if (counts.hasIndex()) {
// we can only reposition if the countsreader has an index. Otherwise, we trust the
// caching counts archive to have created a new reader positioned at the start of the counts sequence.
binAdaptor.reposition(startLocation);
}
binAdaptor.skipTo(startLocation);
int position = binAdaptor.getPosition();
ObjectArrayList<LocusScore> result = new ObjectArrayList<LocusScore>();
result.add(new BasicScore(initialStartPosition, position, 0.0f));
while (binAdaptor.hasNextTransition() && position < endLocation) {