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Refactor so that GenotypeAnnotation and InfoFieldAnnotation share common superclass VariantAnnotatorAnnotation

This commit is contained in:
Mark DePristo 2011-07-25 10:55:09 -04:00
parent 7f8e6a97ee
commit 1a268ff1fd
7 changed files with 51 additions and 18 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAnnotation {
public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
Double ratio = annotateSNP(stratifiedContext, vc, g);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -22,7 +22,7 @@ import java.util.List;
import java.util.Map;
public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnotation {
public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation {
private static String REF_ALLELE = "REF";

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
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@ -49,7 +49,7 @@ import java.util.Map;
* Time: 6:46:25 PM
* To change this template use File | Settings | File Templates.
*/
public class MappingQualityZeroBySample implements GenotypeAnnotation {
public class MappingQualityZeroBySample extends GenotypeAnnotation {
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
AlignmentContext context, VariantContext vc, Genotype g) {
if ( g == null || !g.isCalled() )

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java
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@ -52,7 +52,7 @@ import java.util.Map;
* Time: 3:59:27 PM
* To change this template use File | Settings | File Templates.
*/
public class ReadDepthAndAllelicFractionBySample implements GenotypeAnnotation {
public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
private static String REF_ALLELE = "REF";

11
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
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@ -10,15 +10,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
public interface GenotypeAnnotation {
public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts/genotype split by sample
public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
// return the FORMAT keys
public List<String> getKeyNames();
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
// return the descriptions used for the VCF FORMAT meta field
public List<VCFFormatHeaderLine> getDescriptions();
public abstract List<VCFFormatHeaderLine> getDescriptions();
}

9
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -10,16 +11,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator INFO-field annotations", summary = "VariantAnnotator annotations, written to INFO Field")
public abstract class InfoFieldAnnotation {
public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
// return annotations for the given contexts split by sample
public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
// return the INFO keys
public abstract List<String> getKeyNames();
// return the descriptions used for the VCF INFO meta field
public abstract List<VCFInfoHeaderLine> getDescriptions();
}

41
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java 100644
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@ -0,0 +1,41 @@
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
public abstract class VariantAnnotatorAnnotation {
// return the INFO keys
public abstract List<String> getKeyNames();
}