bfa2c2f391b15d4bcaaba46479e584b86af4d5ad,public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java,RecalDatumNode,calcPenalty,#,254

Before Change


            int i = 0;
            for ( final RecalDatumNode<T> subnode : subnodes ) {
                // use the yates correction to help avoid all zeros => NaN
                counts[i][0] = subnode.getRecalDatum().getNumMismatches() + 1;
                counts[i][1] = subnode.getRecalDatum().getNumObservations() + 2;
                i++;
            }

After Change


            int i = 0;
            for ( final RecalDatumNode<T> subnode : subnodes ) {
                // use the yates correction to help avoid all zeros => NaN
                counts[i][0] = Math.round(subnode.getRecalDatum().getNumMismatches()) + 1L;
                counts[i][1] = Math.round(subnode.getRecalDatum().getNumObservations()) + 2L;
                i++;
            }