Skip to content

feat: add variant-info command to retrieve sample carriersFeat/variant info#20

Merged
dlopez-bioinfo merged 8 commits into
masterfrom
feat/variant-info
Mar 24, 2026
Merged

feat: add variant-info command to retrieve sample carriersFeat/variant info#20
dlopez-bioinfo merged 8 commits into
masterfrom
feat/variant-info

Conversation

@dlopez-bioinfo
Copy link
Copy Markdown
Collaborator

Summary

  • Adds variant-info CLI command and Python API method to list all samples carrying a specific variant
  • Each carrier includes: genotype (het/hom/alt), FILTER status (PASS/FAIL), sex, technology, and phenotype codes
  • Supports the same sample filters as query (--phenotype, --sex, --tech)
  • Output formats: text (aligned table), TSV, and JSON

Closes #18

Test plan

  • pytest tests/test_variant_info.py -v — 26 new tests, all passing
  • pytest --tb=short -q — full suite (470 tests), no regressions
  • afquery variant-info --db demo_db/ --locus chr1:1500 --format text
  • afquery variant-info --db demo_db/ --locus chr1:1500 --ref A --alt T --format json

@codecov-commenter
Copy link
Copy Markdown

codecov-commenter commented Mar 24, 2026

⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 88.42975% with 14 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
src/afquery/query.py 81.35% 6 Missing and 5 partials ⚠️
src/afquery/variant_info.py 66.66% 2 Missing ⚠️
src/afquery/cli.py 97.43% 0 Missing and 1 partial ⚠️

📢 Thoughts on this report? Let us know!

@dlopez-bioinfo dlopez-bioinfo merged commit 25c3805 into master Mar 24, 2026
3 checks passed
@dlopez-bioinfo dlopez-bioinfo deleted the feat/variant-info branch March 24, 2026 14:06
dlopez-bioinfo added a commit that referenced this pull request Mar 26, 2026
feat: add variant-info command to retrieve sample carriersFeat/variant info
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

feat: Add variant-info module to retrieve samples and metadata for a given variant

2 participants