From 4e268ef6ac60d5b1c03a215ac7124add3f3c9aaf Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 28 May 2010 18:27:25 +0000
Subject: [PATCH] Removing the Variant Recalibration Performance test because
 it isn't ready yet.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...ntRecalibrationWalkersPerformanceTest.java | 65 -------------------
 1 file changed, 65 deletions(-)
 delete mode 100755 java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersPerformanceTest.java

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<String, String> paramsFiles = new HashMap<String, String>();
-
-    @Test
-    public void testGenerateVariantClusters() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "b39bde091254e90490b0d7bf9f0ef24a" );
-
-        for ( Map.Entry<String, String> 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<String>(0));
-            List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
-            paramsFiles.put(vcf, result.get(0).getAbsolutePath());
-        }
-    }
-
-    @Test
-    public void testVariantRecalibrator() {
-        HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "412bdb2eb4ca8f7ee9dfb39cda676c95" );
-
-        for ( Map.Entry<String, String> 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<String>(0));
-
-                executeTest("testVariantRecalibrator", spec);
-            }
-        }
-    }
-}