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Merge pull request #1333 from broadinstitute/db_issue_1216 

Replace string literals for annotation groups.  Closes #1216
This commit is contained in:
David Benjamin 2016-04-19 21:55:18 -04:00
parent 70b259a3fb c040da427d
commit 44691f036b
4 changed files with 16 additions and 7 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2.java
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@ -1066,7 +1066,7 @@ public class MuTect2 extends ActiveRegionWalker<List<VariantContext>, Integer> i
* Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups.
*/
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
//protected String[] annotationGroupsToUse = { "Standard" };
//protected String[] annotationGroupsToUse = { StandardAnnotation.class.getSimpleName() };
protected String[] annotationClassesToUse = { };
/**

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
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@ -62,6 +62,8 @@ import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
import org.broadinstitute.gatk.engine.io.DirectOutputTracker;
import org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardHCAnnotation;
import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
import org.broadinstitute.gatk.utils.contexts.AlignmentContextUtils;
import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
@ -328,7 +330,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
* to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
*/
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{ "Standard", "StandardHCAnnotation" }));
protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName(), StandardHCAnnotation.class.getSimpleName() }));
@ArgumentCollection
private HaplotypeCallerArgumentCollection HCAC = new HaplotypeCallerArgumentCollection();

3
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
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@ -54,6 +54,7 @@ package org.broadinstitute.gatk.tools.walkers.variantutils;
import org.broadinstitute.gatk.engine.arguments.DbsnpArgumentCollection;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.CommandLineGATK;
import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
@ -129,7 +130,7 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
* to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
*/
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
protected String[] annotationGroupsToUse = { "Standard" };
protected String[] annotationGroupsToUse = { StandardAnnotation.class.getSimpleName() };
/**

14
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFs.java
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@ -65,7 +65,9 @@ import org.broadinstitute.gatk.engine.walkers.RodWalker;
import org.broadinstitute.gatk.engine.walkers.TreeReducible;
import org.broadinstitute.gatk.engine.walkers.Window;
import org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AS_StandardAnnotation;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.AnnotatorCompatible;
import org.broadinstitute.gatk.tools.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine;
import org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyFailOverAFCalculatorProvider;
@ -169,7 +171,7 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
* to provide a pedigree file for a pedigree-based annotation) may cause the run to fail.
*/
@Argument(fullName="group", shortName="G", doc="One or more classes/groups of annotations to apply to variant calls", required=false)
protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{"Standard"}));
protected List<String> annotationGroupsToUse = new ArrayList<>(Arrays.asList(new String[]{StandardAnnotation.class.getSimpleName()}));
/**
@ -222,9 +224,13 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
annotationEngine = new VariantAnnotatorEngine(annotationGroupsToUse, annotationsToUse, Collections.<String>emptyList(), this, toolkit);
// create the genotyping engine
boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY) || annotationGroupsToUse.contains("AS_Standard");
genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger),
toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping);
// when checking for presence of AS_StandardAnnotation we must deal with annoying feature that
// the class name with or without the trailing "Annotation" are both valid command lines
boolean doAlleleSpecificGenotyping = annotationsToUse.contains(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY)
|| annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName())
|| annotationGroupsToUse.contains(AS_StandardAnnotation.class.getSimpleName().replace("Annotation", ""));
genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(),
GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger), toolkit.getArguments().BAQMode, doAlleleSpecificGenotyping);
// take care of the VCF headers
final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);