usage: __main__.py [-h] [--array ARRAY] --intensities INTENSITIES --out-prefix
                   OUT_PREFIX [--genome GENOME] [--masks MASKS]
                   [--mask-file MASK_FILE] [--control-masks CONTROL_MASKS]
                   [--control-mask-file CONTROL_MASK_FILE]
                   [--random-controls RANDOM_CONTROLS]
                   [--stability-probes STABILITY_PROBES]
                   [--kmer-size KMER_SIZE] [--n-families N_FAMILIES]
                   [--repeats REPEATS] [--caps CAPS] [--seed SEED]
                   [--min-probes MIN_PROBES] [--plot] [--quiet]
                   [{max-probes,mask}]

Calibrate EUbar analysis parameters from probe representation and effect
stability. Use 'max-probes' for the production probe cap or 'mask' to compare
explicit masks.

positional arguments:
  {max-probes,mask}     Calibration target (default: max-probes)

options:
  -h, --help            show this help message and exit
  --array ARRAY         EUbar k-mer positions/array file (required for max-
                        probes calibration)
  --intensities INTENSITIES
                        EUbar resid_log intensity file
  --out-prefix OUT_PREFIX
                        Output prefix
  --genome GENOME       Genome FASTA (required for mask calibration)
  --masks MASKS         Comma-separated explicit 0/1 masks for mask
                        calibration
  --mask-file MASK_FILE
                        Text file containing one or more candidate 0/1 masks
  --control-masks CONTROL_MASKS
                        Comma-separated diagnostic control masks. Controls are
                        fully evaluated and reported but are excluded from the
                        automatic recommendation.
  --control-mask-file CONTROL_MASK_FILE
                        Text file containing diagnostic control masks.
                        Controls are evaluated but excluded from the automatic
                        recommendation.
  --random-controls RANDOM_CONTROLS
                        Mask calibration only: generate this many random
                        diagnostic masks matched to the recommended
                        candidate's span and number of informative positions.
                        First/last positions remain informative. Random
                        controls are excluded from the recommendation
                        (default: 0).
  --stability-probes STABILITY_PROBES
                        Fixed probe count used to compare mask effect
                        stability (default: 100)
  --kmer-size KMER_SIZE
  --n-families N_FAMILIES
                        Representative/evaluated families. Defaults: 100 for
                        max-probes; 500 for mask calibration.
  --repeats REPEATS     Subsamples per family and cap
  --caps CAPS
  --seed SEED
  --min-probes MIN_PROBES
                        Minimum usable probes per family
  --plot                Also write a diagnostic PDF
  --quiet               Suppress progress messages
