58937bf9ba4a233aa3c708635bd539524ccb3c4d,java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java,UnifiedGenotyper,map,#RefMetaDataTracker#ReferenceContext#AlignmentContext#,157
Before Change
// annotate the call, if possible
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}
After Change
if ( UAC.ALL_ANNOTATIONS )
annotations = VariantAnnotator.getAllAnnotations(refContext, fullContext, call.second, call.first);
else
annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}