Merge pull request #140 from epifluidlab/kundan

Simple fix for blacklisting feature on BAM/CRAM

CHANGELOG.md

@@ -7,10 +7,19 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.5] - 2025-1-9
+
+### Changed
+- added `intersect_policy` to `filter_file`
+
+### Fixed
+- blacklist functionality of `filter_file`
+
 ## [0.10.4] - 2025-1-2
 
 ### Changed
-- Changed filter-bam function into filter-file; Now accepts BED and CRAM in addition to BAM
+- Changed `filter-bam` function into `filter-file`; Now accepts BED and CRAM in
+addition to BAM
 - filter-file command can now accept a blacklist file
 
 ## [0.10.3] - 2024-12-21

README.md

@@ -52,7 +52,7 @@ FinaleToolkit has support for the following cell-free DNA fragmentation features
 - Cleavage Profile [![DOI](https://img.shields.io/badge/DOI-10.1073%2Fpnas.2209852119-blue?style=flat-square)](https://doi.org/10.1073/pnas.2209852119)
 
 ### Documentation
-Documentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/finaletoolkit-docs/).
+Documentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/FinaleToolkit/).
 
 ### Wiki/Tutorials
 The wiki and tutorial page for FinaleToolkit can be found [here](https://github.com/epifluidlab/FinaleToolkit/wiki).

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

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

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
 

docs/_build/html/_sources/index.rst.txt

@@ -8,9 +8,9 @@ About
 
 FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
 
-- **Website:** https://epifluidlab.github.io/finaletoolkit-docs/
+- **Website:** https://epifluidlab.github.io/FinaleToolkit/
 - **PyPI:** https://pypi.org/project/finaletoolkit/
-- **Documentation:** https://epifluidlab.github.io/finaletoolkit-docs/documentation
+- **Documentation:** https://epifluidlab.github.io/FinaleToolkit/documentation
 - **Wiki:** https://github.com/epifluidlab/FinaleToolkit/wiki
 - **Source code:** https://github.com/epifluidlab/finaletoolkit
 - **Changelog:** https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md

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 {

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";
 

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"];

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;