Changes

             -d  debug [false]

             -d  debug [false]

             -q  do not print options and summary [false]

             -q  do not print options and summary [false]

             -m  exits when REF is inconsistent with

             -m  warns but does not exit when REF is inconsistent

                 unmasked reference sequence for non SNPs.

                 with masked reference sequence for non SNPs.

                 This overides the -n option [false]

                 This overides the -n option [false]

             -n  warns but does not exit when REF is inconsistent

             -n  warns but does not exit when REF is inconsistent