.tools.walkers.genotyper.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
@ -41,6 +41,8 @@ import java.util.*;
/**
* Read-likelihoods container implementation based on integer indexed arrays.
*
* @param <A> the type of the allele the likelihood makes reference to.
*
* @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
*/
public class ReadLikelihoods<A extends Allele> implements SampleList, AlleleList<A>, Cloneable {