# Python
__pycache__/
*.py[cod]
*$py.class
*.so
*.egg-info/
*.egg
dist/
build/
.eggs/

# Virtual environments
.venv/
venv/
env/

# IDE
.vscode/
.idea/
*.swp
*.swo

# OS
.DS_Store
Thumbs.db

# Testing
.pytest_cache/
.coverage
htmlcov/
coverage.xml

# Type checking
.mypy_cache/

# Nox
.nox/

# MkDocs
site/

# Benchmark outputs (regenerated by run_benchmark.sh)
benchmark-data/output-original/
benchmark-data/output-redux/
benchmark-data/profiles/
benchmark-data/Pairend_StrandSpecific_51mer_Human_hg19.bam
benchmark-data/Pairend_StrandSpecific_51mer_Human_hg19.bam.bai
benchmark-data/hg19_RefSeq.bed
