for (int c = 0; c < table[row].length; c++) {
sum += table[row][c];
}
return sum;
}
<BUG>private static int[][] getContingencyTable(Map<String, AlignmentContext> stratifiedContexts, Allele ref, Allele alt) {
</BUG>
int[][] table = new int[2][2];
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {

for (int c = 0; c < table[row].length; c++) {
sum += table[row][c];
}
return sum;
}
private static int[][] getSNPContingencyTable(Map<String, AlignmentContext> stratifiedContexts, Allele ref, Allele alt) {
int[][] table = new int[2][2];
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {
