Bump version to 0.19.2; rebuild docs

docs/_sources/api/seismicrna.align.tests.rst.txt

@@ -16,7 +16,7 @@ Submodules
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.tests.sim_test
+.. automodule:: seismicrna.align.tests.write_test
    :members:
    :undoc-members:
    :show-inheritance:
@@ -26,3 +26,9 @@ Submodules
    :members:
    :undoc-members:
    :show-inheritance:
+
+
+.. automodule:: seismicrna.align.tests.xamops_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.core.ngs.tests.rst.txt

@@ -14,3 +14,9 @@ Submodules
    :members:
    :undoc-members:
    :show-inheritance:
+
+
+.. automodule:: seismicrna.core.ngs.tests.xam_test
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_sources/api/seismicrna.relate.tests.rst.txt

@@ -10,6 +10,12 @@ Submodules
 ----------
 
 
+.. automodule:: seismicrna.relate.tests.sam_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.relate.tests.sim_test
    :members:
    :undoc-members:

docs/api/seismicrna.align.tests.html

@@ -152,6 +152,32 @@
 
 </dd></dl>
 
+<dl class="py class" id="module-seismicrna.align.tests.write_test">
+<dt class="sig sig-object py" id="seismicrna.align.tests.write_test.TestCalcFlags">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">seismicrna.align.tests.write_test.</span></span><span class="sig-name descname"><span class="pre">TestCalcFlags</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">methodName</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'runTest'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.write_test.TestCalcFlags" title="Link to this definition"></a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">TestCase</span></code></p>
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.write_test.TestCalcFlags.test_f1r2_paired">
+<span class="sig-name descname"><span class="pre">test_f1r2_paired</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.write_test.TestCalcFlags.test_f1r2_paired" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.write_test.TestCalcFlags.test_f1r2_single">
+<span class="sig-name descname"><span class="pre">test_f1r2_single</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.write_test.TestCalcFlags.test_f1r2_single" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.write_test.TestCalcFlags.test_f2r1_paired">
+<span class="sig-name descname"><span class="pre">test_f2r1_paired</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.write_test.TestCalcFlags.test_f2r1_paired" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.write_test.TestCalcFlags.test_f2r1_single">
+<span class="sig-name descname"><span class="pre">test_f2r1_single</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.write_test.TestCalcFlags.test_f2r1_single" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
 <p id="module-seismicrna.align.tests.xamgen_test">Tests for Alignment XAM Generation Module</p>
 <hr class="docutils" />
 <dl class="py class">
@@ -223,6 +249,57 @@
 
 </dd></dl>
 
+<dl class="py class" id="module-seismicrna.align.tests.xamops_test">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds">
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">seismicrna.align.tests.xamops_test.</span></span><span class="sig-name descname"><span class="pre">TestFlagsCmds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">methodName</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'runTest'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds" title="Link to this definition"></a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">TestCase</span></code></p>
+<dl class="py attribute">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.TMP_PFX">
+<span class="sig-name descname"><span class="pre">TMP_PFX</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PosixPath('x/y/z')</span></em><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.TMP_PFX" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.XAM_INP">
+<span class="sig-name descname"><span class="pre">XAM_INP</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PosixPath('a/b/c.bam')</span></em><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.XAM_INP" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py attribute">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.XAM_OUT">
+<span class="sig-name descname"><span class="pre">XAM_OUT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">PosixPath('x/y/z.bam')</span></em><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.XAM_OUT" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_0_flags_bam">
+<span class="sig-name descname"><span class="pre">test_0_flags_bam</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_0_flags_bam" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_0_flags_none">
+<span class="sig-name descname"><span class="pre">test_0_flags_none</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_0_flags_none" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_1_flag_bam">
+<span class="sig-name descname"><span class="pre">test_1_flag_bam</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_1_flag_bam" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_1_flag_none">
+<span class="sig-name descname"><span class="pre">test_1_flag_none</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_1_flag_none" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_2_flags_bam">
+<span class="sig-name descname"><span class="pre">test_2_flags_bam</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_2_flags_bam" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="seismicrna.align.tests.xamops_test.TestFlagsCmds.test_2_flags_none">
+<span class="sig-name descname"><span class="pre">test_2_flags_none</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.align.tests.xamops_test.TestFlagsCmds.test_2_flags_none" title="Link to this definition"></a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
 </section>
 </section>