usage: bogart -o outputName -O ovlStore -G gkpStore -T tigStore

  -O         Mandatory path to an ovlStore.
  -G         Mandatory path to a gkpStore.
  -T         Mandatory path to a tigStore (can exist or not).
  -o prefix  Mandatory name for the output files

  -B b       Target number of fragments per tigStore (consensus) partition

Algorithm Options

  -gs        Genome size in bases.

  -J         Join promiscuous unitigs using unused best edges.

  -SR        Shatter repeats, don't rebuild.
  -R         Shatter repeats (-SR), then rebuild them
  -RL len    Force reads below 'len' bases to be singletons.
               This WILL cause CGW to fail; diagnostic only.

  -threads N Use N compute threads during repeat detection.
               0 - use OpenMP default (default)
               1 - use one thread

Overlap Selection - an overlap will be considered for use in a unitig under
                    the following conditions:

  When constructing the Best Overlap Graph and Promiscuous Unitigs ('g'raph):
    -eg 0.020   no more than 0.020 fraction (2.0%) error   ** DEPRECATED **

  When loading overlaps, an inflated maximum (to allow reruns with different error rates):
    -eM 0.05   no more than 0.05 fraction (5.0%) error in any overlap loaded into bogart
               the maximum used will ALWAYS be at least the maximum of the four error rates

  For all, the lower limit on overlap length
    -el 500     no shorter than 40 bases

Overlap Storage

    -M gb    Use at most 'gb' gigabytes of memory for storing overlaps.
    -N num   Load at most 'num' overlaps per read.

    -create  Only create the overlap graph, save to disk and quit.
    -save    Save the overlap graph to disk, and continue.

Debugging and Logging

  -D <name>  enable logging/debugging for a specific component.
  -d <name>  disable logging/debugging for a specific component.

No output prefix name (-o option) supplied.
No gatekeeper store (-G option) supplied.
No overlap store (-O option) supplied.
No output tigStore (-T option) supplied.