pirl-unc / hitlist / 24195519742
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Jobs 1
Files 15
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coverage: 33.983%. Remained the same
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Issue #19: Fix remaining curation audit findings (#20)

* Issue #19: Fix remaining curation audit findings

- Marino 2020 (32983136): mhc_class I → I+II, add ip_antibody, clarify note
- Fix author: PMID 32157095 "Laumont 2020" → "Chong 2020"
- Ternette 2018 (29786170): fix note (W6/32 IP, not BB7.2), add ip_antibody
- Remove 5 duplicate PMID entries (33298915, 34932366, 29632046, 30833945, 33633747)
- Nicholas 2022 (35051231): fix note (moDCs have HLA-I+II), clarify P1 X31
- Hirama 2021 (34185709): add donors: 6
- Marcu 2021: note 227 vs 225 sample count discrepancy
- Mark 4 n=0 annotation samples with profiled: false
- Standardize classification values (remove verbose non-standard labels)
- Populate all 45 missing titles from PubMed

* Issue #19: Add per-sample MHC field + complete audit fixes

- Add queryable `mhc` column to ms_samples export (export.py)
- Populate per-sample MHC alleles for 108 samples across 33 PMIDs
- Per-sample HLA typing for Sarkizova 2020 validation tumor lines
  (from Supplementary Data 2: 3 CLL, 4 MEL, 1 OV, 3 GBM, 1 ccRCC)
- Complete Abelin 2017 allele list (11 → 16: add A*01:01, A*02:03,
  A*02:07, A*11:01, B*07:02)
- Fix Sarkizova IFN-gamma context (n=6 validation, n=7 proteasomal)
- MHC field convention: "" = uncurated, "unknown" = typing unavailable,
  "HLA-A*02:01 ..." = known alleles
- Bump to 0.9.5

488 of 1436 relevant lines covered (33.98%)

0.34 hits per line

Coverage Regressions

Lines Coverage ∆ File
11
73.12
 0.0% export.py
Jobs
ID Job ID Ran Files Coverage
1 24195519742.1 15
33.98
 GitHub Action Run
Source Files on build 24195519742