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williamdlees committed Oct 25, 2024
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6 changes: 6 additions & 0 deletions docs/_build/html/_sources/index.rst.txt
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

Citation
========
If you use Digger in your research, please cite the following paper:
Digger: directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies.
Bioinformatics, 2024. `DOI: 10.1093/bioinformatics/btae144 <https://doi.org/10.1093/bioinformatics/btae144>`_.
2 changes: 2 additions & 0 deletions docs/_build/html/genindex.html
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Image</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html">Release Notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#changes-in-0-7-3">Changes in 0.7.3</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#id1">Changes in 0.7.3</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Examples</span></p>
<ul>
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10 changes: 10 additions & 0 deletions docs/_build/html/index.html
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Image</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html">Release Notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#changes-in-0-7-3">Changes in 0.7.3</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#id1">Changes in 0.7.3</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Examples</span></p>
<ul>
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Image</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html">Release Notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#changes-in-0-7-3">Changes in 0.7.3</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#id1">Changes in 0.7.3</a></li>
</ul>
</div>
<div class="toctree-wrapper compound">
Expand All @@ -124,6 +128,12 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
<li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
</ul>
</section>
<section id="citation">
<h1>Citation<a class="headerlink" href="#citation" title="Permalink to this heading"></a></h1>
<p>If you use Digger in your research, please cite the following paper:
Digger: directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies.
Bioinformatics, 2024. <a class="reference external" href="https://doi.org/10.1093/bioinformatics/btae144">DOI: 10.1093/bioinformatics/btae144</a>.</p>
</section>


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29 changes: 25 additions & 4 deletions docs/_build/html/news.html
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<li class="toctree-l1"><a class="reference internal" href="overview.html#dig-sequence">dig-sequence</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Image</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Release Notes</a><ul>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Release Notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="#changes-in-0-7-3">Changes in 0.7.3</a></li>
<li class="toctree-l1"><a class="reference internal" href="#id1">Changes in 0.7.3</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-7-2">Changes in 0.7.2</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-7-1">Changes in 0.7.1</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-7-0">Changes in 0.7.0</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-9">Changes in 0.6.9</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-8">Changes in 0.6.8</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-7">Changes in 0.6.7</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id1">Changes in 0.6.7</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id2">Changes in 0.6.7</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-6">Changes in 0.6.6</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-4">Changes in 0.6.4</a></li>
<li class="toctree-l2"><a class="reference internal" href="#changes-in-0-6-3">Changes in 0.6.3:</a></li>
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<section id="release-notes">
<span id="news"></span><h1>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this heading"></a></h1>
</section>
<section id="changes-in-0-7-3">
<h1>Changes in 0.7.3<a class="headerlink" href="#changes-in-0-7-3" title="Permalink to this heading"></a></h1>
<ul class="simple">
<li><p>fix problem with salmonid names, e.g. TRB3V</p></li>
</ul>
</section>
<section id="id1">
<h1>Changes in 0.7.3<a class="headerlink" href="#id1" title="Permalink to this heading"></a></h1>
<ul class="simple">
<li><p>fix crash in compare_annotations.py</p></li>
</ul>
<section id="changes-in-0-7-2">
<h2>Changes in 0.7.2<a class="headerlink" href="#changes-in-0-7-2" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>digger will default to using the starting set of reference genes for comparison, if no sets are specified with -ref_comp.</p></li>
</ul>
</section>
<section id="changes-in-0-7-1">
<h2>Changes in 0.7.1<a class="headerlink" href="#changes-in-0-7-1" title="Permalink to this heading"></a></h2>
<ul class="simple">
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<li><p>include motif files for TRG</p></li>
</ul>
</section>
<section id="id1">
<h2>Changes in 0.6.7<a class="headerlink" href="#id1" title="Permalink to this heading"></a></h2>
<section id="id2">
<h2>Changes in 0.6.7<a class="headerlink" href="#id2" title="Permalink to this heading"></a></h2>
<ul class="simple">
<li><p>better error handling and explanation in parse_imgt_annotations</p></li>
<li><p>Docker image added</p></li>
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<li class="toctree-l1"><a class="reference internal" href="docker.html">Docker Image</a></li>
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html">Release Notes</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#changes-in-0-7-3">Changes in 0.7.3</a></li>
<li class="toctree-l1"><a class="reference internal" href="news.html#id1">Changes in 0.7.3</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Examples</span></p>
<ul>
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

Citation
========
If you use Digger in your research, please cite the following paper:
Digger: directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies.
Bioinformatics, 2024. `DOI: 10.1093/bioinformatics/btae144 <https://doi.org/10.1093/bioinformatics/btae144>`_.
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Metadata-Version: 2.1
Name: receptor_digger
Version: 0.7.3
Version: 0.7.4
Summary: Tools for de novo discovery of genomic germline IG and TR receptor sequences
Home-page: https://github.com/williamdlees/digger
Author: William Lees
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