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

Bug fix for NPE in HC with --dbsnp argument. 

- I had added the framework in the VA engine but should not have hooked it up to the HC yet since the RefMetaDataTracker is always null.
 - Added contracts and docs to the relevant methods in the VA engine so that this doesn't happen in the future.
This commit is contained in:
Eric Banks 2013-02-05 21:59:19 -05:00
parent e7c35a907f
commit 4e5ff3d6f1
2 changed files with 25 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -509,7 +509,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
activeRegion.getLocation(),
getToolkit().getGenomeLocParser(),
activeAllelesToGenotype ) ) {
annotationEngine.annotateDBs(metaDataTracker, getToolkit().getGenomeLocParser().createGenomeLoc(call), call);
// TODO -- uncomment this line once ART-based walkers have a proper RefMetaDataTracker.
// annotationEngine.annotateDBs(metaDataTracker, getToolkit().getGenomeLocParser().createGenomeLoc(call), call);
vcfWriter.add( call );
}

23
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -25,6 +25,8 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -235,6 +237,16 @@ public class VariantAnnotatorEngine {
return builder.genotypes(annotateGenotypes(null, null, null, vc, perReadAlleleLikelihoodMap)).make();
}
/**
* Annotate the ID field and other DBs for the given Variant Context
*
* @param tracker ref meta data tracker (cannot be null)
* @param loc location of the vc
* @param vc variant context to annotate
* @return non-null annotated version of vc
*/
@Requires({"tracker != null && loc != null && vc != null"})
@Ensures("result != null")
public VariantContext annotateDBs(final RefMetaDataTracker tracker, final GenomeLoc loc, VariantContext vc) {
final Map<String, Object> newInfoAnnotations = new HashMap<String, Object>(0);
vc = annotateDBs(tracker, loc, vc, newInfoAnnotations);
@ -247,6 +259,17 @@ public class VariantAnnotatorEngine {
return vc;
}
/**
* Annotate the ID field and other DBs for the given Variant Context
*
* @param tracker ref meta data tracker (cannot be null)
* @param loc location of the vc
* @param vc variant context to annotate
* @param infoAnnotations info annotation map to populate
* @return non-null annotated version of vc
*/
@Requires({"tracker != null && loc != null && vc != null && infoAnnotations != null"})
@Ensures("result != null")
private VariantContext annotateDBs(final RefMetaDataTracker tracker, final GenomeLoc loc, VariantContext vc, final Map<String, Object> infoAnnotations) {
for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {