Merged bug fix from Stable into Unstable

ivy.xml

@@ -76,7 +76,7 @@
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
 
     <!-- snpEff annotator for pipelines -->
-    <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.4rc3" />
+    <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5" />
 
     <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
     <exclude org="javax.servlet" />

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java

@@ -56,7 +56,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
 
     // We refuse to parse SnpEff output files generated by unsupported versions, or
     // lacking a SnpEff version number in the VCF header:
-    public static final String[] SUPPORTED_SNPEFF_VERSIONS = { "2.0.4" };
+    public static final String[] SUPPORTED_SNPEFF_VERSIONS = { "2.0.5" };
     public static final String SNPEFF_VCF_HEADER_VERSION_LINE_KEY = "SnpEffVersion";
     public static final String SNPEFF_VCF_HEADER_COMMAND_LINE_KEY = "SnpEffCmd";
 
@@ -204,11 +204,6 @@ 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());
@@ -228,7 +223,6 @@ 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 ) {

public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -145,19 +145,19 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         }
     }
 
-    @Test(enabled = false)
+    @Test
     public void testSnpEffAnnotations() {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " +
             validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile  " + validationDataLocation +
-            "snpEff2.0.4.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
+            "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429",
             1,
-            Arrays.asList("51258f5c880bd1ca3eb45a1711335c66")
+            Arrays.asList("ffbda45b3682c9b83cb541d83f6c15d6")
         );
         executeTest("Testing SnpEff annotations", spec);
     }
 
-    @Test(enabled = false)
+    @Test
     public void testSnpEffAnnotationsUnsupportedVersion() {
         WalkerTestSpec spec = new WalkerTestSpec(
             "-T VariantAnnotator -R " + hg19Reference + " -NO_HEADER -o %s -A SnpEff --variant " +

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(enabled = false)
+    @Test
     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 " +

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -14,19 +14,19 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     private static String cmdRoot = "-T VariantEval" +
             " -R " + b36KGReference;
 
-    @Test(enabled = false)
+    @Test
     public void testFunctionClassWithSnpeff() {
         WalkerTestSpec spec = new WalkerTestSpec(
                                 buildCommandLine(
                                         "-T VariantEval",
                                         "-R " + b37KGReference,
                                         "--dbsnp " + b37dbSNP132,
-                                        "--eval " + validationDataLocation + "snpEff2.0.4.AFR.unfiltered.VariantAnnotator.output.vcf",
+                                        "--eval " + validationDataLocation + "snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf",
                                         "-noEV",
                                         "-EV TiTvVariantEvaluator",
                                         "-noST",
                                         "-ST FunctionalClass",
-                                        "-L " + validationDataLocation + "snpEff2.0.4.AFR.unfiltered.VariantAnnotator.output.vcf",
+                                        "-L " + validationDataLocation + "snpEff2.0.5.AFR.unfiltered.VariantAnnotator.output.vcf",
                                         "-o %s"
                                 ),
                                 1,

settings/repository/net.sf.snpeff/snpeff-2.0.5.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.4rc3" status="release" />
+    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.5" status="release" />
 </ivy-module>