21096138363
70%

Ran 17 Jan 2026 02:55PM UTC

Jobs 4

Files 21

Run time 1min

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Committed 17 Jan 2026 02:54PM UTC coverage: 45.067% (-9.0%) from 54.087%

Build # 21096138363

Build Type

push

github

Committed by

iskandr

Commit Message

Add Amplify, GEX, and Unify modules for multi-experiment analysis

New modules:
- amplify.py: Load Amplify platform data with SNR/quality filtering
- gex.py: Flexible gene expression augmentation from 10x HDF5 files
- unify.py: Merge clonotype data from multiple experiments

New CLI commands:
- load-amplify: Load Amplify Excel files with quality flags
- unify: Merge multiple clonotype files with occurrence tracking

Updates:
- Sample sheet: Support amplify_path, gex_path, experiment fields
- Config: Add AmplifyConfig, GEXConfig, UnifyConfig classes
- README: Add algorithmic details for all pipeline steps
- Tests: Update to use new alpha_leader/beta_leader API

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Run Details

1640 of 3639 relevant lines covered (45.07%)

1.8 hits per line

Uncovered Existing Lines

Lines	Coverage	∆	File
27	84.92	-9.68%	sample_sheet.py
82	67.58	-0.71%	assemble.py
158	4.95	4.95%	plots.py
342	0.0	0.0%	cli.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	python-3.10 - 21096138363.1	17 Jan 2026 02:55PM UTC	21	45.05	GitHub Action Run
2	python-3.12 - 21096138363.2	17 Jan 2026 02:55PM UTC	21	45.05	GitHub Action Run
3	python-3.11 - 21096138363.3	17 Jan 2026 02:55PM UTC	21	45.05	GitHub Action Run
4	python-3.9 - 21096138363.4	17 Jan 2026 02:55PM UTC	21	45.04	GitHub Action Run

pirl-unc / tcrsift / 21096138363
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pirl-unc / tcrsift / 21096138363 70%

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