coverage: output, storage, & naming

[gfudenberg]

• outputting a 'track' (i.e. bintable+signal) instead of a numpy array for the user-facing function. The following lines can be migrated into api.coverage:

  cooltools/cooltools/cli/coverage.py

  Line 99 in a5341aa

  coverage_table = clr.bins()[:][["chrom", "start", "end"]]

• consider removing store inside cooler option.
  • For:
    • Other functions do not provide this, and it seems to be a legacy of copying the balance.py from cooler. This would streamline the API. (original commit: 4542ee4).
    • Modifies cooler, which is a potentially confusing side-effect of a function.
  • Against:
    • nice to store total cis inside the cooler. @Phlya
• improve naming options for CLI & API.
• decide if use_lock should be set to False or kept in arguments. Description in cooler: https://github.com/open2c/cooler/blob/987e87dd357c99a0a070b8a25cb7aaef86f1655c/cooler/tools.py#L16

continues discussion from PR #385