# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
.claude/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# IDEs and editors
.idea/
.vscode/
*.swp
*.swo
*~
.project
.pydevproject
.settings/
*.sublime-project
*.sublime-workspace

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# ruff
.ruff_cache/

# OS generated files
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db

# Project-specific
*.vcf
*.vcf.gz
*.vcf.gz.tbi
*.bcf
*.bam
*.bam.bai
*.bed
*.fasta
*.fa
*.fasta.fai
*.fa.fai
data/
output/
results/
*.log
