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Remove org.apache.commons.collections.IteratorUtils dependency from the test suite 

-This was a dependency of the test suite, but not the GATK proper,
 which caused problems when running the test suite on the packaged
 GATK jar at release time

-Use GATKVCFUtils.readVCF() instead
This commit is contained in:
David Roazen 2013-08-21 19:41:34 -04:00
parent 4b00c81181
commit 42d771f748
3 changed files with 2 additions and 6 deletions
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6
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -47,7 +47,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import net.sf.samtools.util.BlockCompressedInputStream;
import org.apache.commons.collections.IteratorUtils;
import org.broad.tribble.readers.AsciiLineReader;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -55,7 +54,6 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.variantcontext.Genotype;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.VCFCodec;
import org.testng.Assert;
import org.testng.annotations.Test;
@ -345,12 +343,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
final WalkerTestSpec specAllSamples = new WalkerTestSpec(base, 1, Arrays.asList(""));
specAllSamples.disableShadowBCF();
final File allSamplesVCF = executeTest("testOnlyEmitSampleAllSamples", specAllSamples).first.get(0);
List<VariantContext> allSampleVCs = IteratorUtils.toList(GATKVCFUtils.readAllVCs(allSamplesVCF, new VCFCodec()).getSecond());
final List<VariantContext> allSampleVCs = GATKVCFUtils.readVCF(allSamplesVCF).getSecond();
final WalkerTestSpec onlyHG01879 = new WalkerTestSpec(base + " -onlyEmitSamples HG01879", 1, Arrays.asList(""));
onlyHG01879.disableShadowBCF();
final File onlyHG01879VCF = executeTest("testOnlyEmitSample", onlyHG01879).first.get(0);
List<VariantContext> onlyHG01879VCs = IteratorUtils.toList(GATKVCFUtils.readAllVCs(onlyHG01879VCF, new VCFCodec()).getSecond());
final List<VariantContext> onlyHG01879VCs = GATKVCFUtils.readVCF(onlyHG01879VCF).getSecond();
Assert.assertEquals(allSampleVCs.size(), onlyHG01879VCs.size());
for ( int i = 0; i < allSampleVCs.size(); i++ ) {

1
protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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@ -46,7 +46,6 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.apache.commons.collections.IteratorUtils;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.variantcontext.Genotype;

1
public/java/test/org/broadinstitute/sting/utils/sam/ArtificialBAMBuilderUnitTest.java
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@ -27,7 +27,6 @@ package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import org.apache.commons.collections.IteratorUtils;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.DataProvider;