Bump version to 0.19.0; rebuild docs

docs/api/seismicrna.core.html

@@ -374,7 +374,6 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.count_total_reads"><code class="docutils literal notranslate"><span class="pre">count_total_reads()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.flagstat_cmd"><code class="docutils literal notranslate"><span class="pre">flagstat_cmd()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.idxstats_cmd"><code class="docutils literal notranslate"><span class="pre">idxstats_cmd()</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.index_fasta_cmd"><code class="docutils literal notranslate"><span class="pre">index_fasta_cmd()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.index_xam_cmd"><code class="docutils literal notranslate"><span class="pre">index_xam_cmd()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.parse_flagstat"><code class="docutils literal notranslate"><span class="pre">parse_flagstat()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.parse_idxstats"><code class="docutils literal notranslate"><span class="pre">parse_idxstats()</span></code></a></li>
@@ -383,6 +382,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this hea
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.sort_xam_cmd"><code class="docutils literal notranslate"><span class="pre">sort_xam_cmd()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.view_xam_cmd"><code class="docutils literal notranslate"><span class="pre">view_xam_cmd()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.xam_paired"><code class="docutils literal notranslate"><span class="pre">xam_paired()</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.core.ngs.html#seismicrna.core.ngs.xam.xam_to_fastq_cmd"><code class="docutils literal notranslate"><span class="pre">xam_to_fastq_cmd()</span></code></a></li>
 </ul>
 </li>
 </ul>
@@ -3294,7 +3294,7 @@ <h3>Purpose<a class="headerlink" href="#purpose" title="Link to this heading">
 
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.tmp.release_to_out">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.tmp.</span></span><span class="sig-name descname"><span class="pre">release_to_out</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out_dir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">release_dir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.tmp.release_to_out" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.tmp.</span></span><span class="sig-name descname"><span class="pre">release_to_out</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">out_dir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">release_dir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_path</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/pathlib.html#pathlib.Path" title="(in Python v3.12)"><span class="pre">Path</span></a></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.tmp.release_to_out" title="Link to this definition"></a></dt>
 <dd><p>Move temporary path(s) to the output directory.</p>
 </dd></dl>
 
@@ -3361,12 +3361,12 @@ <h3>Purpose<a class="headerlink" href="#purpose" title="Link to this heading">
 <p id="module-seismicrna.core.version">Version information for SEISMIC-RNA</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.format_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">18</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prtag</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">19</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prtag</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Link to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.parse_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.18.2'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.19.0'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Link to this definition"></a></dt>
 <dd><p>Major and minor versions, patch, and pre-release tag.</p>
 </dd></dl>