Refreshes Retype-generated documentation.

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pdimens · Feb 15, 2023 · 004102c · 004102c
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diff --git a/.nojekyll b/.nojekyll
diff --git a/404.html b/404.html
diff --git a/favicon.png b/favicon.png
diff --git a/index.html b/index.html
diff --git a/install/index.html b/install/index.html
diff --git a/modules/imputation/index.html b/modules/imputation/index.html
diff --git a/modules/initialization/index.html b/modules/initialization/index.html
diff --git a/modules/phasing/index.html b/modules/phasing/index.html
diff --git a/modules/qualitytrimming/index.html b/modules/qualitytrimming/index.html
diff --git a/modules/readmapping/index.html b/modules/readmapping/index.html
diff --git a/modules/variantcalling/index.html b/modules/variantcalling/index.html
diff --git a/resources/css/katex.css b/resources/css/katex.css
diff --git a/resources/css/retype.css b/resources/css/retype.css
diff --git a/resources/fonts/KaTeX_AMS-Regular.ttf b/resources/fonts/KaTeX_AMS-Regular.ttf
diff --git a/resources/fonts/KaTeX_AMS-Regular.woff b/resources/fonts/KaTeX_AMS-Regular.woff
diff --git a/resources/fonts/KaTeX_AMS-Regular.woff2 b/resources/fonts/KaTeX_AMS-Regular.woff2
diff --git a/resources/fonts/KaTeX_Caligraphic-Bold.ttf b/resources/fonts/KaTeX_Caligraphic-Bold.ttf
diff --git a/resources/fonts/KaTeX_Caligraphic-Bold.woff b/resources/fonts/KaTeX_Caligraphic-Bold.woff
diff --git a/resources/fonts/KaTeX_Caligraphic-Bold.woff2 b/resources/fonts/KaTeX_Caligraphic-Bold.woff2
diff --git a/resources/fonts/KaTeX_Caligraphic-Regular.ttf b/resources/fonts/KaTeX_Caligraphic-Regular.ttf
diff --git a/resources/fonts/KaTeX_Caligraphic-Regular.woff b/resources/fonts/KaTeX_Caligraphic-Regular.woff
diff --git a/resources/fonts/KaTeX_Caligraphic-Regular.woff2 b/resources/fonts/KaTeX_Caligraphic-Regular.woff2
diff --git a/resources/fonts/KaTeX_Fraktur-Bold.ttf b/resources/fonts/KaTeX_Fraktur-Bold.ttf
diff --git a/resources/fonts/KaTeX_Fraktur-Bold.woff b/resources/fonts/KaTeX_Fraktur-Bold.woff
diff --git a/resources/fonts/KaTeX_Fraktur-Bold.woff2 b/resources/fonts/KaTeX_Fraktur-Bold.woff2
diff --git a/resources/fonts/KaTeX_Fraktur-Regular.ttf b/resources/fonts/KaTeX_Fraktur-Regular.ttf
diff --git a/resources/fonts/KaTeX_Fraktur-Regular.woff b/resources/fonts/KaTeX_Fraktur-Regular.woff
diff --git a/resources/fonts/KaTeX_Fraktur-Regular.woff2 b/resources/fonts/KaTeX_Fraktur-Regular.woff2
diff --git a/resources/fonts/KaTeX_Main-Bold.ttf b/resources/fonts/KaTeX_Main-Bold.ttf
diff --git a/resources/fonts/KaTeX_Main-Bold.woff b/resources/fonts/KaTeX_Main-Bold.woff
diff --git a/resources/fonts/KaTeX_Main-Bold.woff2 b/resources/fonts/KaTeX_Main-Bold.woff2
diff --git a/resources/fonts/KaTeX_Main-BoldItalic.ttf b/resources/fonts/KaTeX_Main-BoldItalic.ttf
diff --git a/resources/fonts/KaTeX_Main-BoldItalic.woff b/resources/fonts/KaTeX_Main-BoldItalic.woff
diff --git a/resources/fonts/KaTeX_Main-BoldItalic.woff2 b/resources/fonts/KaTeX_Main-BoldItalic.woff2
diff --git a/resources/fonts/KaTeX_Main-Italic.ttf b/resources/fonts/KaTeX_Main-Italic.ttf
diff --git a/resources/fonts/KaTeX_Main-Italic.woff b/resources/fonts/KaTeX_Main-Italic.woff
diff --git a/resources/fonts/KaTeX_Main-Italic.woff2 b/resources/fonts/KaTeX_Main-Italic.woff2
diff --git a/resources/fonts/KaTeX_Main-Regular.ttf b/resources/fonts/KaTeX_Main-Regular.ttf
diff --git a/resources/fonts/KaTeX_Main-Regular.woff b/resources/fonts/KaTeX_Main-Regular.woff
diff --git a/resources/fonts/KaTeX_Main-Regular.woff2 b/resources/fonts/KaTeX_Main-Regular.woff2
diff --git a/resources/fonts/KaTeX_Math-BoldItalic.ttf b/resources/fonts/KaTeX_Math-BoldItalic.ttf
diff --git a/resources/fonts/KaTeX_Math-BoldItalic.woff b/resources/fonts/KaTeX_Math-BoldItalic.woff
diff --git a/resources/fonts/KaTeX_Math-BoldItalic.woff2 b/resources/fonts/KaTeX_Math-BoldItalic.woff2
diff --git a/resources/fonts/KaTeX_Math-Italic.ttf b/resources/fonts/KaTeX_Math-Italic.ttf
diff --git a/resources/fonts/KaTeX_Math-Italic.woff b/resources/fonts/KaTeX_Math-Italic.woff
diff --git a/resources/fonts/KaTeX_Math-Italic.woff2 b/resources/fonts/KaTeX_Math-Italic.woff2
diff --git a/resources/fonts/KaTeX_SansSerif-Bold.ttf b/resources/fonts/KaTeX_SansSerif-Bold.ttf
diff --git a/resources/fonts/KaTeX_SansSerif-Bold.woff b/resources/fonts/KaTeX_SansSerif-Bold.woff
diff --git a/resources/fonts/KaTeX_SansSerif-Bold.woff2 b/resources/fonts/KaTeX_SansSerif-Bold.woff2
diff --git a/resources/fonts/KaTeX_SansSerif-Italic.ttf b/resources/fonts/KaTeX_SansSerif-Italic.ttf
diff --git a/resources/fonts/KaTeX_SansSerif-Italic.woff b/resources/fonts/KaTeX_SansSerif-Italic.woff
diff --git a/resources/fonts/KaTeX_SansSerif-Italic.woff2 b/resources/fonts/KaTeX_SansSerif-Italic.woff2
diff --git a/resources/fonts/KaTeX_SansSerif-Regular.ttf b/resources/fonts/KaTeX_SansSerif-Regular.ttf
diff --git a/resources/fonts/KaTeX_SansSerif-Regular.woff b/resources/fonts/KaTeX_SansSerif-Regular.woff
diff --git a/resources/fonts/KaTeX_SansSerif-Regular.woff2 b/resources/fonts/KaTeX_SansSerif-Regular.woff2
diff --git a/resources/fonts/KaTeX_Script-Regular.ttf b/resources/fonts/KaTeX_Script-Regular.ttf
diff --git a/resources/fonts/KaTeX_Script-Regular.woff b/resources/fonts/KaTeX_Script-Regular.woff
diff --git a/resources/fonts/KaTeX_Script-Regular.woff2 b/resources/fonts/KaTeX_Script-Regular.woff2
diff --git a/resources/fonts/KaTeX_Size1-Regular.ttf b/resources/fonts/KaTeX_Size1-Regular.ttf
diff --git a/resources/fonts/KaTeX_Size1-Regular.woff b/resources/fonts/KaTeX_Size1-Regular.woff
diff --git a/resources/fonts/KaTeX_Size1-Regular.woff2 b/resources/fonts/KaTeX_Size1-Regular.woff2
diff --git a/resources/fonts/KaTeX_Size2-Regular.ttf b/resources/fonts/KaTeX_Size2-Regular.ttf
diff --git a/resources/fonts/KaTeX_Size2-Regular.woff b/resources/fonts/KaTeX_Size2-Regular.woff
diff --git a/resources/fonts/KaTeX_Size2-Regular.woff2 b/resources/fonts/KaTeX_Size2-Regular.woff2
diff --git a/resources/fonts/KaTeX_Size3-Regular.ttf b/resources/fonts/KaTeX_Size3-Regular.ttf
diff --git a/resources/fonts/KaTeX_Size3-Regular.woff b/resources/fonts/KaTeX_Size3-Regular.woff
diff --git a/resources/fonts/KaTeX_Size3-Regular.woff2 b/resources/fonts/KaTeX_Size3-Regular.woff2
diff --git a/resources/fonts/KaTeX_Size4-Regular.ttf b/resources/fonts/KaTeX_Size4-Regular.ttf
diff --git a/resources/fonts/KaTeX_Size4-Regular.woff b/resources/fonts/KaTeX_Size4-Regular.woff
diff --git a/resources/fonts/KaTeX_Size4-Regular.woff2 b/resources/fonts/KaTeX_Size4-Regular.woff2
diff --git a/resources/fonts/KaTeX_Typewriter-Regular.ttf b/resources/fonts/KaTeX_Typewriter-Regular.ttf
diff --git a/resources/fonts/KaTeX_Typewriter-Regular.woff b/resources/fonts/KaTeX_Typewriter-Regular.woff
diff --git a/resources/fonts/KaTeX_Typewriter-Regular.woff2 b/resources/fonts/KaTeX_Typewriter-Regular.woff2
diff --git a/resources/fonts/Poppins-Medium-Latin.woff2 b/resources/fonts/Poppins-Medium-Latin.woff2
diff --git a/resources/fonts/Poppins-Medium-LatinExt.woff2 b/resources/fonts/Poppins-Medium-LatinExt.woff2
diff --git a/resources/fonts/Poppins-Regular-Latin.woff2 b/resources/fonts/Poppins-Regular-Latin.woff2
diff --git a/resources/fonts/Poppins-Regular-LatinExt.woff2 b/resources/fonts/Poppins-Regular-LatinExt.woff2
diff --git a/resources/fonts/Poppins-SemiBold-Latin.woff2 b/resources/fonts/Poppins-SemiBold-Latin.woff2
diff --git a/resources/fonts/Poppins-SemiBold-LatinExt.woff2 b/resources/fonts/Poppins-SemiBold-LatinExt.woff2
diff --git a/resources/js/config.js b/resources/js/config.js
diff --git a/resources/js/katex.js b/resources/js/katex.js
diff --git a/resources/js/lunr.js b/resources/js/lunr.js
diff --git a/resources/js/mermaid.js b/resources/js/mermaid.js
diff --git a/resources/js/prism.js b/resources/js/prism.js
diff --git a/resources/js/retype.js b/resources/js/retype.js
diff --git a/resources/js/search.json b/resources/js/search.json
diff --git a/resources/katex.js.LICENSE.txt b/resources/katex.js.LICENSE.txt
@@ -0,0 +1,8 @@
+/**
+ * KaTeX is a fast, easy-to-use JavaScript library for TeX math rendering on the web.
+ *
+ * @license MIT <https://opensource.org/licenses/MIT>
+ * @author Emily Eisenberg <https://github.com/xymostech>, Sophie Alpert <https://github.com/sophiebits>
+ * @namespace
+ * @public
+ */
diff --git a/resources/lunr.js.LICENSE.txt b/resources/lunr.js.LICENSE.txt
@@ -0,0 +1,61 @@
+/*!
+ * lunr.Builder
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.Index
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.Pipeline
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.Set
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.TokenSet
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.Vector
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.stemmer
+ * Copyright (C) 2020 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */
+
+/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.tokenizer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.trimmer
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/*!
+ * lunr.utils
+ * Copyright (C) 2020 Oliver Nightingale
+ */
+
+/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9
+ * Copyright (C) 2020 Oliver Nightingale
+ * @license MIT
+ */
diff --git a/resources/mermaid.js.LICENSE.txt b/resources/mermaid.js.LICENSE.txt
@@ -0,0 +1,10 @@
+/*! For license information please see mermaid.esm.min.mjs.LICENSE.txt */
+
+/**
+ * Mermaid is a Javascript based diagramming and charting tool that uses Markdown-inspired text definitions and a renderer to create and modify complex diagrams.
+ *
+ * @license MIT <https://opensource.org/licenses/MIT>
+ * @author Knut Sveidqvist <https://github.com/knsv>
+ * @namespace
+ * @public
+ */
diff --git a/resources/prism.js.LICENSE.txt b/resources/prism.js.LICENSE.txt
@@ -0,0 +1,8 @@
+/**
+ * Prism: Lightweight, robust, elegant syntax highlighting
+ *
+ * @license MIT <https://opensource.org/licenses/MIT>
+ * @author Lea Verou <https://lea.verou.me>
+ * @namespace
+ * @public
+ */