pirl-unc / hitlist / 24430177076
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coverage: 43.83% (+0.1%) from 43.724%
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v1.7.1: Upgrade mhc:unknown to class-only when antibody/class informative (#49)

The legacy 'mhc: unknown' sentinel in pmid_overrides.yaml conflated
three states: (a) paper reported nothing, (b) paper used a class-
specific IP antibody (W6/32 / HB-145 / L243) but did not HLA-type
the donor, (c) the genotype was unknown but the class is curated.

Walk every ms_samples[].mhc == 'unknown' entry; where the sample's
mhc_class is 'I' or 'II' (97 entries; mhc_class is curated for 85
of them with a known class), upgrade mhc to 'HLA class I' or
'HLA class II' to match.  This preserves the class-level signal
(useful for downstream class-bucketed joins) while still flagging
'no allele genotype'.

Migration counts:
  upgraded to HLA class I  : 74
  upgraded to HLA class II : 11
  left as 'unknown'        : 12 (all mhc_class: I+II combo samples
                                  where one mhc field can't carry
                                  both classes; flagged for split
                                  in a follow-up)

Code-side: generate_observations_table treats 'unknown', 'HLA class I',
'HLA class II' (and the MHC variant) as class-only sentinels via a
shared _is_class_only_sentinel helper.  Sentinels are excluded from
the per-allele sample-metadata join the same way 'unknown' was —
no allele can be derived from a class-only string.

Test renamed test_ms_samples_mhc_unknown → test_ms_samples_mhc_class_only;
Pat9 (PMID 31844290 ccRCC, no donor HLA typing, W6/32 IP) now
asserts mhc == 'HLA class I' rather than 'unknown'.

1165 of 2658 relevant lines covered (43.83%)

0.44 hits per line

Coverage Regressions

Lines Coverage ∆ File
9
85.82
 0.28% export.py
Jobs
ID Job ID Ran Files Coverage
1 24430177076.1 18
43.83
 GitHub Action Run
Source Files on build 24430177076