diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersPerformanceTest.java deleted file mode 100755 index 13baa958c..000000000 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersPerformanceTest.java +++ /dev/null @@ -1,65 +0,0 @@ -package org.broadinstitute.sting.gatk.walkers.variantrecalibration; - -import org.broadinstitute.sting.WalkerTest; -import org.junit.Test; - -import java.util.*; -import java.io.File; - -public class VariantRecalibrationWalkersPerformanceTest extends WalkerTest { - static HashMap paramsFiles = new HashMap(); - - @Test - public void testGenerateVariantClusters() { - HashMap e = new HashMap(); - e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "b39bde091254e90490b0d7bf9f0ef24a" ); - - for ( Map.Entry entry : e.entrySet() ) { - String vcf = entry.getKey(); - String md5 = entry.getValue(); - - WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + - " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + - " -T GenerateVariantClusters" + - " -B input,VCF," + vcf + - " -nG 6" + - " -nI 5" + - " --ignore_filter GATK_STANDARD" + - " -an QD -an HRun -an SB" + - " -clusterFile /dev/null", - 0, // just one output file - new ArrayList(0)); - List result = executeTest("testGenerateVariantClusters", spec).getFirst(); - paramsFiles.put(vcf, result.get(0).getAbsolutePath()); - } - } - - @Test - public void testVariantRecalibrator() { - HashMap e = new HashMap(); - e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "412bdb2eb4ca8f7ee9dfb39cda676c95" ); - - for ( Map.Entry entry : e.entrySet() ) { - String vcf = entry.getKey(); - String md5 = entry.getValue(); - String paramsFile = paramsFiles.get(vcf); - System.out.printf("PARAMS FOR %s is %s%n", vcf, paramsFile); - if ( paramsFile != null ) { - File file = createTempFile("cluster",".vcf"); - WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + - " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + - " -T VariantRecalibrator" + - " -B input,VCF," + vcf + - " --ignore_filter GATK_STANDARD" + - " -output /dev/null" + - " -clusterFile " + validationDataLocation + "clusterFile", - 0, - new ArrayList(0)); - - executeTest("testVariantRecalibrator", spec); - } - } - } -}