cachedMask [options] cacheDir chromDb [db1.]track1 [[db2.]track2 [o.bama]]

Process baseMasks cached from database tables (tracks). 
cacheDir specifies the root directory where the cache files are stored.
chromDb specifies the database where the chromInfo table can be found.
Tracks can be in different databases, or in the chromDb if their database is
not specified.

If only one input is specified (track1), report bases covered statistics and
generate or update cacheDir/db/track1.bama file if necessary where db is 
either db1 or chromDb if db1 not specified.

If two tracks are specified (track1 and track2) then combine them using
options '-or' or '-and' (union or intersection), and report the resulting
bases covered. If a track specification does not include the database then 
use the chromDb database by default.
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.
  -logTimes  : Log table and cache update times to file cacheDir/db/track.bama.log 
  -orDirectToFile : Write 'or' directly to file range by range,
               bypassing whole chromosome buffering. Might be slower.
  -verbose=n : verbose > 0 prints some details.