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

Fixes for rod bindings

This commit is contained in:
Eric Banks 2011-08-10 23:08:47 -04:00
parent 75985c2fa0
commit f1b09db39e
2 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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

@ -109,7 +109,7 @@ public class VariantAnnotatorEngine {
// check to see whether comp rods were included
final RodBinding<VariantContext> dbsnp = walker.getDbsnpRodBinding();
if ( dbsnp.isBound() )
if ( dbsnp != null && dbsnp.isBound() )
dbAnnotations.put(dbsnp, VCFConstants.DBSNP_KEY);
final List<RodBinding<VariantContext>> comps = walker.getCompRodBindings();

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -69,7 +69,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
*/
@ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return RodBinding.makeUnbound(SnpEffFeature.class); }
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }