Two small modifications to make the -sites filter work when selecting few sites from a large input file:
-> Call readSites in order to populate keepSites correctly;
-> Ensure 0-sized writes (arising when a given chunk contains no variants listed in the -sites file) are not passed to gzwrite, as this results in a file that appears corrupted to applications such as gzip.

Note that the check for 0-sized writes may need to be incorporated at other write points: currently it is only implemented in abcAsso.cpp, as this is the analysis step I am dealing with.