├── .github └── workflows │ ├── publish.yml │ └── test.yml ├── .gitignore ├── LICENSE ├── README.md ├── cinder ├── 404.html ├── __init__.py ├── base.html ├── content.html ├── css │ ├── base.css │ ├── base.min.css │ ├── bootstrap-custom.css │ ├── bootstrap-custom.min.css │ ├── cinder.css │ ├── cinder.min.css │ ├── highlight.css │ └── highlight.min.css ├── fonts │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ └── fontawesome-webfont.woff ├── img │ ├── favicon.ico │ ├── grid1.png │ ├── grid10.png │ ├── grid11.png │ ├── grid12.png │ ├── grid13.png │ ├── grid14.png │ ├── grid15.png │ ├── grid16.png │ ├── grid17.png │ ├── grid18.png │ ├── grid19.png │ ├── grid2.png │ ├── grid20.png │ ├── grid3.png │ ├── grid4.png │ ├── grid5.png │ ├── grid6.png │ ├── grid7.png │ ├── grid8.png │ └── grid9.png ├── js │ ├── base.js │ └── bootstrap-3.0.3.min.js ├── keyboard-modal.html ├── main.html ├── mkdocs_theme.yml ├── nav-sub.html ├── nav.html ├── search-modal.html └── toc.html ├── docs ├── commands.md ├── figs │ ├── COMMD7_GNAS_cluster.html │ ├── GM12878_FRG1EP_cluster.html │ ├── gm12878_FRG1EP.html │ ├── gm12878_FRG1EP_cluster.html │ ├── gm12878_GNAS.html │ ├── gm12878_GNAS.pdf │ ├── gm12878_GNAS_hap.html │ ├── gm12878_GNAS_hap_h3k27ac_h3k4me1.html │ └── gm12878_batch.html ├── img │ ├── favicon.ico │ └── logo.png ├── index.md └── tutorial.md ├── mkdocs.yml ├── modbamtools ├── __init__.py ├── calcregions.py ├── cli.py ├── clustering.py ├── gene_models.py ├── heterogeneity.py ├── modbamviz.py ├── tracks.py ├── tracks_webgl.py └── utils.py ├── setup.py ├── site ├── commands │ └── index.html ├── css │ ├── base.css │ ├── base.min.css │ ├── bootstrap-custom.css │ ├── bootstrap-custom.min.css │ ├── cinder.css │ ├── cinder.min.css │ ├── highlight.css │ └── highlight.min.css ├── figs │ ├── COMMD7_GNAS_cluster.html │ ├── GM12878_FRG1EP_cluster.html │ ├── gm12878_FRG1EP.html │ ├── gm12878_FRG1EP_cluster.html │ ├── gm12878_GNAS.html │ ├── gm12878_GNAS.pdf │ ├── gm12878_GNAS_hap.html │ ├── gm12878_GNAS_hap_h3k27ac_h3k4me1.html │ └── gm12878_batch.html ├── fonts │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ └── fontawesome-webfont.woff ├── img │ ├── favicon.ico │ ├── grid1.png │ ├── grid10.png │ ├── grid11.png │ ├── grid12.png │ ├── grid13.png │ ├── grid14.png │ ├── grid15.png │ ├── grid16.png │ ├── grid17.png │ ├── grid18.png │ ├── grid19.png │ ├── grid2.png │ ├── grid20.png │ ├── grid3.png │ ├── grid4.png │ ├── grid5.png │ ├── grid6.png │ ├── grid7.png │ ├── grid8.png │ ├── grid9.png │ └── logo.png ├── index.html ├── js │ ├── base.js │ └── bootstrap-3.0.3.min.js ├── search │ ├── lunr.js │ ├── main.js │ ├── search_index.json │ └── worker.js ├── sitemap.xml ├── sitemap.xml.gz └── tutorial │ └── index.html └── tests ├── modbamtools.gif ├── modbamviz.html ├── strands.html ├── test.html ├── test.png ├── test_m6a.html ├── test_m6a.html.png └── test_modbamtools.py 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