.gitignore

data/
data*/
real-data*/
old-real-data*/
performance/
raw_data/
!raw_data/alignment.bam
!raw_data/names-mdmg.dmp
!raw_data/nodes-mdmg.dmp
!raw_data/acc2taxid.map.gz
!src/metaDMG/data
.DS_Store
dist/
build/
logs/
config.yaml
config*.yaml
config*.yml
.coverage

metaDMG-lca
metaDMG-cpp
.memoization

*.lca
*.lca.stat
*.uglyprint.*
*.bam.bin
*.csv
*.lca.gz
*.bam

build.sh
publish.sh
pdf_export.pdf

file.log
dask-worker-space/
bla*
*.egg-info/
*.eggs


./docs/build/



# 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/
pip-wheel-metadata/
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/

# 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
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

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

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
.vscode
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/
**__pycache__

# PyCharm
.idea/

# RStudio project files
**.Rproj.user/
**.Rproj.user*
**.Rproj
**.Rhistory

# MacOS
.DS_Store
efd40f0223-config.weight-0.yaml
98ec3bda1f-config.weight-1.yaml
errors.yaml
5922fb11a0-config.weight-0.yaml
5922fb11a0.woltka-mdmg.weight-0/lca/5922fb11a0.lca.txt
5922fb11a0.woltka-mdmg.weight-0/lca/5922fb11a0.mismatches.txt
5922fb11a0.woltka-mdmg.weight-0/lca/5922fb11a0.mismatches.stat.txt
5922fb11a0.woltka-mdmg.weight-0/mismatches/5922fb11a0.mismatches.parquet
config_all.yaml
config_local.yaml


cache/cache.db*

antonio/*
5cdd545807.woltka-mdmg.weight-0/*
5cdd545807-config.weight-0.yaml
config2.yaml
config_getdamage0_subs.yaml
config_getdamage1_subs.yaml
config_old.yaml
config_lca_subs.yaml
pyproject_old.toml
*.code-workspace
config_simulation.yaml
metadamage
src/metaDMG/fit/fits.py
.gitignore
main.py
!src/metaDMG/main.py
config_lda.yaml
binary_classifier.py
config_Bayesian.yaml
src/metaDMG/fit/serial.py
fix_numba.sh
*.gz
*.zip
/logo/*
!/logo/logo.png
c55d4e2df1-config.lca.weight-1.yaml
alignment.mismatches.txt
misincorporation.txt
smallbams.yaml