diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriors.java b/src/main/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriors.java similarity index 92% rename from src/main/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriors.java rename to src/main/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriors.java index a7ddec4e6..3b5c4c4b0 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriors.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriors.java @@ -1,13 +1,18 @@ -package org.broadinstitute.hellbender.tools.exome; +package org.broadinstitute.hellbender.tools.archive; import com.google.common.annotations.VisibleForTesting; -import org.broadinstitute.barclay.argparser.*; import org.broadinstitute.barclay.argparser.Argument; import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; import org.broadinstitute.hdf5.HDF5Library; -import org.broadinstitute.hellbender.cmdline.*; +import org.broadinstitute.hellbender.cmdline.CommandLineProgram; +import org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.tools.exome.ACNVModeledSegment; +import org.broadinstitute.hellbender.tools.exome.HashedListTargetCollection; +import org.broadinstitute.hellbender.tools.exome.SegmentUtils; +import org.broadinstitute.hellbender.tools.exome.TargetCollection; import org.broadinstitute.hellbender.tools.exome.allelefraction.*; import org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCount; import org.broadinstitute.hellbender.tools.exome.alleliccount.AllelicCountCollection; @@ -60,7 +65,7 @@ public class CalculatePulldownPhasePosteriors extends CommandLineProgram { @Argument( doc = "Input file for GATK ACNV allele-fraction global parameters " + - "(with extension " + AllelicCNV.AF_PARAMETER_FILE_SUFFIX + ").", + "(with extension .af.param).", //hard-coded only because protected access to AllelicCNV.AF_PARAMETER_FILE_SUFFIX not available after this tool was archived fullName = ExomeStandardArgumentDefinitions.AF_PARAMETER_FILE_LONG_NAME, shortName = ExomeStandardArgumentDefinitions.AF_PARAMETER_FILE_SHORT_NAME, optional = false diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetector.java b/src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetector.java similarity index 99% rename from src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetector.java rename to src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetector.java index 3328848e1..7bb9fea85 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetector.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetector.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout; +package org.broadinstitute.hellbender.tools.archive; import org.apache.commons.math3.distribution.MixtureMultivariateNormalDistribution; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutResult.java b/src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutResult.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutResult.java rename to src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutResult.java index 9dc6fd2bb..6af65e391 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutResult.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutResult.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout; +package org.broadinstitute.hellbender.tools.archive; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValues.java b/src/main/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValues.java similarity index 95% rename from src/main/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValues.java rename to src/main/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValues.java index 85fd997c0..e445a30c6 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValues.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValues.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome; +package org.broadinstitute.hellbender.tools.archive; import au.com.bytecode.opencsv.CSVWriter; import org.apache.commons.math3.linear.DiagonalMatrix; @@ -8,6 +8,8 @@ import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; import org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.tools.exome.ReadCountCollection; +import org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils; import org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram; import org.broadinstitute.hellbender.utils.svd.SVD; import org.broadinstitute.hellbender.utils.svd.SVDFactory; diff --git a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropout.java b/src/main/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropout.java similarity index 98% rename from src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropout.java rename to src/main/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropout.java index 96985308f..85ea24303 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropout.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropout.java @@ -1,8 +1,8 @@ -package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout; +package org.broadinstitute.hellbender.tools.archive; import org.broadinstitute.barclay.argparser.Argument; -import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; +import org.broadinstitute.hellbender.cmdline.CommandLineProgram; import org.broadinstitute.hellbender.cmdline.programgroups.CopyNumberProgramGroup; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.tools.exome.*; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriorsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriorsIntegrationTest.java similarity index 98% rename from src/test/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriorsIntegrationTest.java rename to src/test/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriorsIntegrationTest.java index 32e3351a6..d13389e6f 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/exome/CalculatePulldownPhasePosteriorsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/archive/CalculatePulldownPhasePosteriorsIntegrationTest.java @@ -1,9 +1,10 @@ -package org.broadinstitute.hellbender.tools.exome; +package org.broadinstitute.hellbender.tools.archive; import org.apache.commons.io.FileUtils; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.ExomeStandardArgumentDefinitions; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; +import org.broadinstitute.hellbender.tools.exome.SegmentedGenome; import org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionIndicator; import org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionSimulatedData; import org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionState; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetectorTest.java b/src/test/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetectorUnitTest.java similarity index 97% rename from src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetectorTest.java rename to src/test/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetectorUnitTest.java index 5fb2e7a85..028e0eb8e 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/CoverageDropoutDetectorTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/archive/CoverageDropoutDetectorUnitTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout; +package org.broadinstitute.hellbender.tools.archive; import org.apache.commons.math3.distribution.NormalDistribution; import org.apache.commons.math3.distribution.UniformRealDistribution; @@ -18,7 +18,7 @@ /** * @author lichtens <lichtens@broadinstitute.org> */ -public final class CoverageDropoutDetectorTest extends BaseTest { +public final class CoverageDropoutDetectorUnitTest extends BaseTest { @DataProvider(name = "randomUnivariateGaussianTargetsLowVariance") diff --git a/src/test/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValuesIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValuesIntegrationTest.java similarity index 96% rename from src/test/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValuesIntegrationTest.java rename to src/test/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValuesIntegrationTest.java index 11dc70ff4..ad1916e24 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/exome/DecomposeSingularValuesIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/archive/DecomposeSingularValuesIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome; +package org.broadinstitute.hellbender.tools.archive; import org.apache.commons.math3.linear.DiagonalMatrix; @@ -6,6 +6,8 @@ import org.apache.commons.math3.linear.QRDecomposition; import org.apache.commons.math3.linear.RealMatrix; import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.tools.exome.ReadCountCollection; +import org.broadinstitute.hellbender.tools.exome.ReadCountCollectionUtils; import org.broadinstitute.hellbender.tools.pon.PoNTestUtils; import org.broadinstitute.hellbender.utils.SparkToggleCommandLineProgram; import org.broadinstitute.hellbender.utils.svd.SVD; diff --git a/src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropoutIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropoutIntegrationTest.java similarity index 98% rename from src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropoutIntegrationTest.java rename to src/test/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropoutIntegrationTest.java index be417b726..98241d534 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/exome/detectcoveragedropout/DetectCoverageDropoutIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/archive/DetectCoverageDropoutIntegrationTest.java @@ -1,4 +1,4 @@ -package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout; +package org.broadinstitute.hellbender.tools.archive; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.testng.Assert;