read.setReadGroup(rg);
final byte [] readQuals = new byte[length];
for (int i = 0; i < length; i++)
readQuals[i] = 20;
read.setBaseQualities(readQuals);
<BUG>final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INSERTIONS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE);
</BUG>
int nKeys = 0;                                                                                                  // keep track of how many keys were produced
final ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);
for (int offset = 0; offset < length; offset++) {

read.setReadGroup(rg);
final byte [] readQuals = new byte[length];
for (int i = 0; i < length; i++)
readQuals[i] = 20;
read.setBaseQualities(readQuals);
final int expectedKeys = expectedNumberOfKeys(4, length, RAC.INDELS_CONTEXT_SIZE, RAC.MISMATCHES_CONTEXT_SIZE);
int nKeys = 0;                                                                                                  // keep track of how many keys were produced
final ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);
for (int offset = 0; offset < length; offset++) {
