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Made the necessary changes to get SnpEff support working with the new rodbinding system.

This commit is contained in:
David Roazen 2011-08-08 23:23:42 -04:00
parent b180a1311a
commit 2efa376619
3 changed files with 24 additions and 15 deletions
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31
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
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@ -24,6 +24,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -43,8 +44,8 @@ import java.util.*;
* (http://snpeff.sourceforge.net/).
*
* For each variant, chooses one of the effects of highest biological impact from the SnpEff
* output file (which must be bound to an RMD track named "SnpEff"), and adds annotations
* on that effect.
* output file (which must be provided on the command line via --snpEffFile:SnpEff <filename>),
* and adds annotations on that effect.
*
* The possible biological effects and their associated impacts are defined in the class:
* org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants
@ -68,28 +69,32 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
public static final String CODON_NUM_KEY = "CODON_NUM";
public static final String CDS_SIZE_KEY = "CDS_SIZE";
// Name of the RMD track bound to the raw SnpEff-generated output file:
public static final String RMD_TRACK_NAME = "SnpEff";
public Map<String, Object> annotate ( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
List<Object> snpEffFeatures = tracker.getReferenceMetaData(RMD_TRACK_NAME);
List<Feature> features = tracker.getValues(Feature.class);
// Add only annotations for one of the most biologically-significant effects as defined in
// the SnpEffConstants class:
SnpEffFeature mostSignificantEffect = getMostSignificantEffect(snpEffFeatures);
SnpEffFeature mostSignificantEffect = getMostSignificantEffect(features);
if ( mostSignificantEffect == null ) {
return null;
}
return generateAnnotations(mostSignificantEffect);
}
private SnpEffFeature getMostSignificantEffect ( List<Object> snpEffFeatures ) {
private SnpEffFeature getMostSignificantEffect ( List<Feature> features ) {
SnpEffFeature mostSignificantEffect = null;
for ( Object feature : snpEffFeatures ) {
SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
for ( Feature feature : features ) {
if ( feature instanceof SnpEffFeature ) {
SnpEffFeature snpEffFeature = (SnpEffFeature)feature;
if ( mostSignificantEffect == null ||
snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
if ( mostSignificantEffect == null ||
snpEffFeature.isHigherImpactThan(mostSignificantEffect) ) {
mostSignificantEffect = snpEffFeature;
mostSignificantEffect = snpEffFeature;
}
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffFeature;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
@ -55,6 +56,9 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;

4
public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -129,8 +129,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testSnpEffAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff -B:variant,VCF " +
validationDataLocation + "1000G.exomes.vcf -B:SnpEff,SnpEff " + validationDataLocation +
"-T VariantAnnotator -R " + b37KGReference + " -NO_HEADER -o %s -A SnpEff --variants:VCF " +
validationDataLocation + "1000G.exomes.vcf --snpEffFile:SnpEff " + validationDataLocation +
"snpEff_1.9.6_1000G.exomes.vcf_hg37.61.out -L 1:26,000,000-26,500,000",
1,
Arrays.asList("c08648a078368c80530bff004b3157f1")