if(maxPermutations != positions.length) throw(new InvalidIndexException(reader.rootDir, "Found invalid number of permutations: " + positions.length+ " for input id: " + id));
for(int i = 0; i < numPermutations; i++)
{
getNeighbors(positions[i], beamRadius, permutationLists[i], sims);
}
return sims.toArray();
}
/**
* Helper method for getSimilars(long id, int beamRadius, int numPermutations).
* @param pos