zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

SnpEff-related fixes. 

-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.

-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
This commit is contained in:
David Roazen 2011-08-12 15:04:33 -04:00
parent 10e873d9c6
commit bb4ced3201
2 changed files with 13 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
View File

@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffConstants;
import org.broadinstitute.sting.utils.codecs.snpEff.SnpEffFeature;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.*;
@ -70,9 +71,11 @@ 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";
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
public Map<String, Object> annotate ( RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc ) {
RodBinding<SnpEffFeature> snpEffRodBinding = walker.getSnpEffRodBinding();
List<SnpEffFeature> features = tracker.getValues(snpEffRodBinding);
validateRodBinding(snpEffRodBinding);
List<SnpEffFeature> features = tracker.getValues(snpEffRodBinding, ref.getLocus());
// Add only annotations for one of the most biologically-significant effects as defined in
// the SnpEffConstants class:
@ -85,6 +88,13 @@ public class SnpEff extends InfoFieldAnnotation implements ExperimentalAnnotatio
return generateAnnotations(mostSignificantEffect);
}
private void validateRodBinding ( RodBinding<SnpEffFeature> snpEffRodBinding ) {
if ( snpEffRodBinding == null || ! snpEffRodBinding.isBound() ) {
throw new UserException("The SnpEff annotator requires that a SnpEff output file be provided " +
"as a rodbinding on the command line, but no SnpEff rodbinding was found.");
}
}
private SnpEffFeature getMostSignificantEffect ( List<SnpEffFeature> snpEffFeatures ) {
SnpEffFeature mostSignificantEffect = null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -64,7 +64,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
* The INFO field will be annotated with information on the most biologically-significant effect
* listed in the SnpEff output file for each variant.
*/
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="A SnpEff output file from which to add annotations", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return snpEffFile; }