Fix build error in tests

broadinstitute · Nov 7, 2018 · b909de3 · b909de3
1 parent 7322bfc
commit b909de3
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Showing 3 changed files with 11 additions and 50 deletions.
diff --git a/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java b/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
@@ -1,46 +1,22 @@
 package org.broadinstitute.hellbender.tools.walkers;
 
-import com.intel.genomicsdb.reader.GenomicsDBFeatureReader;
-import htsjdk.tribble.AbstractFeatureReader;
-import htsjdk.tribble.CloseableTribbleIterator;
-import htsjdk.tribble.readers.LineIterator;
-import htsjdk.tribble.readers.PositionalBufferedStream;
-import htsjdk.variant.bcf2.BCF2Codec;
-import htsjdk.variant.variantcontext.Genotype;
-import htsjdk.variant.variantcontext.GenotypeBuilder;
 import htsjdk.variant.variantcontext.VariantContext;
-import htsjdk.variant.variantcontext.VariantContextBuilder;
-import htsjdk.variant.vcf.VCFCodec;
 import htsjdk.variant.vcf.VCFHeader;
 import org.broadinstitute.hellbender.CommandLineProgramTest;
-import org.broadinstitute.hellbender.Main;
-import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBConstants;
-import org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport;
-import org.broadinstitute.hellbender.utils.IntervalUtils;
+import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
+import org.broadinstitute.hellbender.testutils.GenomicsDBTestUtils;
+import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
 import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.utils.Utils;
-import org.broadinstitute.hellbender.utils.runtime.ProcessController;
-import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder;
-import org.broadinstitute.hellbender.utils.test.BaseTest;
-import org.broadinstitute.hellbender.utils.test.GenomicsDBTestUtils;
-import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils;
-import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
-import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
-import java.io.FileWriter;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.function.BiConsumer;
-import java.util.stream.Collectors;
 
-import static org.broadinstitute.hellbender.utils.test.VariantContextTestUtils.getVariantContexts;
-import static org.testng.Assert.*;
+import static org.broadinstitute.hellbender.testutils.VariantContextTestUtils.getVariantContexts;
 
 /**
  * Created by gauthier on 3/9/18.

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperUnitTest.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.hellbender.tools.walkers;
 
 import htsjdk.variant.variantcontext.*;
-import org.broadinstitute.hellbender.utils.test.VariantContextTestUtils;
+import org.broadinstitute.hellbender.testutils.VariantContextTestUtils;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 

diff --git a/...dinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java b/...dinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtilsUnitTest.java
@@ -12,9 +12,9 @@
 
 import java.util.*;
 
-import static org.broadinstitute.hellbender.utils.test.VariantContextTestUtils.makeG;
-import static org.broadinstitute.hellbender.utils.test.VariantContextTestUtils.makeGwithPLs;
-import static org.broadinstitute.hellbender.utils.test.VariantContextTestUtils.makeVC;
+import static org.broadinstitute.hellbender.testutils.VariantContextTestUtils.makeG;
+import static org.broadinstitute.hellbender.testutils.VariantContextTestUtils.makeGwithPLs;
+import static org.broadinstitute.hellbender.testutils.VariantContextTestUtils.makeVC;
 
 
 @SuppressWarnings("unchecked")
@@ -70,32 +70,17 @@ private int[] _mleparse(final List<Integer> s) {
      */
     private Genotype makeGwithLog10GLs(final String sample, final Allele a1, final Allele a2, final double[] log10GLs) {
         final Genotype gt = new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(log10GLs).make();
-        if ( log10GLs != null && log10GLs.length > 0 ) {
+        if (log10GLs != null && log10GLs.length > 0) {
             Assert.assertNotNull(gt.getPL());
             Assert.assertTrue(gt.getPL().length > 0);
-            for ( final int i : gt.getPL() ) {
+            for (final int i : gt.getPL()) {
                 Assert.assertTrue(i >= 0);
             }
-            Assert.assertNotEquals(Arrays.toString(gt.getPL()),"[0]");
+            Assert.assertNotEquals(Arrays.toString(gt.getPL()), "[0]");
         }
         return gt;
     }
 
-    private Genotype makeG(final String sample, final Allele a1, final Allele a2) {
-        return GenotypeBuilder.create(sample, Arrays.asList(a1, a2));
-    }
-
-    private Genotype makeG(final String sample, final Allele a1, final Allele a2, final int... pls) {
-        return new GenotypeBuilder(sample, Arrays.asList(a1, a2)).PL(pls).make();
-    }
-
-    //NOTE: for deletions use the method makeDeletionVC so stop position validates
-    private VariantContext makeVC(final String source, final List<Allele> alleles, final Genotype... genotypes) {
-        final int start = 10;
-        final int stop = start;
-        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make();
-    }
-
     private VariantContext makeDeletionVC(final String source, final List<Allele> alleles, final int refLength, final Genotype... genotypes) {
         final int start = 10;
         final int stop = start+refLength-1;