.gitignore

# --- migec-specific ---
# NB: .gitignore has no trailing comments -- the whole line is the pattern, so a comment after a
# pattern silently makes it match nothing. Comments go on their own line.

# cmake out-of-tree build, and scikit-build-core's build/{wheel_tag}
build/
# the thread-sanitizer build; see docs/performance.rst for how to make one
build-tsan/
# a second ordinary build, for verifying a change without disturbing the installed extension
build-verify/
# setup.sh creates this
.venv/
# intermediate record files; regenerate with `migec checkout`
*.mig
*.pumi
# local experiments, never committed
scratch/

# --- python ---
__pycache__/
*.py[cod]
*.egg-info/
dist/
.pytest_cache/
.ruff_cache/
.coverage
htmlcov/

# --- docs ---
docs/_build/

# --- os ---
.DS_Store

# Alignment indices pulled down by scripts/read_start_dispersion.py (X1). pysam writes the .bai
# next to wherever it is pointed, which for an HTTP URL is the working directory -- 4.6 MB of it
# reached a published sdist before this line existed.
*.bam
*.bai
*.crai
build-verify/
_migec_error.log