From 506c0e9c9773135a46a3ad3740f1fb2e875eee83 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 23 Dec 2011 16:44:28 -0500
Subject: [PATCH] Disabling SnpEff support in the GATK and SnpEff annotation in
 the HybridSelectionPipeline

SnpEff support will remain disabled until SnpEff 2.0.4 has been officially released
and we've verified the quality of its annotations.
---
 .../broadinstitute/sting/gatk/walkers/annotator/SnpEff.java | 6 ++++++
 .../walkers/annotator/VariantAnnotatorIntegrationTest.java  | 4 ++--
 .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java  | 2 +-
 .../walkers/varianteval/VariantEvalIntegrationTest.java     | 2 +-
 4 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
index 1956dac6c..5d215603a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
@@ -204,6 +204,11 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
     }
 
     public void initialize ( AnnotatorCompatibleWalker walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
+        throw new UserException("SnpEff support is currently disabled in the GATK until SnpEff 2.0.4 is officially released " +
+                                "due to a serious issue with SnpEff versions prior to 2.0.4. Please see this page for more details: " +
+                                "http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Genomic_Annotations_Using_SnpEff_and_VariantAnnotator");
+
+        /*
         // Make sure that we actually have a valid SnpEff rod binding (just in case the user specified -A SnpEff
         // without providing a SnpEff rod via --snpEffFile):
         validateRodBinding(walker.getSnpEffRodBinding());
@@ -223,6 +228,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
         // mistaken in the future for a SnpEff output file:
         headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_VERSION_LINE_KEY, snpEffVersionLine.getValue()));
         headerLines.add(new VCFHeaderLine(OUTPUT_VCF_HEADER_COMMAND_LINE_KEY, snpEffCommandLine.getValue()));
+        */
     }
 
     public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 83c3d3a1e..fa0b62cfd 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -145,7 +145,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test
+    @Test(enabled = false)
     public void testSnpEffAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " +
@@ -157,7 +157,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("Testing SnpEff annotations", spec);
     }
 
-    @Test
+    @Test(enabled = false)
     public void testSnpEffAnnotationsUnsupportedVersion() {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " +
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index ba33108cf..3c6131d6c 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -298,7 +298,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("test MultiSample Phase1 indels with complicated records", spec4);
     }
 
-    @Test
+    @Test(enabled = false)
     public void testSnpEffAnnotationRequestedWithoutRodBinding() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 4e3d38c4f..3ef4e5e9f 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -14,7 +14,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     private static String cmdRoot = "-T VariantEval" +
             " -R " + b36KGReference;
 
-    @Test
+    @Test(enabled = false)
     public void testFunctionClassWithSnpeff() {
         WalkerTestSpec spec = new WalkerTestSpec(
                                 buildCommandLine(