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CNV tools: archive 3 tools and related tests #1130

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CNV tools: archive 3 tools and related tests #1130

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364da0d
archive 3 tools and related tests
May 31, 2017
451fba8
Moved tests, fixed imports, and renamed CoverageDropoutDetectorTest.
samuelklee May 31, 2017
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13 changes: 9 additions & 4 deletions ...ome/CalculatePulldownPhasePosteriors.java → ...ive/CalculatePulldownPhasePosteriors.java
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@@ -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;
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ...eragedropout/CoverageDropoutDetector.java → ...ools/archive/CoverageDropoutDetector.java
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@@ -1,4 +1,4 @@
package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout;
package org.broadinstitute.hellbender.tools.archive;


import org.apache.commons.math3.distribution.MixtureMultivariateNormalDistribution;
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2 changes: 1 addition & 1 deletion ...overagedropout/CoverageDropoutResult.java → .../tools/archive/CoverageDropoutResult.java
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@@ -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;
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4 changes: 3 additions & 1 deletion .../tools/exome/DecomposeSingularValues.java → ...ools/archive/DecomposeSingularValues.java
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@@ -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;
Expand All @@ -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;
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4 changes: 2 additions & 2 deletions ...overagedropout/DetectCoverageDropout.java → .../tools/archive/DetectCoverageDropout.java
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@@ -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.*;
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3 changes: 2 additions & 1 deletion ...lldownPhasePosteriorsIntegrationTest.java → ...lldownPhasePosteriorsIntegrationTest.java
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@@ -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;
Expand Down
4 changes: 2 additions & 2 deletions ...edropout/CoverageDropoutDetectorTest.java → ...hive/CoverageDropoutDetectorUnitTest.java
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@@ -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;
Expand All @@ -18,7 +18,7 @@
/**
* @author lichtens <[email protected]>
*/
public final class CoverageDropoutDetectorTest extends BaseTest {
public final class CoverageDropoutDetectorUnitTest extends BaseTest {


@DataProvider(name = "randomUnivariateGaussianTargetsLowVariance")
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4 changes: 3 additions & 1 deletion ...composeSingularValuesIntegrationTest.java → ...composeSingularValuesIntegrationTest.java
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@@ -1,11 +1,13 @@
package org.broadinstitute.hellbender.tools.exome;
package org.broadinstitute.hellbender.tools.archive;


import org.apache.commons.math3.linear.DiagonalMatrix;
import org.apache.commons.math3.linear.MatrixUtils;
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;
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2 changes: 1 addition & 1 deletion ...DetectCoverageDropoutIntegrationTest.java → ...DetectCoverageDropoutIntegrationTest.java
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package org.broadinstitute.hellbender.tools.exome.detectcoveragedropout;
package org.broadinstitute.hellbender.tools.archive;

import org.broadinstitute.hellbender.CommandLineProgramTest;
import org.testng.Assert;
Expand Down