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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.
This commit is contained in:
David Roazen 2011-12-23 16:44:28 -05:00
parent 24c84da60d
commit 506c0e9c97
4 changed files with 10 additions and 4 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -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 ) {

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -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 " +

2
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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 " +

2
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -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(