Better dna-brnn output filtering

[koisland]

• Added filter_dnabrnn_output.py which filters by the percentile length of a repeat and constant values.
  • Removes small ALRs that incorrectly extend the range of the HOR.
• Added dnabrnn_thresholds.json and dnabrnn_full_alr_region_thresholds.json to set thresholds.
  • Fixes #13
• Adjusted nucfreq.toml defaults.
• Added added_bases to extract_ref_hor_arrays config to allow adding/subtracting bps off the starting ref coords.
• Annotated nucfreq inputs with ancient() to avoid unnecessary reruns.