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Ran 04 Jun 2026 12:30AM UTC

Files 39

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Committed 04 Jun 2026 12:25AM UTC coverage: 79.617% (+0.08%) from 79.54%

Job # 26921876453.3

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

8734 of 10970 relevant lines covered (79.62%)

0.8 hits per line

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main: 81%

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