pirl-unc / mhcgnomes / 33082750947
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coverage: 89.094%. Remained the same
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Add IPD-MHC species and IMGT/HLA genes found missing by sweep (#114)

* Add IPD-MHC species and IMGT/HLA genes found missing by sweep

Swept every IPD-MHC group species listing and the IMGT/HLA gene list
against species.yaml. That sweep found zero prefix mismatches across the
125 IPD species already carried, so everything here is absence rather
than error.

#111 -- 26 species added, bringing IPD-MHC species coverage to complete
for the eleven groups whose listings are reachable:

  10 capuchins (Cebus/Sapajus)  -> Primata sp.
  11 cetaceans                  -> Cetacea sp.
  2 jackals                     -> Canis sp.
  Cuon alpinus, Lycaon pictus   -> Canidae sp. (new)
  Phacochoerus africanus        -> Suidae sp. (new)

The other 2 of the 28 shipped in #108 because they owned prefixes that
were resolving to the wrong animal. Prefixes here are the official
Comparative MHC Nomenclature Committee designations; no loci are
curated for these species, so only the designations are recorded.

Three of them are not in the genus of the group that lists them. Cuon
and Lycaon are canids but not Canis; Phacochoerus is a suid but not Sus.
Filing them under Canis sp./Sus sp. would hand them the DLA/SLA prefix
and those genera's gene lists on no evidence -- the water buffalo
problem in #109. Added Canidae sp. and Suidae sp. instead: real
taxonomic ranks, the same shape as the existing Cetacea sp. and
Galliformes sp. nodes, and what IPD-MHC's Canids and Suids groups cover.
Both prefixes are taxonomic and so are not inherited, leaving DLA on
Canis sp. and SLA on Sus sp. untouched.

#113 -- 10 of 19 genes added: class II pseudogenes DRB2, DQB3, DPA2,
DPA3, DPB2; MIC pseudogenes MICC, MICD, MICE; and immunoproteasome
subunits PSMB8/PSMB9 with LMP7/LMP2 aliases, the same shape as the
existing RING4/RING11 aliases for TAP1/TAP2. All eight pseudogenes carry
pseudogene: true.

The remaining 9 are deliberately held back. IMGT/HLA also names the
class I fragments N, R, S, T, U... (continued)

4011 of 4502 relevant lines covered (89.09%)

0.89 hits per line

Jobs
ID Job ID Ran Files Coverage
1 33082750947.1 40
89.09
 GitHub Action Run
Source Files on build 33082750947