openvax / pyensembl / 25818956626

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Fix #169: add three-tier protein-coding biotype ontology (#357)

Introduces a layered set of flags for "does this transcript make a
polypeptide?":

* `is_protein_coding` - unchanged, strict canonical `protein_coding`
  only. Preserves the contract downstream effect predictors (varcode)
  depend on.
* `is_protein_coding_extended` - widens to IG/TR gene segments and
  translated pseudogenes (`polymorphic_pseudogene`,
  `translated_{processed,unprocessed}_pseudogene`). Excludes NMD/NSD
  because those products are targeted for degradation rather than
  stable accumulation.
* `is_translated` - widest tier. Adds `nonsense_mediated_decay` and
  `non_stop_decay` on top of the extended set. Useful when picking the
  top variant effect or doing RNA-seq peptide analysis where ribosome
  occupancy matters more than stable expression.

Set constants `PROTEIN_CODING_BIOTYPES`,
`EXTENDED_PROTEIN_CODING_BIOTYPES`, and `TRANSLATED_BIOTYPES` are
exposed on `pyensembl.locus_with_genome` so callers can derive their
own categorization if needed.

11 of 11 new or added lines in 2 files covered. (100.0%)

1662 of 1944 relevant lines covered (85.49%)

3.42 hits per line