diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleLikelihoodMatrixMapper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleLikelihoodMatrixMapper.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java index 557dfd0ad..008f194d0 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/AlleleLikelihoodMatrixMapper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleLikelihoodMatrixMapper.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java index 5abb1cd85..33d23c592 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCounts.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java index 4f55b5785..f055362fa 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCounts.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculator.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java index b07334f04..46f6f36de 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculator.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculators.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculators.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java index 4bd5bbaf0..39c4b413a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculators.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingData.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java similarity index 98% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingData.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java index 12214d67e..aabdcceb7 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingData.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingData.java @@ -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 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"); } diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index 8225ba9a5..50a9d0a8c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingLikelihoods.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingLikelihoods.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java index 35787107f..40d296193 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingLikelihoods.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingLikelihoods.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java index 9c84c8962..8021a4897 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/GenotypingModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingModel.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java index ed8d59a94..c4d7a0029 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModel.java @@ -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 diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java index f476d940c..968b869c3 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModel.java @@ -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 permutation = AlleleListUtils.permutation(data,genotypingAlleles); + final AlleleListPermutation permutation = AlleleListUtils.permutation(data, genotypingAlleles); final AlleleLikelihoodMatrixMapper alleleLikelihoodMatrixMapper = AlleleLikelihoodMatrixMapper.newInstance(permutation); final int sampleCount = data.sampleCount(); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/PloidyModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java similarity index 99% rename from protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/PloidyModel.java rename to protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java index 8ca00611e..5c5d7bdce 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/genotyping/PloidyModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/PloidyModel.java @@ -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. diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java index b98c878f3..9a2d123e5 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyper.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java index 22bc09e98..f2bea114a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotypingEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java index 0008f5b28..4a8694161 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java index e2229cd50..ce5e361bd 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index 5e6a519ea..3bb40eaac 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -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.*; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java index 76c8dc772..40cf7196c 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java index a0234a9e6..c263e27a6 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java index aa7305bcf..e5ac47a13 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java index ccc0c18b8..36593b60f 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadLikelihoodCalculationEngine.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java index 116b27009..a8adb94b8 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModel.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java index a798c760f..362e05359 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/indels/PairHMMIndelErrorModel.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java index 9d18e9981..98b849891 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java index e6cc614e6..8b13d2943 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/RegenotypeVariants.java @@ -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; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java index af93892a7..e72915341 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java similarity index 98% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUnitTester.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java index 2eefe64aa..fae233c8b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUnitTester.java @@ -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. *

*

- * 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. *

* diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java similarity index 99% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java index a7e2dce88..917efa9f9 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/AlleleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtilsUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCountsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java similarity index 99% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCountsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java index 8506b96e9..3e802f8e3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeAlleleCountsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCountsUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculatorUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java similarity index 98% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculatorUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java index 99f4c0422..2f280258b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypeLikelihoodCalculatorUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeLikelihoodCalculatorUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypingDataUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java similarity index 97% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypingDataUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java index 59e14e14c..96973ea1d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/GenotypingDataUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingDataUnitTest.java @@ -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 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); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HeterogeneousPloidyModel.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java similarity index 98% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HeterogeneousPloidyModel.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java index 865668093..afd6da5bf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HeterogeneousPloidyModel.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HeterogeneousPloidyModel.java @@ -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. * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java similarity index 98% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java index 030ebf21b..16d29f677 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/HomogeneousPloidyModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/HomogeneousPloidyModelUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedAlleleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java similarity index 97% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedAlleleListUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java index 61bd9f8a7..26b6d9bd7 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedAlleleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleListUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedSampleListUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java similarity index 95% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedSampleListUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java index 138ec0e31..a6e1fa85b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/IndexedSampleListUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleListUnitTest.java @@ -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 <valentin@broadinstitute.org> */ @@ -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 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 sampleNameList = Arrays.asList(sampleNames); final LinkedHashSet 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()]))); } /** diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java similarity index 98% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModelUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java index af4b37b18..616027549 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/InfiniteRandomMatingPopulationModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/InfiniteRandomMatingPopulationModelUnitTest.java @@ -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 { diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/ReadLikelihoodsUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java similarity index 99% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/ReadLikelihoodsUnitTester.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java index 08bfd9f60..a8efd574c 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/ReadLikelihoodsUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTester.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUnitTester.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java similarity index 96% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUnitTester.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java index 9bca352d2..3bd8e9103 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUnitTester.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUnitTester.java @@ -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. * *

- * 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. *

* diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java similarity index 96% rename from protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUtilsUnitTest.java rename to protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java index 71da45838..6e4bc08f6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/genotyping/SampleListUtilsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtilsUnitTest.java @@ -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 <valentin@broadinstitute.org> */ diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index 335c355d2..77c30eb19 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java index d36b1af16..3463fea3d 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java index cb946aafe..06b4f2a47 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java index f268ce535..39f728945 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java @@ -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; diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java index 65fc43579..4c9d093cf 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java @@ -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> sampleToReads = ReadLikelihoodsUnitTester.sampleToReads(sampleList, readCounts); final ReadLikelihoods 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) { diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java index feb41712b..c090010c3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java @@ -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.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java similarity index 96% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java index 2f124ed91..c222529f8 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleList.java @@ -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; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListPermutation.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java similarity index 96% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListPermutation.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java index a2477d053..6677e32d3 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListPermutation.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListPermutation.java @@ -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; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java similarity index 99% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java index dfdfe0945..f734b0990 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/AlleleListUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/AlleleListUtils.java @@ -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; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java similarity index 98% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java index 14de94818..bf5fba8d7 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedAlleleList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedAlleleList.java @@ -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; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java similarity index 98% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java index 277404b96..b761cf3bb 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/IndexedSampleList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/IndexedSampleList.java @@ -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; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java similarity index 96% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java index 3ac8b5ef7..f9eff35a5 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleList.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleList.java @@ -24,7 +24,7 @@ */ -package org.broadinstitute.gatk.genotyping; +package org.broadinstitute.gatk.tools.walkers.genotyper; /** * A indexed set of samples. diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java similarity index 99% rename from public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java rename to public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java index f3787568a..90ecba79f 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/genotyping/SampleListUtils.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/SampleListUtils.java @@ -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.*; diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java index 8deb30f49..0cdcadc44 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java @@ -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 the type of the allele the likelihood makes reference to. + * * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> */ public class ReadLikelihoods implements SampleList, AlleleList, Cloneable {