From b099e2b4ae8d4ae72fddf6b3c5081a1220362859 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 8 Jan 2013 09:34:08 -0500 Subject: [PATCH] Moving integration tests to protected --- .../sting/gatk/walkers/annotator/SnpEffUnitTest.java | 0 .../gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java | 0 .../sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java | 0 .../sting/gatk/walkers/beagle/BeagleIntegrationTest.java | 0 .../sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java | 0 .../sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java | 0 .../walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java | 0 .../walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java | 0 .../sting/gatk/walkers/diffengine/DiffEngineUnitTest.java | 0 .../sting/gatk/walkers/diffengine/DiffNodeUnitTest.java | 0 .../sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java | 0 .../sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java | 0 .../sting/gatk/walkers/diffengine/DifferenceUnitTest.java | 0 .../walkers/fasta/FastaAlternateReferenceIntegrationTest.java | 0 .../gatk/walkers/filters/VariantFiltrationIntegrationTest.java | 0 .../gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java | 0 .../sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java | 0 .../gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java | 0 .../gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java | 0 .../sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java | 0 .../sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java | 0 .../walkers/indels/RealignerTargetCreatorIntegrationTest.java | 0 .../gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java | 0 .../gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java | 0 .../gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java | 0 .../walkers/validation/ValidationAmpliconsIntegrationTest.java | 0 .../walkers/validation/ValidationSiteSelectorIntegrationTest.java | 0 .../gatk/walkers/varianteval/VariantEvalIntegrationTest.java | 0 .../sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java | 0 .../stratifications/manager/StratificationManagerUnitTest.java | 0 .../variantrecalibration/VariantGaussianMixtureModelUnitTest.java | 0 .../VariantRecalibrationWalkersIntegrationTest.java | 0 .../gatk/walkers/variantutils/CombineVariantsIntegrationTest.java | 0 .../sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java | 0 .../walkers/variantutils/LeftAlignVariantsIntegrationTest.java | 0 .../walkers/variantutils/LiftoverVariantsIntegrationTest.java | 0 .../gatk/walkers/variantutils/SelectVariantsIntegrationTest.java | 0 .../variantutils/SelectVariantsParallelIntegrationTest.java | 0 .../gatk/walkers/variantutils/VCFStreamingIntegrationTest.java | 0 .../walkers/variantutils/ValidateVariantsIntegrationTest.java | 0 .../walkers/variantutils/VariantsToBinaryPedIntegrationTest.java | 0 .../gatk/walkers/variantutils/VariantsToTableIntegrationTest.java | 0 .../gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java | 0 43 files changed, 0 insertions(+), 0 deletions(-) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java (100%) rename {public => protected}/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java (100%) diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/WalkerTestIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java similarity index 100% rename from public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java rename to protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java