25200000098
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Ran 01 May 2026 02:54AM UTC

Jobs 1

Files 27

Run time 1min

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Committed 01 May 2026 02:53AM UTC coverage: 70.924%. Remained the same

Build # 25200000098

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.22: Raise class-II implausible cutoff from 31aa to 40aa (#209) (#210)

The class-II severity-tier ``implausible`` upper threshold was set to
``>=31`` in v1.30.17 based on canonical class-II length range
(11-30aa from textbook references). Real-data audit after v1.30.20's
PTM-suffix fix shows that's too strict:

- 16,885 class-II rows currently flagged implausible
- 13,268 (78%) are from Stražar 2023 alone -- their published
  mono-allelic HLA-II ligands span up to 51aa, with bulk in 31-39aa
  (proteasome-edited / DM-extended biology, not curation drift)
- 1,600 from Abelin 2019 MAPTAC class-II portion, similar story

Users passing --exclude-class-label-implausible (introduced in
v1.30.18) currently lose ~13K legitimate Stražar mono-allelic
training rows, which is the opposite of what the filter is meant
to do.

Empirical break in real-data length distribution sits ~40aa: rows
30-39aa are dense across multiple curated supplements; rows >=40aa
are rare enough to be worth flagging. Class-I cutoff (>=18aa) is
unchanged -- bulged class-I peptides cap around 17aa.

Adds two boundary cases to the severity-tier regression test:
35aa class-II = ok (was implausible), 40aa class-II = implausible.

Coverage Stats

3676 of 5183 relevant lines covered (70.92%)

0.71 hits per line

Coverage Regressions

Lines	Coverage	∆	File
1	94.52	0.0%	observations.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25200000098.1	01 May 2026 02:54AM UTC	27	70.92	GitHub Action Run

pirl-unc / hitlist / 25200000098
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