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remove empty defaults
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@dylanpilz
dylanpilz committed Mar 25, 2024
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6 changes: 6 additions & 0 deletions docs/_build/html/src/installation.html
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<li class="toctree-l1"><a class="reference internal" href="usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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6 changes: 6 additions & 0 deletions docs/_build/html/src/usage/aggregate.html
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<li class="toctree-l1"><a class="reference internal" href="boot.html">freyja boot</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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6 changes: 6 additions & 0 deletions docs/_build/html/src/usage/boot.html
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<li class="toctree-l1 current"><a class="current reference internal" href="#">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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5 changes: 3 additions & 2 deletions docs/_build/html/src/usage/covariants.html
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<script src="../../_static/js/theme.js"></script>
<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="Command Line Workflow" href="../wiki/command_line_workflow.html" />
<link rel="next" title="freyja plot-covariants" href="plot-covariants.html" />
<link rel="prev" title="freyja filter" href="filter.html" />
</head>

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<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
Expand Down Expand Up @@ -226,7 +227,7 @@ <h1>freyja covariants<a class="headerlink" href="#freyja-covariants" title="Link
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="filter.html" class="btn btn-neutral float-left" title="freyja filter" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="../wiki/command_line_workflow.html" class="btn btn-neutral float-right" title="Command Line Workflow" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
<a href="plot-covariants.html" class="btn btn-neutral float-right" title="freyja plot-covariants" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>

<hr/>
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<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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8 changes: 0 additions & 8 deletions docs/_build/html/src/usage/demix.html
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Expand Up @@ -120,20 +120,12 @@ <h1>freyja demix<a class="headerlink" href="#freyja-demix" title="Link to this h
<dt class="sig sig-object std" id="cmdoption-freyja-demix-barcodes">
<span class="sig-name descname"><span class="pre">--barcodes</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;barcodes&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-demix-barcodes" title="Link to this definition"></a></dt>
<dd><p>Path to custom barcode file</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p></p></dd>
</dl>
</dd></dl>

<dl class="std option">
<dt class="sig sig-object std" id="cmdoption-freyja-demix-meta">
<span class="sig-name descname"><span class="pre">--meta</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;meta&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-demix-meta" title="Link to this definition"></a></dt>
<dd><p>custom lineage to variant metadata file</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p></p></dd>
</dl>
</dd></dl>

<dl class="std option">
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<li class="toctree-l1 current"><a class="current reference internal" href="#">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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1 change: 1 addition & 0 deletions docs/_build/html/src/usage/filter.html
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<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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14 changes: 1 addition & 13 deletions docs/_build/html/src/usage/plot.html
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<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
Expand Down Expand Up @@ -175,31 +176,18 @@ <h1>freyja plot<a class="headerlink" href="#freyja-plot" title="Link to this hea
<dt class="sig sig-object std" id="cmdoption-freyja-plot-lineageyml">
<span class="sig-name descname"><span class="pre">--lineageyml</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;lineageyml&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-plot-lineageyml" title="Link to this definition"></a></dt>
<dd><p>Custom lineage hierarchy file</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p></p></dd>
</dl>
</dd></dl>

<dl class="std option">
<dt class="sig sig-object std" id="cmdoption-freyja-plot-thresh">
<span class="sig-name descname"><span class="pre">--thresh</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;thresh&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-plot-thresh" title="Link to this definition"></a></dt>
<dd><p>pass a minimum lineage abundance</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p><code class="docutils literal notranslate"><span class="pre">0.01</span></code></p>
</dd>
</dl>
</dd></dl>

<dl class="std option">
<dt class="sig sig-object std" id="cmdoption-freyja-plot-writegrouped">
<span class="sig-name descname"><span class="pre">--writegrouped</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;writegrouped&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-plot-writegrouped" title="Link to this definition"></a></dt>
<dd><p>path to write grouped lineage data</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p></p></dd>
</dl>
</dd></dl>

<p class="rubric">Arguments</p>
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Expand Up @@ -204,10 +204,6 @@ <h1>freyja relgrowthrate<a class="headerlink" href="#freyja-relgrowthrate" title
<dt class="sig sig-object std" id="cmdoption-freyja-relgrowthrate-lineageyml">
<span class="sig-name descname"><span class="pre">--lineageyml</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;lineageyml&gt;</span></span><a class="headerlink" href="#cmdoption-freyja-relgrowthrate-lineageyml" title="Link to this definition"></a></dt>
<dd><p>lineage hierarchy file</p>
<dl class="field-list simple">
<dt class="field-odd">Default<span class="colon">:</span></dt>
<dd class="field-odd"><p></p></dd>
</dl>
</dd></dl>

<p class="rubric">Arguments</p>
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6 changes: 6 additions & 0 deletions docs/_build/html/src/usage/update.html
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<li class="toctree-l1"><a class="reference internal" href="boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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1 change: 1 addition & 0 deletions docs/_build/html/src/usage/variants.html
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<li class="toctree-l1"><a class="reference internal" href="extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul>
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10 changes: 8 additions & 2 deletions docs/_build/html/src/wiki/command_line_workflow.html
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<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="next" title="Cryptic Variant Detection" href="cryptic_variants.html" />
<link rel="prev" title="freyja plot" href="../usage/plot.html" />
<link rel="prev" title="freyja plot-covariants" href="../usage/plot-covariants.html" />
</head>

<body class="wy-body-for-nav">
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
Expand Down Expand Up @@ -145,7 +151,7 @@ <h1>Command Line Workflow<a class="headerlink" href="#command-line-workflow" tit
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="../usage/plot.html" class="btn btn-neutral float-left" title="freyja plot" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="../usage/plot-covariants.html" class="btn btn-neutral float-left" title="freyja plot-covariants" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="cryptic_variants.html" class="btn btn-neutral float-right" title="Cryptic Variant Detection" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>

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6 changes: 6 additions & 0 deletions docs/_build/html/src/wiki/cryptic_variants.html
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
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6 changes: 6 additions & 0 deletions docs/_build/html/src/wiki/custom_plotting_tutorial.html
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
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6 changes: 6 additions & 0 deletions docs/_build/html/src/wiki/lineage_barcode_extract.html
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
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6 changes: 6 additions & 0 deletions docs/_build/html/src/wiki/read_analysis_tutorial.html
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
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<li class="toctree-l1"><a class="reference internal" href="../usage/boot.html">freyja boot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/aggregate.html">freyja aggregate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot.html">freyja plot</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/dash.html">freyja dash</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/relgrowthrate.html">freyja relgrowthrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/extract.html">freyja extract</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/filter.html">freyja filter</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/covariants.html">freyja covariants</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage/plot-covariants.html">freyja plot-covariants</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Wiki:</span></p>
<ul class="current">
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