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theiagen · Nov 21, 2024 · b645574 · b645574
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diff --git a/v2.2.1/algorithm/technical/index.html b/v2.2.1/algorithm/technical/index.html
@@ -89,7 +89,7 @@
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-        <a href="#calculating-percent-gene-coverage" class="md-skip">
+        <a href="#technical-code-breakdown" class="md-skip">
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       <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
 
 
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         <label class="md-nav__link md-nav__link--active" for="__toc">
 
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@@ -1014,10 +1018,13 @@
 
 
 
-  <h1>Technical Code Breakdown</h1>
-
+<div class="admonition tip inline end">
+<p class="admonition-title">Examples from TBProfiler v4.4.2</p>
+<p>The examples in this document are based on the output of TBProfiler v4.4.2. However, the general principles apply to all versions of TBProfiler and tbp-parser.</p>
+</div>
+<h1 id="technical-code-breakdown">Technical Code Breakdown<a class="headerlink" href="#technical-code-breakdown" title="Permanent link">&para;</a></h1>
 <p><code>tbp-parser</code> is object-oriented, with each class representing either <em>an output file</em>, <em>a part of an output file</em>, or <em>a part of the input JSON file</em> produced by TBProfiler.</p>
-<p>The first class that is invoked by the <code>tbp-parser.py</code> script is <code>Parser</code> which is a control class that orchestrates the creation of the different output reports. </p>
+<p>The first class that is invoked by the <code>tbp-parser.py</code> script is <code>Parser</code> which is a control class that orchestrates the creation of the different output reports.</p>
 <h2 id="calculating-percent-gene-coverage">Calculating percent gene coverage<a class="headerlink" href="#calculating-percent-gene-coverage" title="Permanent link">&para;</a></h2>
 <p>Before creating any reports, <code>Parser</code> calls the <code>Coverage</code> class to calculate the percent gene coverage over a specified minimum depth (default: 10) for the coding regions of all genes included in the TBDB (the database used in TBProfiler to generate the drug resistance annotations). This requires as input the BAM and BAI files produced by TBProfiler during alignment to the H37Rv reference genome. The percent gene coverage results are then stored in a global dictionary that is accessed multiple times for QC purposes during the creation of the final reports.</p>
 <h2 id="creating-the-laboratorian-report">Creating the Laboratorian report<a class="headerlink" href="#creating-the-laboratorian-report" title="Permanent link">&para;</a></h2>
@@ -1228,7 +1235,7 @@ <h2 id="creating-the-coverage-report">Creating the coverage report<a class="head
     <span class="md-icon" title="Last update">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg>
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-    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-08-20</span>
+    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-11-21</span>
   </span>
 
 

diff --git a/v2.2.1/assets/tbp-parser_versioning.png b/v2.2.1/assets/tbp-parser_versioning.png
diff --git a/v2.2.1/index.html b/v2.2.1/index.html
@@ -980,6 +980,16 @@ <h1 id="tbp-parser">tbp-parser<a class="headerlink" href="#tbp-parser" title="Pe
 <p class="admonition-title">Not for Diagnostic Use</p>
 <p><strong>CAUTION</strong>: The information produced by this program should <strong>not</strong> be used for clinical reporting unless and until extensive validation has occured in your laboratory on a stable version. Otherwise, the outputs of tbp-parser are for research use only.</p>
 </div>
+<div class="admonition dna">
+<p class="admonition-title">FUTURE DEPRECATION NOTICE</p>
+<p><mark><strong>At the time of the PHB v2.3.0 release:</strong></mark></p>
+<ul>
+<li><strong>all</strong> branches on Terra that have been mentioned in this documentation will be deleted. Please use the v2.3.0 version of TheiaProk moving forward.</li>
+<li>the <code>main</code> branch of tbp-parser will host v2.1.0 and above; earlier versions of tbp-parser will no longer be supported</li>
+<li>future releases of tbp-parser will only support outputs generated by TBProfiler v6.0.0 and above.</li>
+</ul>
+<p><strong>Versions of TBProfiler prior to v6.0.0 are not compatible with v2+ of tbp-parser.</strong> Please ensure that you are using the correct version of tbp-parser for your version of TBProfiler.</p>
+</div>
 <h2 id="overview">Overview<a class="headerlink" href="#overview" title="Permanent link">&para;</a></h2>
 <p><code>tbp-parser</code> is a tool developed in partnership with the California Department of Health (CDPH) to parse the output of <a href="https://github.com/jodyphelan/TBProfiler">Jody Phelan’s TBProfiler tool</a> into four additional files:</p>
 <ol>
@@ -1011,7 +1021,7 @@ <h2 id="overview">Overview<a class="headerlink" href="#overview" title="Permanen
     <span class="md-icon" title="Last update">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg>
     </span>
-    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-08-20</span>
+    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-11-21</span>
   </span>
 
 

diff --git a/v2.2.1/inputs/inputs/index.html b/v2.2.1/inputs/inputs/index.html
@@ -1042,7 +1042,7 @@ <h1>Command-line Arguments</h1>
 
 <p>The inputs on this page reflect the parameters that are applicable for the command-line tool. To see the inputs required for <code>tbp-parser</code> when run as part of the TheiaProk workflow series, please refer to the <a href="../theiaprok/">TheiaProk Inputs</a> page.</p>
 <h2 id="required-inputs">Required Inputs<a class="headerlink" href="#required-inputs" title="Permanent link">&para;</a></h2>
-<p><code>tbp-parser</code> is designed to run immediately after <a href="https://github.com/jodyphelan/TBProfiler">Jody Phelan’s TB-Profiler tool</a>. Only two inputs are required: the JSON file produced by <code>TB-Profiler</code> and the BAM file produced by <code>TB-Profiler</code>.</p>
+<p><code>tbp-parser</code> is designed to run immediately after <a href="https://github.com/jodyphelan/TBProfiler">Jody Phelan’s TBProfiler tool</a>. Only two inputs are required: the JSON file produced by <code>TBProfiler</code> and the BAM file produced by <code>TBProfiler</code>.</p>
 <p>The JSON file contains information about the mutations detected in the sample: the quality, the type, and if that mutation confers resistance to an antimicrobial drug. The BAM file contains the alignment information for the sample and is needed for determining sequencing quality. </p>
 <table>
 <thead>
@@ -1054,16 +1054,16 @@ <h2 id="required-inputs">Required Inputs<a class="headerlink" href="#required-in
 <tbody>
 <tr>
 <td style="text-align: left;">input_json</td>
-<td style="text-align: left;">The path to the JSON file that was produced by <code>TB-Profiler</code></td>
+<td style="text-align: left;">The path to the JSON file that was produced by <code>TBProfiler</code></td>
 </tr>
 <tr>
 <td style="text-align: left;">input_bam</td>
-<td style="text-align: left;">The path to the BAM file that was produced by <code>TB-Profiler</code></td>
+<td style="text-align: left;">The path to the BAM file that was produced by <code>TBProfiler</code></td>
 </tr>
 </tbody>
 </table>
 <div class="admonition info">
-<p class="admonition-title">Info</p>
+<p class="admonition-title">BAM index file required</p>
 <p>The BAM file must have the accompanying BAI file in the same directory. It must also be named exactly the same as the BAM file but ending with a <code>.bai</code> suffix.</p>
 </div>
 <h2 id="optional-inputs">Optional Inputs<a class="headerlink" href="#optional-inputs" title="Permanent link">&para;</a></h2>
@@ -1109,7 +1109,7 @@ <h3 id="quality-control-arguments">Quality Control Arguments<a class="headerlink
 <td style="text-align: left;">-r</td>
 <td style="text-align: left;">--coverage_regions</td>
 <td style="text-align: left;">A BED file containing the regions to calculate percent coverage for</td>
-<td style="text-align: left;"><a href="https://github.com/theiagen/tbp-parser/blob/v1.6.0/data/tbdb-modified-regions.bed">/data/tbdb-modified-regions.md</a></td>
+<td style="text-align: left;"><a href="https://github.com/theiagen/tbp-parser/blob/main/data/tbdb-modified-regions.bed">/data/tbdb-modified-regions.md</a></td>
 </tr>
 </tbody>
 </table>
@@ -1164,7 +1164,7 @@ <h3 id="lims-arguments">LIMS Arguments<a class="headerlink" href="#lims-argument
 </tbody>
 </table>
 <h3 id="tngs-specific-arguments">tNGS-specific Arguments<a class="headerlink" href="#tngs-specific-arguments" title="Permanent link">&para;</a></h3>
-<p>These options are primarily used for tNGS data, although all frequency arguments are compatible with WGS data.</p>
+<p>These options are primarily used for tNGS data, although all frequency and read support arguments are compatible with WGS data.</p>
 <table>
 <thead>
 <tr>
@@ -1182,7 +1182,7 @@ <h3 id="tngs-specific-arguments">tNGS-specific Arguments<a class="headerlink" hr
 <tr>
 <td style="text-align: left;">--tngs_expert_regions</td>
 <td style="text-align: left;">A BED file containing the regions to calculate coverage for expert rule regions. This is used to determine coverage quality in the regions where resistance-conferring mutations are found, or where a CDC expert rule is applied. This is not used for QC purposes</td>
-<td style="text-align: left;"><a href="https://github.com/theiagen/tbp-parser/blob/v1.6.0/data/tbdb-expert-regions.bed">/data/tbdb-expert-regions.bed</a></td>
+<td style="text-align: left;"><a href="https://github.com/theiagen/tbp-parser/blob/main/data/tbdb-expert-regions.bed">/data/tbdb-expert-regions.bed</a></td>
 </tr>
 <tr>
 <td style="text-align: left;">--rrs_frequency</td>
@@ -1217,11 +1217,28 @@ <h3 id="tngs-specific-arguments">tNGS-specific Arguments<a class="headerlink" hr
 </tbody>
 </table>
 <h3 id="logging-arguments">Logging Arguments<a class="headerlink" href="#logging-arguments" title="Permanent link">&para;</a></h3>
-<p>These options change the verbosity of the <code>stdout</code> log
-| Name | Description | Default Value |
-| :--- | :---------- | :------------ |
-| --verbose | Increases the output verbosity to describe which stage of the analysis is currently running | false |
-| --debug | The highest level of output verbosity detailing every step of the analysis and logic implemented; overwrites --verbose | false |</p>
+<p>These options change the verbosity of the <code>stdout</code> log</p>
+<table>
+<thead>
+<tr>
+<th style="text-align: left;">Name</th>
+<th style="text-align: left;">Description</th>
+<th style="text-align: left;">Default Value</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td style="text-align: left;">--verbose</td>
+<td style="text-align: left;">Increases the output verbosity to describe which stage of the analysis is currently running</td>
+<td style="text-align: left;">false</td>
+</tr>
+<tr>
+<td style="text-align: left;">--debug</td>
+<td style="text-align: left;">The highest level of output verbosity detailing every step of the analysis and logic implemented; overwrites --verbose</td>
+<td style="text-align: left;">false</td>
+</tr>
+</tbody>
+</table>
 
 
 
@@ -1244,7 +1261,7 @@ <h3 id="logging-arguments">Logging Arguments<a class="headerlink" href="#logging
     <span class="md-icon" title="Last update">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg>
     </span>
-    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-08-20</span>
+    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-11-21</span>
   </span>