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filter-bam into filter-file #138

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Jan 3, 2025
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d54f4fd
filter-bam into filter-file
Jan 2, 2025
65175a0
test and changelog
Jan 2, 2025
74da919
update version
jamesli124 Jan 2, 2025
709e61d
Make suffix always in scope, check input->output extension agreement
Kudostoy0u Jan 3, 2025
93eb025
minor formatting and typing changes
jamesli124 Jan 3, 2025
b9ec456
regenerate docs
jamesli124 Jan 3, 2025
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/_build/html/_static/basic.css
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Expand Up @@ -55,7 +55,7 @@ div.sphinxsidebarwrapper {

div.sphinxsidebar {
float: left;
width: 270px;
width: 230px;
margin-left: -100%;
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14 changes: 7 additions & 7 deletions docs/_build/html/_static/webpack-macros.html
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Expand Up @@ -5,20 +5,20 @@

{% macro head_pre_assets() %}
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<link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
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<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>
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<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>
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<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 %}
44 changes: 25 additions & 19 deletions docs/_build/html/documentation/api_reference/basicfeatures.html
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document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
</script>
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this give us a css class that will be invisible only if js is disabled
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this give us a css class that will be invisible only if js is disabled
-->
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<style>
Expand All @@ -27,16 +27,16 @@
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<link href="../../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
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<link href="../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
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<script src="../../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
<script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
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<script src="../../_static/documentation_options.js?v=5929fcd5"></script>
<script src="../../_static/doctools.js?v=9a2dae69"></script>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>

Expand All @@ -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>
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<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>

<footer class="bd-footer">
<div class="bd-footer__inner bd-page-width">
Expand Down Expand Up @@ -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>
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44 changes: 25 additions & 19 deletions docs/_build/html/documentation/api_reference/cleavageprofile.html
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Expand Up @@ -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>
Expand All @@ -27,16 +27,16 @@
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<link href="../../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
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<script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
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<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" />
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<script src="../../_static/documentation_options.js?v=5929fcd5"></script>
<script src="../../_static/doctools.js?v=9a2dae69"></script>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>

Expand All @@ -462,8 +467,8 @@ <h1>Cleavage Profile<a class="headerlink" href="#cleavage-profile" title="Link t
</div>

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<script defer src="../../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
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<script defer src="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>

<footer class="bd-footer">
<div class="bd-footer__inner bd-page-width">
Expand Down Expand Up @@ -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>
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44 changes: 25 additions & 19 deletions docs/_build/html/documentation/api_reference/delfi.html
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Expand Up @@ -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>
Expand All @@ -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" />
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<script src="../../_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
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<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
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<script src="../../_static/documentation_options.js?v=5929fcd5"></script>
<script src="../../_static/doctools.js?v=9a2dae69"></script>
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<div id="ethical-ad-placement"
class="flat"
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data-ea-type="readthedocs-sidebar"
data-ea-manual="true">
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Expand Down Expand Up @@ -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>

Expand All @@ -493,8 +498,8 @@ <h1>DELFI<a class="headerlink" href="#delfi" title="Link to this heading">#</a><
</div>

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Expand Down Expand Up @@ -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.
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