diff --git a/docs/_images/example_01.png b/docs/_images/example_01.png
index 74c1bed..1ee485d 100644
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diff --git a/docs/_images/example_02.png b/docs/_images/example_02.png
index 37002ee..2eb8ccf 100644
Binary files a/docs/_images/example_02.png and b/docs/_images/example_02.png differ
diff --git a/docs/_images/example_05.png b/docs/_images/example_05.png
index da9dc6f..b7d390b 100644
Binary files a/docs/_images/example_05.png and b/docs/_images/example_05.png differ
diff --git a/docs/_images/example_06.png b/docs/_images/example_06.png
index 0ef2243..5dfcdf5 100644
Binary files a/docs/_images/example_06.png and b/docs/_images/example_06.png differ
diff --git a/docs/_images/example_06b.png b/docs/_images/example_06b.png
index ed0dde8..e86c45e 100644
Binary files a/docs/_images/example_06b.png and b/docs/_images/example_06b.png differ
diff --git a/docs/_images/example_08.png b/docs/_images/example_08.png
index afdd3e7..cc0d9df 100644
Binary files a/docs/_images/example_08.png and b/docs/_images/example_08.png differ
diff --git a/docs/_images/example_13.png b/docs/_images/example_13.png
index cfe717e..918c679 100644
Binary files a/docs/_images/example_13.png and b/docs/_images/example_13.png differ
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 2e45e84..f29af04 100644
--- 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
index 1ee485d..f4ccda1 100644
Binary files a/docs/_static/example_01.png and b/docs/_static/example_01.png differ
diff --git a/docs/_static/example_02.png b/docs/_static/example_02.png
index 2eb8ccf..22a2bfe 100644
Binary files a/docs/_static/example_02.png and b/docs/_static/example_02.png differ
diff --git a/docs/_static/example_06.png b/docs/_static/example_06.png
index 5dfcdf5..0ef2243 100644
Binary files a/docs/_static/example_06.png and b/docs/_static/example_06.png differ
diff --git a/docs/_static/example_06b.png b/docs/_static/example_06b.png
index e86c45e..a87c7e2 100644
Binary files a/docs/_static/example_06b.png and b/docs/_static/example_06b.png differ
diff --git a/docs/_static/example_08.png b/docs/_static/example_08.png
index cc0d9df..ba46c29 100644
Binary files a/docs/_static/example_08.png and b/docs/_static/example_08.png differ
diff --git a/docs/_static/example_13.png b/docs/_static/example_13.png
index 918c679..9172d06 100644
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diff --git a/docs/_static/example_pa_01.pdf b/docs/_static/example_pa_01.pdf
index 9c9c33e..db3b912 100644
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diff --git a/docs/_static/example_pa_02.pdf b/docs/_static/example_pa_02.pdf
index 8226f96..8b8e868 100644
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diff --git a/docs/_static/example_pa_03.pdf b/docs/_static/example_pa_03.pdf
index a8b8906..9303b3a 100644
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diff --git a/docs/_static/example_pa_04.pdf b/docs/_static/example_pa_04.pdf
index 0d33b73..7b501d3 100644
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diff --git a/docs/_static/merge_ologram_stats_01.pdf b/docs/_static/merge_ologram_stats_01.pdf
index 1314de4..86454df 100644
Binary files a/docs/_static/merge_ologram_stats_01.pdf and b/docs/_static/merge_ologram_stats_01.pdf differ
diff --git a/docs/_static/treeified.pdf b/docs/_static/treeified.pdf
index d146b3a..e69de29 100644
Binary files a/docs/_static/treeified.pdf and b/docs/_static/treeified.pdf differ
diff --git a/docs/about.html b/docs/about.html
index c0e0322..4ad1a0e 100644
--- 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
index 2ffaa01..186d35a 100644
--- 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
index 614f007..0f38804 100644
--- 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
index 3139370..0133a50 100644
--- 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
index a49a8ef..dba58e0 100644
--- 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
index f0a83b3..3ef4f00 100644
--- 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>
diff --git a/docs/coverage.html b/docs/coverage.html
index 6589a0a..6dbadd2 100644
--- a/docs/coverage.html
+++ b/docs/coverage.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘coverage’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘coverage’ &#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="sequence.html" title="Commands from section ‘sequence’"
              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 ‘coverage’</a></li> 
       </ul>
     </div>  
@@ -216,22 +216,22 @@ <h2>profile<a class="headerlink" href="#profile" title="Permalink to this headli
 <p><strong>Basic profiles</strong></p>
 <p>A simple overlayed profile of all epigenetic marks around promoter. Here <em>—group-by</em> is, by default set to <em>bwig</em> and <em>—facet-var</em> is set to None. Thus a single plot with several lines corresponding to bwig coverage is obtained.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -o profile_prom -pf png -if  example_01.png
- |-- 14:52-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_01.png"><img alt="_images/example_01.png" src="_images/example_01.png" style="width: 75%;" /></a>
 <p>Changing colors and applying color order can be done using the following syntax:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -c &#39;red,blue,violet&#39; -d H3K79me,H3K4me3,H3K36me3 -o profile_prom -pf png -if  example_01b.png
- |-- 14:52-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_01b.png"><img alt="_images/example_01b.png" src="_images/example_01b.png" style="width: 75%;" /></a>
 <p>Transcript coverage is obtained using the <em>mini_real_tx.zip</em> matrix. This provides a simple overlayed profile of all epigenetic marks along the transcript body extended in 5’ and 3’ regions:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx.zip -o profile_tx -pf png -if  example_02.png
- |-- 14:52-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-WARNING-profile : --group-by not set. Choosing &#39;bwig&#39;.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_02.png"><img alt="_images/example_02.png" src="_images/example_02.png" style="width: 75%;" /></a>
@@ -239,118 +239,118 @@ <h2>profile<a class="headerlink" href="#profile" title="Permalink to this headli
 <p>Faceted plot of epigenetic profiles. The groups (i.e colors/lines) can be set to bwig classes and the facets to transcript classes. Things can be simply done by providing an additional file containing the transcript and their associated classes.</p>
 <p><strong>Example:</strong></p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -f tx_classes -g bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_05.png -e -V 2 -fc 2
- |-- 14:52-DEBUG-profile : Using pandas version 1.2.4
- |-- 14:52-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:52-DEBUG-profile : Using numpy version 1.20.3
- |-- 14:52-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:52-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:52-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:52-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_wr7zmkxq
- |-- 14:52-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_wr7zmkxq
- |-- 14:52-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_wr7zmkxq/mini_real_promoter
- |-- 14:52-INFO-profile : Getting configuration info from input file.
- |-- 14:52-INFO-profile : Reading transcript file.
- |-- 14:52-INFO-profile : Deleting duplicates in transcript-file.
- |-- 14:52-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 14:52-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 14:52-DEBUG-profile : Color order : [&#39;H3K36me3&#39;, &#39;H3K79me&#39;, &#39;H3K4me3&#39;]
- |-- 14:52-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 14:52-INFO-profile : Searching coverage columns.
- |-- 14:52-INFO-profile : Melting.
- |-- 14:52-INFO-profile : Ceiling
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 14:52-INFO-profile : Computing column ordering.
- |-- 14:52-INFO-profile : Preparing diagram
- |-- 14:52-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:52-INFO-profile : Preparing x axis
- |-- 14:52-INFO-profile : facet_col 2
- |-- 14:52-INFO-profile : Page width set to 6
- |-- 14:52-INFO-profile : Page height set to 5.0
- |-- 14:52-INFO-profile : Saving diagram to file : example_05.png
- |-- 14:52-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:52-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_wr7zmkxq
+ |-- 11:02-DEBUG-profile : Using pandas version 1.2.4
+ |-- 11:02-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 11:02-DEBUG-profile : Using numpy version 1.20.3
+ |-- 11:02-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 11:02-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 11:02-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 11:02-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_cxvl97ol
+ |-- 11:02-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_cxvl97ol
+ |-- 11:02-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_cxvl97ol/mini_real_promoter
+ |-- 11:02-INFO-profile : Getting configuration info from input file.
+ |-- 11:02-INFO-profile : Reading transcript file.
+ |-- 11:02-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 11:02-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 11:02-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 11:02-DEBUG-profile : Color order : [&#39;H3K36me3&#39;, &#39;H3K79me&#39;, &#39;H3K4me3&#39;]
+ |-- 11:02-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:02-INFO-profile : Searching coverage columns.
+ |-- 11:02-INFO-profile : Melting.
+ |-- 11:02-INFO-profile : Ceiling
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-INFO-profile : Computing column ordering.
+ |-- 11:02-INFO-profile : Preparing diagram
+ |-- 11:02-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:02-INFO-profile : Preparing x axis
+ |-- 11:02-INFO-profile : facet_col 2
+ |-- 11:02-INFO-profile : Page width set to 6
+ |-- 11:02-INFO-profile : Page height set to 5.0
+ |-- 11:02-INFO-profile : Saving diagram to file : example_05.png
+ |-- 11:02-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:02-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_cxvl97ol
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_05.png"><img alt="_images/example_05.png" src="_images/example_05.png" style="width: 75%;" /></a>
 <p>Alternatively, the groups can be set to chromosomes or transcript classes:</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -g tx_classes -f bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_06.png -V 2 -nm ranging
- |-- 14:52-DEBUG-profile : Using pandas version 1.2.4
- |-- 14:52-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:52-DEBUG-profile : Using numpy version 1.20.3
- |-- 14:52-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:52-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:52-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:52-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_px_ama3f
- |-- 14:52-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_px_ama3f
- |-- 14:52-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_px_ama3f/mini_real_promoter
- |-- 14:52-INFO-profile : Getting configuration info from input file.
- |-- 14:52-INFO-profile : Reading transcript file.
- |-- 14:52-INFO-profile : Deleting duplicates in transcript-file.
- |-- 14:52-INFO-profile : Checking how many transcripts where found in the transcript list.
- |-- 14:52-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
- |-- 14:52-DEBUG-profile : Color order : [&#39;antisense&#39;, &#39;protein_coding&#39;, &#39;lincRNA&#39;]
- |-- 14:52-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
- |-- 14:52-INFO-profile : Searching coverage columns.
- |-- 14:52-INFO-profile : Melting.
- |-- 14:52-INFO-profile : Ceiling
- |-- 14:52-INFO-profile : Normalizing (ranging)
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 14:52-INFO-profile : Computing column ordering.
- |-- 14:52-INFO-profile : Preparing diagram
- |-- 14:52-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:52-INFO-profile : Preparing x axis
- |-- 14:52-INFO-profile : facet_col 3
- |-- 14:52-INFO-profile : Page width set to 9
- |-- 14:52-INFO-profile : Page height set to 2.0
- |-- 14:52-INFO-profile : Saving diagram to file : example_06.png
- |-- 14:52-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:52-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_px_ama3f
+ |-- 11:02-DEBUG-profile : Using pandas version 1.2.4
+ |-- 11:02-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 11:02-DEBUG-profile : Using numpy version 1.20.3
+ |-- 11:02-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 11:02-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 11:02-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 11:02-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f198it4c
+ |-- 11:02-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f198it4c
+ |-- 11:02-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f198it4c/mini_real_promoter
+ |-- 11:02-INFO-profile : Getting configuration info from input file.
+ |-- 11:02-INFO-profile : Reading transcript file.
+ |-- 11:02-INFO-profile : Deleting duplicates in transcript-file.
+ |-- 11:02-INFO-profile : Checking how many transcripts where found in the transcript list.
+ |-- 11:02-INFO-profile : Keeping 804 transcript out of 833 in input transcript list.
+ |-- 11:02-DEBUG-profile : Color order : [&#39;lincRNA&#39;, &#39;antisense&#39;, &#39;protein_coding&#39;]
+ |-- 11:02-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#00bb00&#39;, &#39;#cccccc&#39;]
+ |-- 11:02-INFO-profile : Searching coverage columns.
+ |-- 11:02-INFO-profile : Melting.
+ |-- 11:02-INFO-profile : Ceiling
+ |-- 11:02-INFO-profile : Normalizing (ranging)
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-INFO-profile : Computing column ordering.
+ |-- 11:02-INFO-profile : Preparing diagram
+ |-- 11:02-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:02-INFO-profile : Preparing x axis
+ |-- 11:02-INFO-profile : facet_col 3
+ |-- 11:02-INFO-profile : Page width set to 9
+ |-- 11:02-INFO-profile : Page height set to 2.0
+ |-- 11:02-INFO-profile : Saving diagram to file : example_06.png
+ |-- 11:02-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:02-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_f198it4c
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_06.png"><img alt="_images/example_06.png" src="_images/example_06.png" style="width: 75%;" /></a>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_promoter.zip -g chrom -f bwig  -t tx_classes.txt -o profile_prom  -pf png -if  example_06b.png -V 2 -nm ranging
- |-- 14:52-DEBUG-profile : Using pandas version 1.2.4
- |-- 14:52-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
- |-- 14:52-DEBUG-profile : Using numpy version 1.20.3
- |-- 14:52-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
- |-- 14:52-DEBUG-profile : Using plotnine version 0.8.0
- |-- 14:52-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
- |-- 14:52-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_1d2wsyma
- |-- 14:52-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_1d2wsyma
- |-- 14:52-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_1d2wsyma/mini_real_promoter
- |-- 14:52-INFO-profile : Getting configuration info from input file.
- |-- 14:52-DEBUG-profile : Color order : [&#39;chr21&#39;, &#39;chr11&#39;, &#39;chr13&#39;, &#39;chr22&#39;, &#39;chr12&#39;, &#39;chrX&#39;, &#39;chr8&#39;, &#39;chr18&#39;, &#39;chr4&#39;, &#39;chr5&#39;, &#39;chr7&#39;, &#39;chr2&#39;, &#39;chr17&#39;, &#39;chr6&#39;, &#39;chr19&#39;, &#39;chr3&#39;, &#39;chr1&#39;, &#39;chr9&#39;, &#39;chr10&#39;, &#39;chr16&#39;, &#39;chr15&#39;, &#39;chr14&#39;, &#39;chr20&#39;]
- |-- 14:52-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#6c007c&#39;, &#39;#850096&#39;, &#39;#2500a5&#39;, &#39;#0000ca&#39;, &#39;#0041dd&#39;, &#39;#0086dd&#39;, &#39;#009fca&#39;, &#39;#00aaa1&#39;, &#39;#00a76f&#39;, &#39;#009c00&#39;, &#39;#00bb00&#39;, &#39;#00da00&#39;, &#39;#00f900&#39;, &#39;#88ff00&#39;, &#39;#dbf400&#39;, &#39;#f7db00&#39;, &#39;#ffb500&#39;, &#39;#ff6100&#39;, &#39;#f60000&#39;, &#39;#da0000&#39;, &#39;#cc1313&#39;, &#39;#cccccc&#39;]
- |-- 14:52-INFO-profile : Searching coverage columns.
- |-- 14:52-INFO-profile : Melting.
- |-- 14:52-INFO-profile : Ceiling
- |-- 14:52-INFO-profile : Normalizing (ranging)
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 14:53-INFO-profile : Computing column ordering.
- |-- 14:53-INFO-profile : Preparing diagram
- |-- 14:53-INFO-profile : Theming and ordering. Please be patient...
- |-- 14:53-INFO-profile : Preparing x axis
- |-- 14:53-INFO-profile : facet_col 3
- |-- 14:53-INFO-profile : Page width set to 9
- |-- 14:53-INFO-profile : Page height set to 2.0
- |-- 14:53-INFO-profile : Saving diagram to file : example_06b.png
- |-- 14:53-INFO-profile : Be patient. This may be long for large datasets.
- |-- 14:53-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_1d2wsyma
+ |-- 11:02-DEBUG-profile : Using pandas version 1.2.4
+ |-- 11:02-DEBUG-profile : Pandas location /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pandas/__init__.py
+ |-- 11:02-DEBUG-profile : Using numpy version 1.20.3
+ |-- 11:02-DEBUG-profile : Pandas numpy /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/numpy/__init__.py
+ |-- 11:02-DEBUG-profile : Using plotnine version 0.8.0
+ |-- 11:02-DEBUG-profile : Pandas plotnine /Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/plotnine/__init__.py
+ |-- 11:02-DEBUG-profile : Creating directory : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_woyx5gcz
+ |-- 11:02-DEBUG-profile : Uncompressing : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_woyx5gcz
+ |-- 11:02-DEBUG-profile : Reading : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_woyx5gcz/mini_real_promoter
+ |-- 11:02-INFO-profile : Getting configuration info from input file.
+ |-- 11:02-DEBUG-profile : Color order : [&#39;chr1&#39;, &#39;chr6&#39;, &#39;chr15&#39;, &#39;chr7&#39;, &#39;chr9&#39;, &#39;chr5&#39;, &#39;chr8&#39;, &#39;chr14&#39;, &#39;chr11&#39;, &#39;chr19&#39;, &#39;chr3&#39;, &#39;chr4&#39;, &#39;chr10&#39;, &#39;chr16&#39;, &#39;chr2&#39;, &#39;chrX&#39;, &#39;chr17&#39;, &#39;chr21&#39;, &#39;chr12&#39;, &#39;chr18&#39;, &#39;chr22&#39;, &#39;chr13&#39;, &#39;chr20&#39;]
+ |-- 11:02-DEBUG-profile : Profile color : [&#39;#000000&#39;, &#39;#6c007c&#39;, &#39;#850096&#39;, &#39;#2500a5&#39;, &#39;#0000ca&#39;, &#39;#0041dd&#39;, &#39;#0086dd&#39;, &#39;#009fca&#39;, &#39;#00aaa1&#39;, &#39;#00a76f&#39;, &#39;#009c00&#39;, &#39;#00bb00&#39;, &#39;#00da00&#39;, &#39;#00f900&#39;, &#39;#88ff00&#39;, &#39;#dbf400&#39;, &#39;#f7db00&#39;, &#39;#ffb500&#39;, &#39;#ff6100&#39;, &#39;#f60000&#39;, &#39;#da0000&#39;, &#39;#cc1313&#39;, &#39;#cccccc&#39;]
+ |-- 11:02-INFO-profile : Searching coverage columns.
+ |-- 11:02-INFO-profile : Melting.
+ |-- 11:02-INFO-profile : Ceiling
+ |-- 11:02-INFO-profile : Normalizing (ranging)
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-INFO-profile : Computing column ordering.
+ |-- 11:02-INFO-profile : Preparing diagram
+ |-- 11:02-INFO-profile : Theming and ordering. Please be patient...
+ |-- 11:02-INFO-profile : Preparing x axis
+ |-- 11:02-INFO-profile : facet_col 3
+ |-- 11:02-INFO-profile : Page width set to 9
+ |-- 11:02-INFO-profile : Page height set to 2.0
+ |-- 11:02-INFO-profile : Saving diagram to file : example_06b.png
+ |-- 11:02-INFO-profile : Be patient. This may be long for large datasets.
+ |-- 11:02-DEBUG-profile : Deleting temp file : /var/folders/zy/wl3dj2_n76zfc8sdvny1q06c0000gn/T/profile_matrix__pygtftk_woyx5gcz
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_06b.png"><img alt="_images/example_06b.png" src="_images/example_06b.png" style="width: 75%;" /></a>
 <p>Note that facets may also be associated to epigenetic marks. In this case each the –group-by can be set to <em>tx_classes</em> or <em>chrom</em>.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx.zip -g tx_classes -t tx_classes.txt -f bwig  -o profile_tx -pf png -if  example_07.png -w -nm ranging
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 14:53-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {&#39;ha&#39;} specified two times.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:02-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {&#39;ha&#39;} specified two times.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_07.png"><img alt="_images/example_07.png" src="_images/example_07.png" style="width: 75%;" /></a>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk profile -D -i mini_real_tx.zip -g chrom -f bwig  -o profile_tx -pf png -if  example_08.png  -w -nm ranging
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
-/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.8-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
- |-- 14:53-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {&#39;ha&#39;} specified two times.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:815: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+/Users/puthier/anaconda3/envs/python_dev_388/lib/python3.8/site-packages/pygtftk-1.2.9-py3.8-macosx-10.9-x86_64.egg/pygtftk/plugins/profile.py:890: FutureWarning: Index.ravel returning ndarray is deprecated; in a future version this will return a view on self.
+ |-- 11:03-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {&#39;ha&#39;} specified two times.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_08.png"><img alt="_images/example_08.png" src="_images/example_08.png" style="width: 75%;" /></a>
@@ -473,13 +473,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="sequence.html" title="Commands from section ‘sequence’"
              >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 ‘coverage’</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/developers.html b/docs/developers.html
index c2a5bee..0584505 100644
--- a/docs/developers.html
+++ b/docs/developers.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Writing your own commands &#8212; gtftk 1.2.8 documentation</title>
+    <title>Writing your own commands &#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" />
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@@ -41,7 +41,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="bwig_coverage.html" title="The pygtftk.bwig.bw_coverage module"
              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="">Writing your own commands</a></li> 
       </ul>
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@@ -232,13 +232,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="bwig_coverage.html" title="The pygtftk.bwig.bw_coverage module"
              >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="">Writing your own commands</a></li> 
       </ul>
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     <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.
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     </div>
   </body>
diff --git a/docs/editing.html b/docs/editing.html
index 86c4e2d..c40aac4 100644
--- a/docs/editing.html
+++ b/docs/editing.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘Editing’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘Editing’ &#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" />
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@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="information.html" title="Commands from section ‘information’"
              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 ‘Editing’</a></li> 
       </ul>
     </div>  
@@ -431,7 +431,7 @@ <h2>discretize_key<a class="headerlink" href="#discretize-key" title="Permalink
 </pre></div>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk join_attr -i simple.gtf -j simple.join_mat -k gene_id -m | gtftk discretize_key -k S1 -d S1_d -n 2 -l A,B  | gtftk select_by_key -k feature -v gene
- |-- 14:53-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;]
+ |-- 11:03-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;]
 chr1	gtftk	gene	125	138	.	+	.	gene_id &quot;G0001&quot;;
 chr1	gtftk	gene	180	189	.	+	.	gene_id &quot;G0002&quot;;
 chr1	gtftk	gene	50	61	.	-	.	gene_id &quot;G0003&quot;; S1 &quot;0.2322&quot;; S2 &quot;0.4&quot;; S1_d &quot;A&quot;;
@@ -450,7 +450,7 @@ <h2>discretize_key<a class="headerlink" href="#discretize-key" title="Permalink
 <p>The <em>profile</em> command that could be used to asses the associated epigenetic marks of these 10 gene classes.</p>
 </div>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t gene | gtftk discretize_key -k exprs -p -d exprs_class -n 10 -l A,B,C,D,E,F,G,H,I,J  | gtftk tabulate -k exprs_class -Hn | sort | uniq -c
- |-- 14:53-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;, &#39;C&#39;, &#39;D&#39;, &#39;E&#39;, &#39;F&#39;, &#39;G&#39;, &#39;H&#39;, &#39;I&#39;, &#39;J&#39;]
+ |-- 11:03-INFO-discretize_key : Categories: [&#39;A&#39;, &#39;B&#39;, &#39;C&#39;, &#39;D&#39;, &#39;E&#39;, &#39;F&#39;, &#39;G&#39;, &#39;H&#39;, &#39;I&#39;, &#39;J&#39;]
   96 A
   83 B
   89 C
@@ -567,13 +567,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="information.html" title="Commands from section ‘information’"
              >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 ‘Editing’</a></li> 
       </ul>
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     <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/example_01.png b/docs/example_01.png
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diff --git a/docs/example_06.png b/docs/example_06.png
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diff --git a/docs/example_pa_01.pdf b/docs/example_pa_01.pdf
index 77f68b3..9c9c33e 100644
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diff --git a/docs/example_pa_02.pdf b/docs/example_pa_02.pdf
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diff --git a/docs/example_pa_03.pdf b/docs/example_pa_03.pdf
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diff --git a/docs/example_pa_04.pdf b/docs/example_pa_04.pdf
index ca8b7d0..0d33b73 100644
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diff --git a/docs/genindex.html b/docs/genindex.html
index 2dc8b71..3ccb722 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Index &#8212; gtftk 1.2.8 documentation</title>
+    <title>Index &#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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</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="">Index</a></li> 
       </ul>
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@@ -729,13 +729,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</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="">Index</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/gtftk_args.html b/docs/gtftk_args.html
index 1ed4540..19b64b2 100644
--- a/docs/gtftk_args.html
+++ b/docs/gtftk_args.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Help on gtftk Unix commands &#8212; gtftk 1.2.8 documentation</title>
+    <title>Help on gtftk Unix commands &#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" />
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@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing pygtftk/gtftk"
              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 gtftk Unix commands</a></li> 
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@@ -297,13 +297,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing pygtftk/gtftk"
              >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 gtftk Unix commands</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.
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     </div>
   </body>
diff --git a/docs/index.html b/docs/index.html
index 403284b..25507a0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -19,7 +19,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Welcome to pygtftk documentation page &#8212; gtftk 1.2.8 documentation</title>
+    <title>Welcome to pygtftk documentation page &#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" />
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@@ -43,7 +43,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="Warning about supported GTF file formats"
              accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Welcome to pygtftk documentation page</a></li> 
       </ul>
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@@ -238,13 +238,13 @@ <h3>Navigation</h3>
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           <a href="about.html" title="Warning about supported GTF file formats"
              >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">gtftk 1.2.8 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">gtftk 1.2.9 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Welcome to pygtftk documentation page</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/information.html b/docs/information.html
index 2366bb6..438ca25 100644
--- a/docs/information.html
+++ b/docs/information.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘information’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘information’ &#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="gtftk_args.html" title="Help on gtftk Unix commands"
              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 ‘information’</a></li> 
       </ul>
     </div>  
@@ -69,10 +69,10 @@ <h2>apropos<a class="headerlink" href="#apropos" title="Permalink to this headli
 <p><strong>Description:</strong> Search in all command description files those related to a user-defined keyword.</p>
 <p><strong>Example:</strong> Search all commands related to promoters.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk apropos -k promoter
- |-- 14:54-INFO-apropos : &gt;&gt; Keyword &#39;promoter&#39; was found in the following command:
-	- divergent.
-	- coverage.
+ |-- 11:03-INFO-apropos : &gt;&gt; Keyword &#39;promoter&#39; was found in the following command:
 	- ologram.
+	- coverage.
+	- divergent.
 </pre></div>
 </div>
 <p><strong>Arguments:</strong></p>
@@ -724,13 +724,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="gtftk_args.html" title="Help on gtftk Unix commands"
              >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 ‘information’</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/installation.html b/docs/installation.html
index 59a84f5..ef4cb43 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -17,7 +17,7 @@
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-    <title>Installing pygtftk/gtftk &#8212; gtftk 1.2.8 documentation</title>
+    <title>Installing pygtftk/gtftk &#8212; gtftk 1.2.9 documentation</title>
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              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="">Installing pygtftk/gtftk</a></li> 
       </ul>
     </div>  
@@ -109,13 +109,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="about.html" title="Warning about supported GTF file formats"
              >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="">Installing pygtftk/gtftk</a></li> 
       </ul>
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     <div class="footer" role="contentinfo">
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-      Last updated on Jun 15, 2021.
+      Last updated on Jun 17, 2021.
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diff --git a/docs/merge_ologram_stats_01.pdf b/docs/merge_ologram_stats_01.pdf
index 1314de4..86454df 100644
Binary files a/docs/merge_ologram_stats_01.pdf and b/docs/merge_ologram_stats_01.pdf differ
diff --git a/docs/miscellaneous.html b/docs/miscellaneous.html
index 0dbc1f2..df4f8b8 100644
--- a/docs/miscellaneous.html
+++ b/docs/miscellaneous.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘miscellaneous’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘miscellaneous’ &#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" />
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@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="coverage.html" title="Commands from section ‘coverage’"
              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 ‘miscellaneous’</a></li> 
       </ul>
     </div>  
@@ -69,13 +69,13 @@ <h2>control_list<a class="headerlink" href="#control-list" title="Permalink to t
 <p><strong>Description:</strong> Returns a list of gene matched for expression based on reference values. Based on a reference gene list (or more generally IDs) this command tries to extract a set of other genes/IDs matched for signal/expression. The –reference-gene-file contains the list of reference IDs while the –inputfile contains a tuple gene/signal for all genes.</p>
 <p><strong>Example:</strong></p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk control_list -i mini_real_counts_ENCFF630HEX.tsv -r mini_real_control_1.txt -D -V 2 -s -l -p 1 -ju -if example_13.png -pf png
- |-- 14:54-INFO-control_list : 0 duplicate lines have been deleted in reference file.
- |-- 14:54-INFO-control_list : Found 50 genes of the reference in the provided signal file
- |-- 14:54-INFO-control_list : All reference genes were found.
- |-- 14:54-INFO-control_list : Searching for genes with matched signal.
- |-- 14:54-INFO-control_list : Preparing a dataframe for plotting.
- |-- 14:54-INFO-control_list : Saving diagram to file : example_13.png
- |-- 14:54-INFO-control_list : Be patient. This may be long for large datasets.
+ |-- 11:04-INFO-control_list : 0 duplicate lines have been deleted in reference file.
+ |-- 11:04-INFO-control_list : Found 50 genes of the reference in the provided signal file
+ |-- 11:04-INFO-control_list : All reference genes were found.
+ |-- 11:04-INFO-control_list : Searching for genes with matched signal.
+ |-- 11:04-INFO-control_list : Preparing a dataframe for plotting.
+ |-- 11:04-INFO-control_list : Saving diagram to file : example_13.png
+ |-- 11:04-INFO-control_list : Be patient. This may be long for large datasets.
 </pre></div>
 </div>
 <a class="reference external image-reference" href="_static/example_13.png"><img alt="_images/example_13.png" src="_images/example_13.png" /></a>
@@ -235,13 +235,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="coverage.html" title="Commands from section ‘coverage’"
              >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 ‘miscellaneous’</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.
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   </body>
diff --git a/docs/objects.inv b/docs/objects.inv
index 6ee469f..57ba1fe 100644
Binary files a/docs/objects.inv and b/docs/objects.inv differ
diff --git a/docs/ologram.html b/docs/ologram.html
index 95ed5dc..3765af5 100644
--- a/docs/ologram.html
+++ b/docs/ologram.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘ologram’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘ologram’ &#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" />
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@@ -45,7 +45,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="annotation.html" title="Commands from section ‘annotation’"
              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 ‘ologram’</a></li> 
       </ul>
     </div>  
@@ -103,8 +103,8 @@ <h2>ologram<a class="headerlink" href="#ologram" title="Permalink to this headli
 </div>
 <p><strong>Example:</strong> Perform a basic annotation. We are searching whether H3K4me3 peaks tends to be enriched in some specific genomic elements. The bars in the bar plot diagram will be ordered according to ‘summed_bp_overlaps_pvalue’.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk ologram -i hg38_chr1.gtf.gz -p ENCFF112BHN_H3K4me3_chr1.bed -c hg38_chr1.genome -u 1500 -d 1500 -D  -pf example_pa_01.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 14:54-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 14:55-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean &gt;= var ; var was set to mean+1 (start_codon)
+ |-- 11:04-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 11:05-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean &gt;= var ; var was set to mean+1 (start_codon)
 </pre></div>
 </div>
 <br>
@@ -119,7 +119,7 @@ <h2>ologram<a class="headerlink" href="#ologram" title="Permalink to this headli
 <br>
 <br><p><strong>Example:</strong> We are now using the gene_biotype key (note that a list of keys can be provided). This will tell us whether H3K4me3 tends to be located in particular transcripts (protein coding, LncRNAs…). The –no-basic-feature argument tells ologram not to test basic genomic elements (gene, transcripts…).</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk select_by_key -i mini_real.gtf.gz -k gene_biotype -v protein_coding,lincRNA,antisense,processed_transcript  |  gtftk ologram  -m gene_biotype -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n  -pf example_pa_02.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 14:56-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 11:06-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 </pre></div>
 </div>
 <br>
@@ -138,8 +138,8 @@ <h2>ologram<a class="headerlink" href="#ologram" title="Permalink to this headli
 </div>
 <p><strong>Example:</strong> A more complex example where the key is created on the fly. Expression data are loaded as a novel key using the join_attr command and associated to gene features. This novel key (exprs) is then discretized to created 6 classes of genes with increasing expression (based on percentiles, -p) which are tested for enrichment in H3K36me3.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk join_attr -i mini_real.gtf.gz -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t exon | gtftk discretize_key -k exprs -p -d exprs_class -n 6  -u | gtftk ologram -p ENCFF119BYM_H3K36me3_K562_sub.bed -c hg38 -D -n -m exprs_class -pf example_pa_03.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 14:56-INFO-discretize_key : Categories: [&#39;[0.0_183.0]&#39;, &#39;(183.0_549.0]&#39;, &#39;(549.0_1018.0]&#39;, &#39;(1018.0_1631.0]&#39;, &#39;(1631.0_3139.0]&#39;, &#39;(3139.0_41703.0]&#39;]
- |-- 14:56-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 11:06-INFO-discretize_key : Categories: [&#39;[0.0_183.0]&#39;, &#39;(183.0_549.0]&#39;, &#39;(549.0_1018.0]&#39;, &#39;(1018.0_1631.0]&#39;, &#39;(1631.0_3139.0]&#39;, &#39;(3139.0_41703.0]&#39;]
+ |-- 11:06-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 </pre></div>
 </div>
 <br>
@@ -154,8 +154,8 @@ <h2>ologram<a class="headerlink" href="#ologram" title="Permalink to this headli
 <br>
 <br><p><strong>Example:</strong> Using the add_exon_nb, we add the exon number transcript-wise (numbering from 5’ to 3’) and discretize this novel key into 5 classes tested for enrichment.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk add_exon_nb -k exon_nbr -i mini_real.gtf.gz | gtftk discretize_key -p -d exon_nbr_cat -n 5  -k exon_nbr | gtftk ologram -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38 -D -n -m exon_nbr_cat -pf example_pa_04.pdf -k 8 -j summed_bp_overlaps_pvalue
- |-- 14:57-INFO-discretize_key : Categories: [&#39;[1.0_2.0]&#39;, &#39;(2.0_4.0]&#39;, &#39;(4.0_6.0]&#39;, &#39;(6.0_12.0]&#39;, &#39;(12.0_107.0]&#39;]
- |-- 14:57-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 11:07-INFO-discretize_key : Categories: [&#39;[1.0_2.0]&#39;, &#39;(2.0_4.0]&#39;, &#39;(4.0_6.0]&#39;, &#39;(6.0_12.0]&#39;, &#39;(12.0_107.0]&#39;]
+ |-- 11:07-WARNING-ologram : Using only 8 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
 </pre></div>
 </div>
 <br>
@@ -184,14 +184,14 @@ <h2>ologram (multiple overlaps)<a class="headerlink" href="#ologram-multiple-ove
 <p><strong>Simple example:</strong></p>
 <p>Comparing the query (-p) against two other BED files, analyzing multiple overlaps.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk ologram -z -w -q -c simple_07.chromInfo -p simple_07_peaks.bed --more-bed simple_07_peaks.1.bed simple_07_peaks.2.bed --more-bed-multiple-overlap
- |-- 14:58-WARNING : Converting to bed6 format (simple_07_peaks.bed).
- |-- 14:58-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
- |-- 14:58-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
- |-- 14:58-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
- |-- 14:58-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
- |-- 14:58-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 14:58-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
- |-- 14:58-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean &gt;= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
+ |-- 11:08-WARNING : Converting to bed6 format (simple_07_peaks.bed).
+ |-- 11:08-WARNING : Converting to bed6 format (simple_07_peaks.1.bed).
+ |-- 11:08-WARNING : Converting to bed6 format (simple_07_peaks.2.bed).
+ |-- 11:08-WARNING-ologram : Using only 1 threads, but 16 cores are available. Consider changing the --nb-threads parameter.
+ |-- 11:08-WARNING-ologram : --more-bed-labels was not set, automatically defaulting to --more-bed file names.
+ |-- 11:08-WARNING-ologram : [Query + simple_07_peaks_1 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 11:08-WARNING-ologram : [Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ]: there may be a poor fit for this feature. Check fit quality in the results. This is likely due to there being too few regions.
+ |-- 11:08-WARNING-ologram : Computing log(p-val) for a Neg Binom with mean &gt;= var ; var was set to mean+1 ([Query + simple_07_peaks_1 + simple_07_peaks_2 + ... ])
 </pre></div>
 </div>
 <p><strong>Detailed example:</strong></p>
@@ -504,7 +504,6 @@ <h2>ologram_modl_treeify<a class="headerlink" href="#ologram-modl-treeify" title
 <p>The tsv result file can be edited before passing it to the command, for example by keeping only the combinations you are interested in.
 You can either (1) run OLOGRAM-MODl with no filtering and get a tree of all combinations, (2) use MODL to get a pre-selection that can be tailored, or (3) take the run with all combinations from the possibility 1 and use the -t argument to take the most frequent combinations.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk ologram_modl_treeify -i multiple_overlap_trivial_ologram_stats.tsv -o treeified.pdf -l ThisWasTheNameOfTheQuery
- |-- 14:58-ERROR-ologram_modl_treeify : gtftk ologram_modl_treeify needs graphviz to be installed on your system.
 </pre></div>
 </div>
 <br>
@@ -681,13 +680,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="annotation.html" title="Commands from section ‘annotation’"
              >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 ‘ologram’</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.
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index f9ac33c..076dd33 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -16,7 +16,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
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-    <title>Python Module Index &#8212; gtftk 1.2.8 documentation</title>
+    <title>Python Module Index &#8212; gtftk 1.2.9 documentation</title>
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+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
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@@ -163,13 +163,13 @@ <h3>Navigation</h3>
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              >modules</a> |</li>
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+        <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="">Python Module Index</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.
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diff --git a/docs/search.html b/docs/search.html
index 01b946b..c13cfbd 100644
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+++ b/docs/search.html
@@ -16,7 +16,7 @@
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       })();
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-    <title>Search &#8212; gtftk 1.2.8 documentation</title>
+    <title>Search &#8212; gtftk 1.2.9 documentation</title>
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@@ -42,7 +42,7 @@ <h3>Navigation</h3>
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+        <li class="nav-item nav-item-0"><a href="index.html">gtftk 1.2.9 documentation</a> &#187;</li>
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@@ -101,13 +101,13 @@ <h3>Navigation</h3>
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              >modules</a> |</li>
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+        <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="">Search</a></li> 
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     <div class="footer" role="contentinfo">
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+      Last updated on Jun 17, 2021.
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diff --git a/docs/searchindex.js b/docs/searchindex.js
index 83dfa45..c67db9f 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs/selection.html b/docs/selection.html
index cb794ec..8b2248c 100644
--- a/docs/selection.html
+++ b/docs/selection.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘selection’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘selection’ &#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="editing.html" title="Commands from section ‘Editing’"
              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 ‘selection’</a></li> 
       </ul>
     </div>  
@@ -440,8 +440,8 @@ <h2>random_list<a class="headerlink" href="#random-list" title="Permalink to thi
 <p><strong>Example:</strong> Select randomly 3 transcripts.</p>
 <div class="highlight-text notranslate"><div class="highlight"><pre><span></span>$ gtftk random_list -n 3 -i simple.gtf | gtftk count
 transcript	3
-exon	4
-CDS	3
+exon	6
+CDS	5
 </pre></div>
 </div>
 <p><strong>Arguments:</strong></p>
@@ -484,10 +484,10 @@ <h2>random_tx<a class="headerlink" href="#random-tx" title="Permalink to this he
 G0003	G0003T001
 G0004	G0004T001
 G0005	G0005T001
-G0006	G0006T001
+G0006	G0006T002
 G0007	G0007T001
 G0008	G0008T001
-G0009	G0009T002
+G0009	G0009T001
 G0010	G0010T001
 </pre></div>
 </div>
@@ -805,13 +805,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="editing.html" title="Commands from section ‘Editing’"
              >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 ‘selection’</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/sequence.html b/docs/sequence.html
index ebf9bc8..19c11ad 100644
--- a/docs/sequence.html
+++ b/docs/sequence.html
@@ -17,7 +17,7 @@
         var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
       })();
     </script>
-    <title>Commands from section ‘sequence’ &#8212; gtftk 1.2.8 documentation</title>
+    <title>Commands from section ‘sequence’ &#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="coordinates.html" title="Commands from section ‘coordinates’"
              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 ‘sequence’</a></li> 
       </ul>
     </div>  
@@ -234,13 +234,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="coordinates.html" title="Commands from section ‘coordinates’"
              >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 ‘sequence’</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/source/_static/example_01.png b/docs/source/_static/example_01.png
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index a8b8906..9303b3a 100644
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index 0d33b73..7b501d3 100644
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diff --git a/docs/source/_static/merge_ologram_stats_01.pdf b/docs/source/_static/merge_ologram_stats_01.pdf
index 86454df..3291f80 100644
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index e69de29..1478791 100644
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diff --git a/docs/source/conf.py b/docs/source/conf.py
index f54ce4e..3de342a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -58,10 +58,10 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.8'
+version = u'1.2.9'
 
 # The full version, including alpha/beta/rc tags.
-release = u'1.2.8'
+release = u'1.2.9'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/docs/source/example_01.png b/docs/source/example_01.png
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index 5dfcdf5..0ef2243 100644
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index e86c45e..a87c7e2 100644
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index cc0d9df..ba46c29 100644
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index 918c679..9172d06 100644
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diff --git a/docs/source/example_pa_01.pdf b/docs/source/example_pa_01.pdf
index 9c9c33e..db3b912 100644
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index 8226f96..8b8e868 100644
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diff --git a/docs/source/example_pa_03.pdf b/docs/source/example_pa_03.pdf
index a8b8906..9303b3a 100644
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index 0d33b73..7b501d3 100644
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diff --git a/docs/source/merge_ologram_stats_01.pdf b/docs/source/merge_ologram_stats_01.pdf
index 86454df..3291f80 100644
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diff --git a/docs/source/treeified.pdf b/docs/source/treeified.pdf
index e69de29..1478791 100644
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diff --git a/docs/treeified.pdf b/docs/treeified.pdf
index d146b3a..e69de29 100644
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diff --git a/pygtftk/version.py b/pygtftk/version.py
index 8dcc746..31f010a 100644
--- a/pygtftk/version.py
+++ b/pygtftk/version.py
@@ -1,2 +1,2 @@
-__base_version__='1.2.8'
-__version__='1.2.8'
+__base_version__='1.2.9'
+__version__='1.2.9'
diff --git a/setup.cfg b/setup.cfg
index fe81d9d..f025796 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = pygtftk
-version = 1.2.8
+version = 1.2.9
 author = D. Puthier, F. Lopez and Q. Ferre
 author-email = denis.puthier@univ-amu.fr