Add output file with # of alignment records used and ignored

Hi Brent,

Would it be easy to output along with the coverage files, counts of alignment records parsed during the analysis ?

According to the `--flag` option value in the command line, we can have a small file which contains something like:

    READS_USED    4567
    READS_IGNORED    1234

This would allow to compute a theoretical (or intended) coverage for the experiment and to compare for instance with what is really on-target without having to parse the BAM elsewhere. 

Thanks,
Anthony
