int numReadGroups = 0;
<BUG>for( List<? extends Comparable> readGroupList : dataManager.getCollapsedTable(0).keySet() ) {
</BUG>
if(NUM_READ_GROUPS_TO_PROCESS == -1 || ++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS) {
<BUG>String readGroup = readGroupList.get(0).toString();
</BUG>
System.out.println("Analyzing read group: " + readGroup);
for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
Covariate cov = requestedCovariates.get(iii);
try {

int numReadGroups = 0;
for( Object readGroupKey : dataManager.getCollapsedTable(0).data.keySet() ) {
if(NUM_READ_GROUPS_TO_PROCESS == -1 || ++numReadGroups <= NUM_READ_GROUPS_TO_PROCESS) {
String readGroup = readGroupKey.toString();
System.out.println("Analyzing read group: " + readGroup);
for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
Covariate cov = requestedCovariates.get(iii);
try {
