pirl-unc / tcrsift / 25558062992
71%

DEFAULT BRANCH: main
Ran
Jobs 4
Files 24
Run time 1min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 70.812% (-0.2%) from 70.986%
25558062992

push

github

web-flow 
Bucket filtered output by donor sharing (#15 chunk 4 — closes #15) (#17)

Final slice of #15. With donor/method aggregations populated by
chunk 2 and the filter knobs / named modes from chunk 3, surface the
two natural output buckets users have been computing post-hoc:

  data/
    filtered_private_to_donor.csv      # n_donors == 1 (or NaN)
    filtered_public_across_donors.csv  # n_donors >= 2

Both are written when the n_donors column is present on the filtered
table; empty buckets are skipped so single-donor cohorts don't get a
zero-row public_across_donors.csv. Existing tier CSVs continue to be
written under filter_mode=fdr; the bucket files coexist alongside.

Mode-named summary outputs:

  data/filtered_shared_high_freq.csv      under shared-high-freq
  data/filtered_cross_donor_public.csv    under cross-donor-public

Lets users find the "passes the named mode" set without reading FDR
tier CSVs that don't carry tier semantics under non-FDR modes.

Same outputs from `tcrsift filter` (subcommand) for parity:
all_shared_high_freq.csv / all_cross_donor_public.csv,
private_to_donor.csv / public_across_donors.csv.

Tests cover: empty when n_donors missing; correct split on n_donors;
single-donor cohorts only emit private bucket; all-public cohorts
only emit public bucket; NaN treated as 1 (private).

Bumps version to 0.5.1 — output files are additive, no breaking
change.

Closes #15. (#9 — broader axis generalization to timepoints / APCs /
TIL-overlap — remains open; that explicitly waits on #8/#15.)

4185 of 5910 relevant lines covered (70.81%)

2.83 hits per line

Coverage Regressions

Lines Coverage ∆ File
196
55.68
 -1.06% cli.py
Jobs
ID Job ID Ran Files Coverage
1 python-3.10 - 25558062992.1 24
70.8
 GitHub Action Run
2 python-3.11 - 25558062992.2 24
70.8
 GitHub Action Run
3 python-3.12 - 25558062992.3 24
70.8
 GitHub Action Run
4 python-3.9 - 25558062992.4 24
70.77
 GitHub Action Run
Source Files on build 25558062992