pirl-unc / mhcgnomes / 33456854862
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coverage: 89.182%. Remained the same
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Put the four macaques under their genus node (#145)

#123 listed five primates sitting outside an existing genus node. Four
are macaques and move under Macaca sp., going from 24-34 genes to the 68
the genus provides, so Mafu-A*01:01 and Maas-DRB1*01:01 parse instead of
returning None.

The fifth does not move, and checking why was the useful part. NCBI
Taxonomy accepts Cebuella pygmaea (taxid 9493, lineage ...
Callitrichinae > Cebuella) and lists Callithrix pygmaea as a homotypic
synonym -- which is where the entry's old prefix Cepy comes from. It is
not a Callithrix, so Callithrix sp. would be the wrong parent even
though the key says otherwise. Recorded on the entry.

Two existing tests encoded the old inconsistency rather than a rule:

  Maar-A normalized to A1 because M. arctoides declared A1 but not A.
  Mamu-A, Mafa-A and Mane-A all leave A alone, so the old answer was the
  odd one out.

  An adversarial stickiness test used Maar-A2 as a name that must not
  parse. It parses now, but to M. arctoides itself rather than by
  switching species, so it no longer tests stickiness. Replaced with
  Maar-BLB2 and Maar-UAA, which do.

0 of 11,558 corpus names change. Four entries change old_mhc_prefix to
RhLA, the umbrella every other macaque already carries.

Closes #123

Claude-Session: https://claude.ai/code/session_012s4siLj2Vm33eNMGjNSazH

4130 of 4631 relevant lines covered (89.18%)

0.89 hits per line

Jobs
ID Job ID Ran Files Coverage
1 33456854862.1 41
89.18
 GitHub Action Run
Source Files on build 33456854862