Merge pull request #138 from epifluidlab/kundan

filter-bam into filter-file
epifluidlab · Jan 3, 2025 · 698452f · 698452f
2 parents 0058482 + b9ec456
commit 698452f
Show file tree

Hide file tree

Showing 59 changed files with 877 additions and 668 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,12 @@ The format is based on
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.10.4] - 2025-1-2
+
+### Changed
+- 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
 
 ### Fixed

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/_static/basic.css b/docs/_build/html/_static/basic.css
@@ -55,7 +55,7 @@ div.sphinxsidebarwrapper {
 
 div.sphinxsidebar {
     float: left;
-    width: 270px;
+    width: 230px;
     margin-left: -100%;
     font-size: 90%;
     word-wrap: break-word;

diff --git a/docs/_build/html/_static/scripts/pydata-sphinx-theme.js b/docs/_build/html/_static/scripts/pydata-sphinx-theme.js
diff --git a/docs/_build/html/_static/scripts/pydata-sphinx-theme.js.map b/docs/_build/html/_static/scripts/pydata-sphinx-theme.js.map
diff --git a/docs/_build/html/_static/styles/pydata-sphinx-theme.css b/docs/_build/html/_static/styles/pydata-sphinx-theme.css
diff --git a/docs/_build/html/_static/styles/pydata-sphinx-theme.css.map b/docs/_build/html/_static/styles/pydata-sphinx-theme.css.map
diff --git a/docs/_build/html/_static/webpack-macros.html b/docs/_build/html/_static/webpack-macros.html
@@ -5,20 +5,20 @@
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=8878045cc6db502f8baf" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=8878045cc6db502f8baf" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
   <!-- So that users can add custom icons -->
-  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8878045cc6db502f8baf" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8878045cc6db502f8baf" />
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=8878045cc6db502f8baf"></script>
+<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=8878045cc6db502f8baf"></script>
 {% endmacro %}
diff --git a/docs/_build/html/documentation/api_reference/basicfeatures.html b/docs/_build/html/documentation/api_reference/basicfeatures.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,16 +27,16 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="../../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <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" />
 
   <!-- So that users can add custom icons -->
-  <script src="../../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<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>
@@ -302,9 +302,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -519,13 +524,13 @@ <h1>Basic Features<a class="headerlink" href="#basic-features" title="Link to th
   </nav></div>
 
   <div class="sidebar-secondary-item">
-
-  <div class="tocsection sourcelink">
-    <a href="../../_sources/documentation/api_reference/basicfeatures.rst.txt">
-      <i class="fa-solid fa-file-lines"></i> Show Source
-    </a>
-  </div>
-</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation/api_reference/basicfeatures.rst.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div></div>
 
 </div></div>
 
@@ -540,8 +545,8 @@ <h1>Basic Features<a class="headerlink" href="#basic-features" title="Link to th
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -574,7 +579,8 @@ <h1>Basic Features<a class="headerlink" href="#basic-features" title="Link to th
 
         <div class="footer-item">
 <p class="theme-version">
-  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.0.
+  <!-- # L10n: Setting the PST URL as an argument as this does not need to be localized -->
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.1.
 </p></div>
 
     </div>

diff --git a/docs/_build/html/documentation/api_reference/cleavageprofile.html b/docs/_build/html/documentation/api_reference/cleavageprofile.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,16 +27,16 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="../../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <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" />
 
   <!-- So that users can add custom icons -->
-  <script src="../../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<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>
@@ -302,9 +302,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -441,13 +446,13 @@ <h1>Cleavage Profile<a class="headerlink" href="#cleavage-profile" title="Link t
   </nav></div>
 
   <div class="sidebar-secondary-item">
-
-  <div class="tocsection sourcelink">
-    <a href="../../_sources/documentation/api_reference/cleavageprofile.rst.txt">
-      <i class="fa-solid fa-file-lines"></i> Show Source
-    </a>
-  </div>
-</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation/api_reference/cleavageprofile.rst.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div></div>
 
 </div></div>
 
@@ -462,8 +467,8 @@ <h1>Cleavage Profile<a class="headerlink" href="#cleavage-profile" title="Link t
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -496,7 +501,8 @@ <h1>Cleavage Profile<a class="headerlink" href="#cleavage-profile" title="Link t
 
         <div class="footer-item">
 <p class="theme-version">
-  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.0.
+  <!-- # L10n: Setting the PST URL as an argument as this does not need to be localized -->
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.1.
 </p></div>
 
     </div>

diff --git a/docs/_build/html/documentation/api_reference/delfi.html b/docs/_build/html/documentation/api_reference/delfi.html
@@ -16,8 +16,8 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-  <!-- 
-    this give us a css class that will be invisible only if js is disabled 
+  <!--
+    this give us a css class that will be invisible only if js is disabled
   -->
   <noscript>
     <style>
@@ -27,16 +27,16 @@
   </noscript>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
-<link href="../../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+  <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" />
 
   <!-- So that users can add custom icons -->
-  <script src="../../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
-<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+  <link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
+<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>
@@ -302,9 +302,14 @@
 
 
   <div class="sidebar-primary-items__end sidebar-primary__section">
+      <div class="sidebar-primary-item">
+<div id="ethical-ad-placement"
+      class="flat"
+      data-ea-publisher="readthedocs"
+      data-ea-type="readthedocs-sidebar"
+      data-ea-manual="true">
+</div></div>
   </div>
-
-  <div id="rtd-footer-container"></div>
 
 
       </div>
@@ -472,13 +477,13 @@ <h1>DELFI<a class="headerlink" href="#delfi" title="Link to this heading">#</a><
   </nav></div>
 
   <div class="sidebar-secondary-item">
-
-  <div class="tocsection sourcelink">
-    <a href="../../_sources/documentation/api_reference/delfi.rst.txt">
-      <i class="fa-solid fa-file-lines"></i> Show Source
-    </a>
-  </div>
-</div>
+  <div role="note" aria-label="source link">
+    <h3>This Page</h3>
+    <ul class="this-page-menu">
+      <li><a href="../../_sources/documentation/api_reference/delfi.rst.txt"
+            rel="nofollow">Show Source</a></li>
+    </ul>
+   </div></div>
 
 </div></div>
 
@@ -493,8 +498,8 @@ <h1>DELFI<a class="headerlink" href="#delfi" title="Link to this heading">#</a><
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script defer src="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
-<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+  <script defer src="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
+<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -527,7 +532,8 @@ <h1>DELFI<a class="headerlink" href="#delfi" title="Link to this heading">#</a><
 
         <div class="footer-item">
 <p class="theme-version">
-  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.0.
+  <!-- # L10n: Setting the PST URL as an argument as this does not need to be localized -->
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.1.
 </p></div>
 
     </div>