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epifluidlab · Jan 9, 2025 · 90d29ec · 90d29ec
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diff --git a/docs/_build/doctrees/documentation/api_reference/basicfeatures.doctree b/docs/_build/doctrees/documentation/api_reference/basicfeatures.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/cleavageprofile.doctree b/docs/_build/doctrees/documentation/api_reference/cleavageprofile.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/delfi.doctree b/docs/_build/doctrees/documentation/api_reference/delfi.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/endmotifs.doctree b/docs/_build/doctrees/documentation/api_reference/endmotifs.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/fragfile.doctree b/docs/_build/doctrees/documentation/api_reference/fragfile.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/genomeutils.doctree b/docs/_build/doctrees/documentation/api_reference/genomeutils.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/index.doctree b/docs/_build/doctrees/documentation/api_reference/index.doctree
diff --git a/docs/_build/doctrees/documentation/api_reference/wps.doctree b/docs/_build/doctrees/documentation/api_reference/wps.doctree
diff --git a/docs/_build/doctrees/documentation/cli_reference/index.doctree b/docs/_build/doctrees/documentation/cli_reference/index.doctree
diff --git a/docs/_build/doctrees/documentation/index.doctree b/docs/_build/doctrees/documentation/index.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/features.doctree b/docs/_build/doctrees/documentation/user_guide/features.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/help.doctree b/docs/_build/doctrees/documentation/user_guide/help.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/index.doctree b/docs/_build/doctrees/documentation/user_guide/index.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/inputdata.doctree b/docs/_build/doctrees/documentation/user_guide/inputdata.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/installation.doctree b/docs/_build/doctrees/documentation/user_guide/installation.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/intersectpolicy.doctree b/docs/_build/doctrees/documentation/user_guide/intersectpolicy.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/quickstart.doctree b/docs/_build/doctrees/documentation/user_guide/quickstart.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/structure.doctree b/docs/_build/doctrees/documentation/user_guide/structure.doctree
diff --git a/docs/_build/doctrees/documentation/user_guide/what.doctree b/docs/_build/doctrees/documentation/user_guide/what.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 670efaa449e3fccfe64f8fb2cf4a7d46
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a6a7c49fe85dc34358516258c905dd38
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 670efaa449e3fccfe64f8fb2cf4a7d46
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/documentation/api_reference/fragfile.rst.txt b/docs/_build/html/_sources/documentation/api_reference/fragfile.rst.txt
@@ -1,7 +1,7 @@
 Frag File Utilities
 ======================================
 
-.. autofunction:: finaletoolkit.utils.filter_bam
+.. autofunction:: finaletoolkit.utils.filter_file
 
 .. autofunction:: finaletoolkit.utils.agg_bw
 

diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css
@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {

diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js
@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 

diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js
@@ -1,13 +1,6 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];

diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css
diff --git a/docs/_build/html/_static/searchtools.js b/docs/_build/html/_static/searchtools.js
@@ -1,12 +1,5 @@
 /*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
  * Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
     // and returns the new score.
     /*
     score: result => {
-      const [docname, title, anchor, descr, score, filename] = result
+      const [docname, title, anchor, descr, score, filename, kind] = result
       return score
     },
     */
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
   };
 }
 
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+    static get index() { return  "index"; }
+    static get object() { return "object"; }
+    static get text() { return "text"; }
+    static get title() { return "title"; }
+}
+
 const _removeChildren = (element) => {
   while (element && element.lastChild) element.removeChild(element.lastChild);
 };
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
   const contentRoot = document.documentElement.dataset.content_root;
 
-  const [docName, title, anchor, descr, score, _filename] = item;
+  const [docName, title, anchor, descr, score, _filename, kind] = item;
 
   let listItem = document.createElement("li");
+  // Add a class representing the item's type:
+  // can be used by a theme's CSS selector for styling
+  // See SearchResultKind for the class names.
+  listItem.classList.add(`kind-${kind}`);
   let requestUrl;
   let linkUrl;
   if (docBuilder === "dirhtml") {
@@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => {
       "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
     );
   else
-    Search.status.innerText = _(
-      "Search finished, found ${resultCount} page(s) matching the search query."
+    Search.status.innerText = Documentation.ngettext(
+      "Search finished, found one page matching the search query.",
+      "Search finished, found ${resultCount} pages matching the search query.",
+      resultCount,
     ).replace('${resultCount}', resultCount);
 };
 const _displayNextItem = (
@@ -138,7 +145,7 @@ const _displayNextItem = (
   else _finishSearch(resultCount);
 };
 // Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
 // Order the results by score (in opposite order of appearance, since the
 // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
 const _orderResultsByScoreThenName = (a, b) => {
@@ -248,6 +255,7 @@ const Search = {
     searchSummary.classList.add("search-summary");
     searchSummary.innerText = "";
     const searchList = document.createElement("ul");
+    searchList.setAttribute("role", "list");
     searchList.classList.add("search");
 
     const out = document.getElementById("search-results");
@@ -318,7 +326,7 @@ const Search = {
     const indexEntries = Search._index.indexentries;
 
     // Collect multiple result groups to be sorted separately and then ordered.
-    // Each is an array of [docname, title, anchor, descr, score, filename].
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
     const normalResults = [];
     const nonMainIndexResults = [];
 
@@ -337,6 +345,7 @@ const Search = {
             null,
             score + boost,
             filenames[file],
+            SearchResultKind.title,
           ]);
         }
       }
@@ -354,6 +363,7 @@ const Search = {
             null,
             score,
             filenames[file],
+            SearchResultKind.index,
           ];
           if (isMain) {
             normalResults.push(result);
@@ -475,6 +485,7 @@ const Search = {
         descr,
         score,
         filenames[match[0]],
+        SearchResultKind.object,
       ]);
     };
     Object.keys(objects).forEach((prefix) =>
@@ -585,6 +596,7 @@ const Search = {
         null,
         score,
         filenames[file],
+        SearchResultKind.text,
       ]);
     }
     return results;

diff --git a/docs/_build/html/documentation/api_reference/basicfeatures.html b/docs/_build/html/documentation/api_reference/basicfeatures.html
diff --git a/docs/_build/html/documentation/api_reference/cleavageprofile.html b/docs/_build/html/documentation/api_reference/cleavageprofile.html
@@ -30,7 +30,7 @@
   <link href="../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 <link href="../../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
 
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
 
   <!-- So that users can add custom icons -->
   <script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
@@ -39,7 +39,7 @@
 <link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />
 
     <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'documentation/api_reference/cleavageprofile';</script>
     <link rel="icon" href="../../_static/favicon.ico"/>
@@ -362,7 +362,7 @@
 <h1>Cleavage Profile<a class="headerlink" href="#cleavage-profile" title="Link to this heading">#</a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="finaletoolkit.frag.cleavage_profile">
-<span class="sig-prename descclassname"><span class="pre">finaletoolkit.frag.</span></span><span class="sig-name descname"><span class="pre">cleavage_profile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">FragFile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chrom_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contig</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">left</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_length</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_length</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quality_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">30</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fraction_low</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fraction_high</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">np.ndarray</span></span></span><a class="headerlink" href="#finaletoolkit.frag.cleavage_profile" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">finaletoolkit.frag.</span></span><span class="sig-name descname"><span class="pre">cleavage_profile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">PathLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">AlignmentFile</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">TabixFile</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chrom_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">contig</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">left</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_length</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_length</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">quality_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">30</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fraction_low</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fraction_high</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="headerlink" href="#finaletoolkit.frag.cleavage_profile" title="Link to this definition">#</a></dt>
 <dd><p>Cleavage profile calculated over a single interval.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -488,7 +488,7 @@ <h3>This Page</h3>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.1.3.
     <br/>
   </p>
 </div>