baseMask [options] in1.bama [in2.bama [o.bama]]

Process baseMasks. 
If only one file in1.bama is specified, report bases covered statistics.
If two baseMasks in1.bama and in2.bama are specified then combine them using
options '-or' or '-and' (union or intersection), and report the resulting
bases covered.
Create output baseMask file o.bama, if specified.

Options:
  -or        : 'or' the basemasks together (union).
               (output file will have all chroms in 
               either file, and all ranges will be merged.)
  -and       : 'and' the basemasks together (intersection).
               (output file will have the subset of chroms and 
               bases, or ranges, common to both files.)
  -quiet     : Do not calculate or output the base cover
               statistics. Might be slightly faster.
  -saveMem   : Try and reduce memory usage. Might be slightly
               slower.
  -orDirectToFile : Write 'or' directly to file range by range,
               bypassing whole chromosome buffering. Might be slower.
  -verbose=n : verbose > 0 prints some details.