byte[] bases = clippedRead.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
final int readLength = clippedRead.getReadLength();
for (int i = 0; i < readLength; i++) {
<BUG>values.addCovariate(contextWith(bases, i, mismatchesContextSize), contextWith(bases, i, insertionsContextSize), contextWith(bases, i, deletionsContextSize), (negativeStrand ? readLength - i - 1 : i));
}</BUG>
}
@Override
public final Object getValue(final String str) {

byte[] bases = clippedRead.getReadBases();
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
final int readLength = clippedRead.getReadLength();
for (int i = 0; i < readLength; i++) {
final long indelKey = contextWith(bases, i, indelsContextSize);
values.addCovariate(contextWith(bases, i, mismatchesContextSize), indelKey, indelKey, (negativeStrand ? readLength - i - 1 : i));
}
}
@Override
public final Object getValue(final String str) {
