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++;
}