pirl-unc / tsarina / 26976504813
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coverage: 70.875% (+0.05%) from 70.824%
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Add XAGE1A/XAGE1B group + XAGE family alias backfill (#77) (#85)

* Group XAGE1A/XAGE1B as one antigen + backfill XAGE/MAGEB6 aliases (#77)

XAGE1A and XAGE1B encode the identical 81-aa XAGE-1 protein, so they are a
single antigen at the pMHC level — group them like CTAG1A/CTAG1B (NY-ESO-1)
via a new _XAGE1_GROUP_LABEL/_XAGE1_ALIASES pair, and route both groups through
a single _GROUP_ALIAS_TO_LABEL map (XAGE1C/D/E and GAGED2 resolve too).

Backfill HGNC synonyms onto the XAGE family + MAGEB6 rows so alias-based lookups
resolve (XAGE1A/B/2/3/5, MAGEB6). Fix MAGEB6 CT-number comment (CT3.2->CT3.4).
Bump 1.4.3 -> 1.4.4.

* Add XAGE1A/XAGE1B group + XAGE family alias backfill (#77)

XAGE1A and XAGE1B encode the identical 81-aa XAGE-1 protein (XAGE1C/D/E are
Ensembl synonyms of XAGE1B; GAGED2 is the legacy symbol), so they are one
antigen at the pMHC level. Group them like CTAG1A/CTAG1B (NY-ESO-1):

- Add a XAGE1A/XAGE1B explicit group + alias set (XAGE1, XAGE1A-E, GAGED2)
  resolving to the group for panel selection/display. Generalize the
  CTAG1-specific alias->group resolution into a shared _GROUP_ALIAS_TO_LABEL.
- Fix explicit-group member tracking: recover the underlying member genes from
  _CTA_GROUPS instead of reporting the collapsed group label as its own member.
  This also fixes the previously-untested CTAG1 case (members now CTAG1A;CTAG1B).
- Backfill the Aliases column for the XAGE family + MAGEB6 with HGNC synonyms
  (a first concrete chunk of #77): XAGE1A/B, XAGE2, XAGE3, XAGE5, MAGEB6.
- Repoint the identical-peptide-set grouping test to CT45A1/CT45A2 (XAGE1A/B
  now route through the explicit group) and add XAGE1 group/alias coverage.
- Correct MAGEB6 designation comment CT3.2 -> CT3.4.

Version 1.4.4.

2414 of 3406 relevant lines covered (70.87%)

0.71 hits per line

Coverage Regressions

Lines Coverage ∆ File
85
90.96
 0.06% spanning.py
Jobs
ID Job ID Ran Files Coverage
1 26976504813.1 35
70.87
 GitHub Action Run
Source Files on build 26976504813