26917880104

Committed 03 Jun 2026 10:48PM UTC coverage: 79.588% (+0.06%) from 79.53%

Build # 26917880104

Build Type

push

github

Committed by

web-flow

Commit Message

Per-sample clonal-expansion QC + unexpanded-repertoire warning (#161) (#162)

A one-line expansion fingerprint that flags an unexpanded/near-polyclonal
sample (failed expansion, sample swap, or baseline sort) instead of via a
half-day forensic dig.

- qc.clonal_expansion_metrics(long_df, group_col=sample|donor): per-group
  top1/top10 clone fraction, effective_clones=exp(Shannon), clonality,
  gini_simpson, fraction_cells_in_clones_ge_N, and an 'unexpanded' flag +
  warning when top1<1% AND effective/observed clones >0.8 (near-polyclonal).
- qc.cdr3_anchor_integrity: % of CDR3 ending in a conserved F/W anchor
  (low → assembly/anchor trouble; the OLGA Pgen=0 cause).
- run pipeline emits expansion_qc.csv per sample and prints a ⚠️ warning for
  any unexpanded sample. Verified on B1-2 (correctly NOT flagged; the
  B1-4-style near-uniform case fires).

Bump 2.27.0.

Coverage Stats

8660 of 10881 relevant lines covered (79.59%)

3.18 hits per line

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55.89

/cli.py

Source Not Available

The file "cli.py" isn't available on github. Either it's been removed, or the repo root directory needs to be updated.

pirl-unc / tcrsift / 26917880104

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