e96b1791abd3b65c939b214730cd6999cb2464f8,java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/SNPGenotypeConcordance.java,SNPGenotypeConcordance,computeConcordance,#RefMetaDataTracker#ReferenceContext#,54

Before Change


    }

    public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
        Variation call1 = (Variation)tracker.lookup("callset1", null);
        Variation call2 = (Variation)tracker.lookup("callset2", null);

        // the only reason they would be null is a lack of coverage

After Change


    }

    public void computeConcordance(RefMetaDataTracker tracker, ReferenceContext ref) {
        RODRecordList<ReferenceOrderedDatum> call1List = tracker.getTrackData("callset1", null);
        RODRecordList<ReferenceOrderedDatum> call2List = tracker.getTrackData("callset2", null);
        Variation call1 = (call1List == null ? null : (Variation)call1List.getRecords().get(0));
        Variation call2 = (call2List == null ? null : (Variation)call2List.getRecords().get(0));

        // the only reason they would be null is a lack of coverage