# OS/editor files
.DS_Store
Thumbs.db
*~
.idea/
.vscode/

# Python caches and packaging output
__pycache__/
*.py[cod]
*.pyo
*.pyd
*.egg-info/
.pytest_cache/
.ruff_cache/
.mypy_cache/
.coverage
coverage.xml
htmlcov/
build/
dist/
site/

# Local environments
.venv/
venv/
env/
.env
.env.*
!.env.example

# Local-only legacy snapshot retained for reference
legacy/
AGENTS*

# Runtime outputs
outputs/
results/
work/
tmp/
*.log

# Bioinformatics intermediates and indexes
*.sam
*.bam
*.bai
*.cram
*.crai
*.vcf
*.vcf.gz
*.bcf
*.tbi
*.csi
*.mmi
*.fai
*.amb
*.ann
*.bwt*
*.pac
*.0123
