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Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-02 00:22:15 +00:00
parent 4ddbaeed07
commit 9dbdfff786
26 changed files with 38 additions and 45 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicPoolVariantAnalysis.java
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.genotype.Variation;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/BasicVariantAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/BasicVariantAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/CallableBasesAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CallableBasesAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ChipConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ChipConcordance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.Genotype;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ClusterCounterAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ClusterCounterAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.IntervalRod;
@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
/**

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ConcordanceTruthTable.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.genotype.Genotype;

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeAnalysis.java
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@ -1,7 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
package org.broadinstitute.sting.gatk.walkers.varianteval;
/**
* The Broad Institute

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/HardyWeinbergEquilibrium.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import cern.jet.math.Arithmetic;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/Histogram.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/Histogram.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import java.util.ArrayList;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/IndelMetricsAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/NeighborDistanceAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/NeighborDistanceAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.IntervalRod;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PoolAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PoolAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
/**
* Created by IntelliJ IDEA.

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledConcordance.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledConcordance.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.utils.StingException;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledFrequencyAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PooledFrequencyAnalysis.java
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@ -1,9 +1,8 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import java.util.List;
import java.util.ArrayList;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PopulationAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/PopulationAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
/**
* The Broad Institute

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/TransitionTranversionAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/TransitionTranversionAnalysis.java
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@ -1,9 +1,8 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.ArrayList;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ValidationDataAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/ValidationDataAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantAnalysis.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantAnalysis.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantCounter.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantCounter.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantDBCoverage.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantDBCoverage.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantMatcher.java → java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantMatcher.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
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@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.VariantBackedByGenotype;
import org.broadinstitute.sting.playground.gatk.walkers.poolseq.PowerBelowFrequencyWalker;
import org.broadinstitute.sting.playground.gatk.walkers.varianteval.ConcordanceTruthTable;
import org.broadinstitute.sting.gatk.walkers.varianteval.ConcordanceTruthTable;
import java.io.*;
import java.util.LinkedList;

26
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java → java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
@ -18,8 +18,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalVariantROD() {
HashMap<String, String> md5 = new HashMap<String, String>();
md5.put("", "4b5a43cb4fa1b82e1bb361632754eaa1");
md5.put("-A", "7dd6aa5379ea5422fe7db4e79baad1f7");
md5.put("", "9cfda40f521d75a3e8bafc44a663c14a");
md5.put("-A", "8fea7cc25f551ce170636fc35c5ae0fe");
/**
* the above MD5 was calculated from running the following command:
@ -52,7 +52,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalVariantRODConfSix() {
List<String> md5 = new ArrayList<String>();
md5.add("cfcc2a8e0587cb288f0472118a9bdc1d");
md5.add("11d636d105f902680c46b9f2e330d922");
/**
* the above MD5 was calculated from running the following command:
@ -84,7 +84,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalVariantRODOutputViolations() {
List<String> md5 = new ArrayList<String>();
md5.add("ce708258676bbd4e71e8714828e7d695");
md5.add("12ecd457d62329e9d4e593de904a457d");
/**
* the above MD5 was calculated from running the following command:
@ -116,7 +116,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalGenotypeROD() {
List<String> md5 = new ArrayList<String>();
md5.add("4df6a9c9d09a7bf034f29db24fb7a923");
md5.add("cbe45debc69e83d2b90988ee72042074");
/**
* the above MD5 was calculated after running the following command:
*
@ -150,7 +150,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalMarksGenotypingExample() {
List<String> md5 = new ArrayList<String>();
md5.add("f79448f380cfb56be3585547b794a48c");
md5.add("2694cf3eb73a9fecdda8cf5b76d0135d");
/**
* Run with the following commands:
*
@ -177,7 +177,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testEvalRuntimeWithLotsOfIntervals() {
List<String> md5 = new ArrayList<String>();
md5.add("4d01485ed2d3cb5edbff24cc0c05b205");
md5.add("6a90341517fc3c5026529301d9970c7b");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T VariantEval -R " + oneKGLocation + "reference/human_b36_both.fasta " +
"-B eval,Variants," + validationDataLocation + "NA12878.pilot_3.all.geli.calls " +
@ -193,11 +193,11 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
@Test
public void testVCFVariantEvals() {
HashMap<String, String> md5 = new HashMap<String, String>();
md5.put("", "9702cba801cf216324607c8ecb7871e4");
md5.put("-A", "e9e02eba2e3423bde18ddb0a33a50e34");
md5.put("-A --includeFilteredRecords", "f0cb51e2c7917e502ca510cc9a3382a9");
md5.put("-A --sampleName NA12878", "b936723b0de69ed2698ab2af4b70a1e8");
md5.put("-A -vcfInfoSelector AF=0.50", "a8299c6ba370bf9334327ec03e8885b7");
md5.put("", "a1c5c8e9b185108969528e8c9fbef15e");
md5.put("-A", "2ae1456de2375502689c4af8f40b8693");
md5.put("-A --includeFilteredRecords", "9b2f446f0f42ab10d9d27f5221748f5e");
md5.put("-A --sampleName NA12878", "38deda8ab3816f083f0aeb97ccf8c347");
md5.put("-A -vcfInfoSelector AF=0.50", "715ea2da250f58aa35004386a890f5ba");
for ( Map.Entry<String, String> e : md5.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java
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@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.genotype.Genotype;
import org.broadinstitute.sting.utils.genotype.BasicGenotype;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.playground.gatk.walkers.varianteval.ConcordanceTruthTable;
import org.broadinstitute.sting.gatk.walkers.varianteval.ConcordanceTruthTable;
import org.broadinstitute.sting.BaseTest;
import java.util.List;