From d625186796ec8d5c7c67e938523031df3c2ac6e3 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Sep 2010 15:00:41 +0000
Subject: [PATCH] I think the VR integration tests are fine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
---
 ...ntRecalibrationWalkersIntegrationTest.java | 53 +++++++++----------
 1 file changed, 26 insertions(+), 27 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 9836001b5..f12507c98 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -11,35 +11,34 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     static HashMap<String, String> tranchesFiles = new HashMap<String, String>();
     static HashMap<String, String> inputVCFFiles = new HashMap<String, String>();
 
-    // commented out until fixed in SVN
-    // @Test
-    // public void testGenerateVariantClusters() {
-    //     HashMap<String, String> e = new HashMap<String, String>();
-    //     e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "7c5431a560e9ca257523cf68b808b058" );
-    //     e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "a438635bc96a80c5e6f090d82a394819" );
+    @Test
+    public void testGenerateVariantClusters() {
+        HashMap<String, String> e = new HashMap<String, String>();
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "7c5431a560e9ca257523cf68b808b058" );
+        e.put( validationDataLocation + "lowpass.N3.chr1.raw.vcf", "a438635bc96a80c5e6f090d82a394819" );
 
-    //     for ( Map.Entry<String, String> entry : e.entrySet() ) {
-    //         String vcf = entry.getKey();
-    //         String md5 = entry.getValue();
+        for ( Map.Entry<String, String> entry : e.entrySet() ) {
+            String vcf = entry.getKey();
+            String md5 = entry.getValue();
 
-    //         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-    //                 "-R " + b36KGReference +
-    //                         " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
-    //                         " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/genotypes_r27_nr.b36_fwd.vcf" +
-    //                         " -weightDBSNP 0.2 -weightHapMap 1.0" +
-    //                         " -T GenerateVariantClusters" +
-    //                         " -B:input,VCF " + vcf +
-    //                         " -L 1:50,000,000-200,000,000" +
-    //                         " -qual 50.0" +
-    //                         " --ignore_filter GATK_STANDARD" +
-    //                         " -an QD -an HRun -an SB" +
-    //                         " -clusterFile %s",
-    //                 1, // just one output file
-    //                 Arrays.asList(md5));
-    //         List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
-    //         clusterFiles.put(vcf, result.get(0).getAbsolutePath());
-    //     }
-    // }
+            WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                    "-R " + b36KGReference +
+                            " --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
+                            " -B:hapmap,VCF " + comparisonDataLocation + "Validated/HapMap/3.2/genotypes_r27_nr.b36_fwd.vcf" +
+                            " -weightDBSNP 0.2 -weightHapMap 1.0" +
+                            " -T GenerateVariantClusters" +
+                            " -B:input,VCF " + vcf +
+                            " -L 1:50,000,000-200,000,000" +
+                            " -qual 50.0" +
+                            " --ignore_filter GATK_STANDARD" +
+                            " -an QD -an HRun -an SB" +
+                            " -clusterFile %s",
+                    1, // just one output file
+                    Arrays.asList(md5));
+            List<File> result = executeTest("testGenerateVariantClusters", spec).getFirst();
+            clusterFiles.put(vcf, result.get(0).getAbsolutePath());
+        }
+    }
 
     @Test
     public void testVariantRecalibrator() {