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pirl-unc / tcrsift / 26921876453
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DEFAULT BRANCH: main
Ran 04 Jun 2026 12:29AM UTC
Jobs 4
Files 39
Run time 1min
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04 Jun 2026 12:25AM UTC coverage: 79.665% (+0.08%) from 79.588%
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Per-sample integrity QC: GEX↔VDJ overlap + barcode Jaccard + cellranger ID (#161) (#163)

Completes the #161 QC-report surfacing — turns the swap/duplicate/mislabel
check into a glance:

- qc.gex_vdj_overlap: per-sample fraction of GEX cells with a VDJ call
  (low → wrong VDJ library / barcode-suffix mismatch / swap).
- qc.inter_sample_barcode_jaccard: sample×sample Jaccard over base cell
  barcodes (suffix stripped). Independent samples share ≈0; a high
  off-diagonal flags an accidentally duplicated/copied input. Verified:
  independent A↔B=0.0, duplicate A↔C=1.0.
- qc.read_cellranger_metrics: best-effort metrics_summary.csv Sample ID /
  chemistry / library lookup from adata.obs['gex_dir'] (never raises).
- qc.sample_integrity_qc: combines the above + per-sample CDR3 anchor
  integrity into one table + warnings (low overlap, duplicate input, low
  anchor).
- run pipeline emits sample_qc.csv + sample_barcode_jaccard.csv and prints
  ⚠️ warnings per flagged sample.

All computed from adata.obs already in scope (barcodes=obs_names,
sample/CDR3 columns). 6 new tests. Bump 2.28.0.

8740 of 10971 relevant lines covered (79.66%)

3.19 hits per line

Coverage Regressions

Lines Coverage ∆ File
130
56.28
0.39% cli.py
10
84.76
0.82% qc.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.10 - 26921876453.1 04 Jun 2026 12:29AM UTC 39
79.66
GitHub Action Run
2 python-3.12 - 26921876453.2 04 Jun 2026 12:29AM UTC 39
79.66
GitHub Action Run
3 python-3.9 - 26921876453.3 04 Jun 2026 12:30AM UTC 39
79.62
GitHub Action Run
4 python-3.11 - 26921876453.4 04 Jun 2026 12:29AM UTC 39
79.66
GitHub Action Run
Source Files on build 26921876453
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  • Changed 3
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Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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