Merge branch 'release/v1.2.9'

dputhier · Jun 17, 2021 · 494bcb1 · 494bcb1
2 parents c33ee3a + 19f307b
commit 494bcb1
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diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png
diff --git a/docs/_images/example_02.png b/docs/_images/example_02.png
diff --git a/docs/_images/example_05.png b/docs/_images/example_05.png
diff --git a/docs/_images/example_06.png b/docs/_images/example_06.png
diff --git a/docs/_images/example_06b.png b/docs/_images/example_06b.png
diff --git a/docs/_images/example_08.png b/docs/_images/example_08.png
diff --git a/docs/_images/example_13.png b/docs/_images/example_13.png
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.2.8',
+    VERSION: '1.2.9',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/example_01.png b/docs/_static/example_01.png
diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png
diff --git a/docs/_static/example_06.png b/docs/_static/example_06.png
diff --git a/docs/_static/example_06b.png b/docs/_static/example_06b.png
diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png
diff --git a/docs/_static/example_13.png b/docs/_static/example_13.png
diff --git a/docs/_static/example_pa_01.pdf b/docs/_static/example_pa_01.pdf
diff --git a/docs/_static/example_pa_02.pdf b/docs/_static/example_pa_02.pdf
diff --git a/docs/_static/example_pa_03.pdf b/docs/_static/example_pa_03.pdf
diff --git a/docs/_static/example_pa_04.pdf b/docs/_static/example_pa_04.pdf
diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf
diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf
diff --git a/docs/about.html b/docs/about.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Warning about supported GTF file formats &#8212; gtftk 1.2.8 documentation</title>
+    <title>Warning about supported GTF file formats &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to pygtftk documentation page"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Warning about supported GTF file formats</a></li> 
       </ul>
     </div>  
@@ -201,13 +201,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to pygtftk documentation page"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Warning about supported GTF file formats</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/annotation.html b/docs/annotation.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘annotation’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘annotation’ &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="conversion.html" title="Commands from section ‘conversion’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘annotation’</a></li> 
       </ul>
     </div>  
@@ -475,13 +475,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="conversion.html" title="Commands from section ‘conversion’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘annotation’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/api.html b/docs/api.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Help on Python package (pygtftk) &#8212; gtftk 1.2.8 documentation</title>
+    <title>Help on Python package (pygtftk) &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="miscellaneous.html" title="Commands from section ‘miscellaneous’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Help on Python package (pygtftk)</a></li> 
       </ul>
     </div>  
@@ -1042,7 +1042,7 @@ <h1>Help on Python package (pygtftk)<a class="headerlink" href="#help-on-python-
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">pygtftk.gtf_interface</span> <span class="kn">import</span> <span class="n">GTF</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">a_file</span> <span class="o">=</span> <span class="n">get_example_file</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">a_gtf</span> <span class="o">=</span> <span class="n">GTF</span><span class="p">(</span><span class="n">a_file</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a_gtf</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">res</span> <span class="o">=</span> <span class="n">a_gtf</span><span class="o">.</span><span class="n">head</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">returned</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </dd></dl>
@@ -1443,7 +1443,7 @@ <h1>Help on Python package (pygtftk)<a class="headerlink" href="#help-on-python-
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">pygtftk.gtf_interface</span> <span class="kn">import</span> <span class="n">GTF</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">a_file</span> <span class="o">=</span> <span class="n">get_example_file</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">a_gtf</span> <span class="o">=</span> <span class="n">GTF</span><span class="p">(</span><span class="n">a_file</span><span class="p">)</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">a_gtf</span><span class="o">.</span><span class="n">tail</span><span class="p">(</span><span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">res</span> <span class="o">=</span> <span class="n">a_gtf</span><span class="o">.</span><span class="n">tail</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">returned</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </dd></dl>
@@ -3681,13 +3681,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="miscellaneous.html" title="Commands from section ‘miscellaneous’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Help on Python package (pygtftk)</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/bwig_coverage.html b/docs/bwig_coverage.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>The pygtftk.bwig.bw_coverage module &#8212; gtftk 1.2.8 documentation</title>
+    <title>The pygtftk.bwig.bw_coverage module &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="api.html" title="Help on Python package (pygtftk)"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">The pygtftk.bwig.bw_coverage module</a></li> 
       </ul>
     </div>  
@@ -178,13 +178,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="api.html" title="Help on Python package (pygtftk)"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">The pygtftk.bwig.bw_coverage module</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/conversion.html b/docs/conversion.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘conversion’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘conversion’ &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selection.html" title="Commands from section ‘selection’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘conversion’</a></li> 
       </ul>
     </div>  
@@ -320,13 +320,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="selection.html" title="Commands from section ‘selection’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘conversion’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>

diff --git a/docs/coordinates.html b/docs/coordinates.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘coordinates’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘coordinates’ &#8212; gtftk 1.2.9 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/nature.css" />
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="ologram.html" title="Commands from section ‘ologram’"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘coordinates’</a></li> 
       </ul>
     </div>  
@@ -423,13 +423,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="ologram.html" title="Commands from section ‘ologram’"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Commands from section ‘coordinates’</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, F. Lopez and D. Puthier.
-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
       Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.0.2.
     </div>
   </body>