#smulated inputs
# simulated_inputs/
#
#logs
logs/

#cursor
.cursorrules
.cursorignore

# continue
.continueignore
.continuerules

#tmp
tmp/

# outputs
*.tar.gz
*.tsv.zst
*.tar.zst
*.tsv.gz
*.sam.gz
*fa.gz
slurmsout/
outputs/
imgvr4_data/
imgvr4_data/crispr-host-prediction/nucleotide_db/
**/raw_outputs
**/simulated_data
**/ground_truth.tsv
**/bash_scripts
**/tools_results.tsv
**/.parquet
results/real_data/raw_outputs/
results/real_data/results/
**/tools_results.tsv
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

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

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.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/
cover/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
Pipfile.lock

# UV
uv.lock

# poetry
poetry.lock

# pdm
pdm.lock
.pdm.toml
.pdm-python
.pdm-build/

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

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

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

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

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
.idea/

# PyPI configuration file
.pypirc

# vscode
.vscode/
.vscode/*
# quarto
.quarto/
# public/

# /.quarto/

# rust_simulator/
rust_simulator/src/target/debug/

# run_t_*
results/simulated/run_t_*
# pixi environments
.pixi
*.egg-info


results/*
results_mismatches/*
*.tsv

.ruff_cache/
IMGVR4_SEQUENCES.fna.zst

# temporary - will comment this once done
draft/
src/tests/
tests/
src/bench/obsolete/

datasets
data/test_outputs
dori_wrapper.sh