.gitattributes
.gitignore
.pre-commit-config.yaml
LICENSE
README.md
environment.yml
pyproject.toml
.github/workflows/ci.yml
.github/workflows/codeql.yml
assets/pyllelic_demo.gif
assets/pyllelic_logo.png
assets/tert_genome.txt
assets/test/fh_22RV1_chr5.bam
assets/test/fh_22RV1_chr5.bam.bai
docs/.buildinfo
docs/.nojekyll
docs/genindex.html
docs/index.html
docs/modules.html
docs/objects.inv
docs/py-modindex.html
docs/pyllelic.html
docs/search.html
docs/searchindex.js
docs/_modules/index.html
docs/_modules/pathlib.html
docs/_modules/pyllelic/config.html
docs/_modules/pyllelic/process.html
docs/_modules/pyllelic/pyllelic.html
docs/_modules/pyllelic/quma.html
docs/_modules/pyllelic/visualization.html
docs/_sources/index.rst.txt
docs/_sources/modules.rst.txt
docs/_sources/pyllelic.rst.txt
docs/_static/basic.css
docs/_static/doctools.js
docs/_static/documentation_options.js
docs/_static/file.png
docs/_static/jquery-3.5.1.js
docs/_static/jquery.js
docs/_static/jquery.min.map
docs/_static/language_data.js
docs/_static/material.css
docs/_static/minus.png
docs/_static/plus.png
docs/_static/pygments.css
docs/_static/searchtools.js
docs/_static/underscore-1.12.0.js
docs/_static/underscore-1.13.1.js
docs/_static/underscore-1.3.1.js
docs/_static/underscore.js
docs/_static/css/badge_only.css
docs/_static/css/theme.css
docs/_static/css/fonts/Roboto-Slab-Bold.woff
docs/_static/css/fonts/Roboto-Slab-Bold.woff2
docs/_static/css/fonts/Roboto-Slab-Regular.woff
docs/_static/css/fonts/Roboto-Slab-Regular.woff2
docs/_static/css/fonts/fontawesome-webfont.eot
docs/_static/css/fonts/fontawesome-webfont.svg
docs/_static/css/fonts/fontawesome-webfont.ttf
docs/_static/css/fonts/fontawesome-webfont.woff
docs/_static/css/fonts/fontawesome-webfont.woff2
docs/_static/css/fonts/lato-bold-italic.woff
docs/_static/css/fonts/lato-bold-italic.woff2
docs/_static/css/fonts/lato-bold.woff
docs/_static/css/fonts/lato-bold.woff2
docs/_static/css/fonts/lato-normal-italic.woff
docs/_static/css/fonts/lato-normal-italic.woff2
docs/_static/css/fonts/lato-normal.woff
docs/_static/css/fonts/lato-normal.woff2
docs/_static/fonts/Inconsolata-Bold.ttf
docs/_static/fonts/Inconsolata-Regular.ttf
docs/_static/fonts/Inconsolata.ttf
docs/_static/fonts/Lato-Bold.ttf
docs/_static/fonts/Lato-Regular.ttf
docs/_static/fonts/RobotoSlab-Bold.ttf
docs/_static/fonts/RobotoSlab-Regular.ttf
docs/_static/fonts/font-awesome.css
docs/_static/fonts/fontawesome-webfont.eot
docs/_static/fonts/fontawesome-webfont.svg
docs/_static/fonts/fontawesome-webfont.ttf
docs/_static/fonts/fontawesome-webfont.woff
docs/_static/fonts/fontawesome-webfont.woff2
docs/_static/fonts/material-icons.css
docs/_static/fonts/Lato/lato-bold.eot
docs/_static/fonts/Lato/lato-bold.ttf
docs/_static/fonts/Lato/lato-bold.woff
docs/_static/fonts/Lato/lato-bold.woff2
docs/_static/fonts/Lato/lato-bolditalic.eot
docs/_static/fonts/Lato/lato-bolditalic.ttf
docs/_static/fonts/Lato/lato-bolditalic.woff
docs/_static/fonts/Lato/lato-bolditalic.woff2
docs/_static/fonts/Lato/lato-italic.eot
docs/_static/fonts/Lato/lato-italic.ttf
docs/_static/fonts/Lato/lato-italic.woff
docs/_static/fonts/Lato/lato-italic.woff2
docs/_static/fonts/Lato/lato-regular.eot
docs/_static/fonts/Lato/lato-regular.ttf
docs/_static/fonts/Lato/lato-regular.woff
docs/_static/fonts/Lato/lato-regular.woff2
docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.eot
docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.ttf
docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff
docs/_static/fonts/RobotoSlab/roboto-slab-v7-bold.woff2
docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.eot
docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.ttf
docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff
docs/_static/fonts/RobotoSlab/roboto-slab-v7-regular.woff2
docs/_static/fonts/specimen/FontAwesome.ttf
docs/_static/fonts/specimen/FontAwesome.woff
docs/_static/fonts/specimen/FontAwesome.woff2
docs/_static/fonts/specimen/MaterialIcons-Regular.ttf
docs/_static/fonts/specimen/MaterialIcons-Regular.woff
docs/_static/fonts/specimen/MaterialIcons-Regular.woff2
docs/_static/images/favicon.png
docs/_static/images/icons/bitbucket.1b09e088.svg
docs/_static/images/icons/bitbucket.svg
docs/_static/images/icons/github.f0b8504a.svg
docs/_static/images/icons/github.svg
docs/_static/images/icons/gitlab.6dd19c00.svg
docs/_static/images/icons/gitlab.svg
docs/_static/javascripts/application.js
docs/_static/javascripts/modernizr.js
docs/_static/javascripts/version_dropdown.js
docs/_static/javascripts/lunr/lunr.da.js
docs/_static/javascripts/lunr/lunr.de.js
docs/_static/javascripts/lunr/lunr.du.js
docs/_static/javascripts/lunr/lunr.es.js
docs/_static/javascripts/lunr/lunr.fi.js
docs/_static/javascripts/lunr/lunr.fr.js
docs/_static/javascripts/lunr/lunr.hu.js
docs/_static/javascripts/lunr/lunr.it.js
docs/_static/javascripts/lunr/lunr.ja.js
docs/_static/javascripts/lunr/lunr.jp.js
docs/_static/javascripts/lunr/lunr.multi.js
docs/_static/javascripts/lunr/lunr.nl.js
docs/_static/javascripts/lunr/lunr.no.js
docs/_static/javascripts/lunr/lunr.pt.js
docs/_static/javascripts/lunr/lunr.ro.js
docs/_static/javascripts/lunr/lunr.ru.js
docs/_static/javascripts/lunr/lunr.stemmer.support.js
docs/_static/javascripts/lunr/lunr.sv.js
docs/_static/javascripts/lunr/lunr.th.js
docs/_static/javascripts/lunr/lunr.tr.js
docs/_static/javascripts/lunr/tinyseg.js
docs/_static/javascripts/lunr/wordcut.js
docs/_static/js/badge_only.js
docs/_static/js/html5shiv-printshiv.min.js
docs/_static/js/html5shiv.min.js
docs/_static/js/modernizr.min.js
docs/_static/js/theme.js
docs/_static/stylesheets/application-fixes.css
docs/_static/stylesheets/application-palette.css
docs/_static/stylesheets/application.css
notebooks/fixing_best_match.ipynb
notebooks/more_stats_tests.ipynb
notebooks/pyllelic_binder_example.ipynb
notebooks/pyllelic_notebook.ipynb
pyllelic/__init__.py
pyllelic/__main__.py
pyllelic/__version__.py
pyllelic/config.py
pyllelic/process.py
pyllelic/pyllelic.py
pyllelic/quma.py
pyllelic/visualization.py
pyllelic.egg-info/PKG-INFO
pyllelic.egg-info/SOURCES.txt
pyllelic.egg-info/dependency_links.txt
pyllelic.egg-info/requires.txt
pyllelic.egg-info/top_level.txt
tests/__init__.py
tests/inputs.py
tests/test__main.py
tests/test_process.py
tests/test_pyllelic.py
tests/test_quma.py
tests/test_visualization.py