diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index fe297a68e..5aeadfd10 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -44,6 +44,7 @@ public abstract class BaseTest { protected static String oneKGLocation = "/broad/1KG/"; protected static String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/"; protected static String validationDataLocation = GATKDataLocation + "Validation_Data/"; + protected static String evaluationDataLocation = GATKDataLocation + "Evaluation_Data/"; protected static String testDir = "testdata/"; protected static boolean alreadySetup = false; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java new file mode 100755 index 000000000..d9340e8a1 --- /dev/null +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java @@ -0,0 +1,69 @@ +package org.broadinstitute.sting.gatk.walkers.recalibration; + +import org.broadinstitute.sting.WalkerTest; +import org.junit.Test; + +import java.util.ArrayList; + +public class RecalibrationWalkersPerformanceTest extends WalkerTest { + + @Test + public void testCountCovariatesWholeGenome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T CountCovariates" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-50,000,000" + + " -standard" + + " -OQ" + + " -recalFile /dev/null", + 0, + new ArrayList(0)); + executeTest("testCountCovariatesWholeGenome", spec); + } + + @Test + public void testCountCovariatesWholeExome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T CountCovariates" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + + " -standard" + + " -OQ" + + " -recalFile /dev/null", + 0, + new ArrayList(0)); + executeTest("testCountCovariatesWholeExome", spec); + } + + @Test + public void testTableRecalibratorWholeGenome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T TableRecalibration" + + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -L chr1:1-50,000,000" + + " -OQ" + + " -recalFile " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.recal.csv" + + " -outputBam /dev/null", + 0, + new ArrayList(0)); + executeTest("testTableRecalibratorWholeGenome", spec); + } + + @Test + public void testTableRecalibratorWholeExome() { + WalkerTestSpec spec = new WalkerTestSpec( + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + " -T TableRecalibration" + + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + + " -OQ" + + " -recalFile " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.recal.csv" + + " -outputBam /dev/null", + 0, + new ArrayList(0)); + executeTest("testTableRecalibratorWholeExome", spec); + } +} \ No newline at end of file