26921876453
81%

Ran 04 Jun 2026 12:29AM UTC

Jobs 4

Files 39

Run time 1min

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Committed 04 Jun 2026 12:25AM UTC coverage: 79.665% (+0.08%) from 79.588%

Build # 26921876453

Build Type

push

github

Committed by

web-flow

Commit Message

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.

Coverage Stats

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

pirl-unc / tcrsift / 26921876453
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