diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ed0efde7f1b82319dcbc96fbf4d20f4ac3811040..4793817ff6896453c58b0d2029b64acb364e0d23 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,7 +13,7 @@ pages:
     - pip3 install sphinx
     - yum install -y make
     - pip3 install sphinx
-    - pip3 install sphinxcontrib-bibtex
+    - pip3 install sphinxcontrib-bibtex sphinx_rtd_theme sphinx-argparse
     - pip3 install -r jass_preprocessing/requirements.txt
     - cd doc
     - sphinx-apidoc -f -o ./source/_autosummary/ ../jass_preprocessing/
diff --git a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree
index d0913191263b087a2eb7716892dc73279b33e9cb..f63ae09cfdfcd8b45cc4aa8ea86a829b1d0de6f2 100644
Binary files a/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree and b/doc/_build/doctrees/_autosummary/jass_preprocessing.doctree differ
diff --git a/doc/_build/doctrees/_autosummary/modules.doctree b/doc/_build/doctrees/_autosummary/modules.doctree
index d81bf9478aba49c75c023312084bedfb7da10a8b..27e69465a3f3a5f52f0a552a07a3b5fae79b0de3 100644
Binary files a/doc/_build/doctrees/_autosummary/modules.doctree and b/doc/_build/doctrees/_autosummary/modules.doctree differ
diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle
index a25385815e8157b8176f6a3de98f8f3998f8d13c..37ed4b08a279ba895c90c7a1e3e3234dced8b63f 100644
Binary files a/doc/_build/doctrees/environment.pickle and b/doc/_build/doctrees/environment.pickle differ
diff --git a/doc/_build/doctrees/index.doctree b/doc/_build/doctrees/index.doctree
index 5b61a86be1dbf42d20c6b122cd6a38b0dc169d47..554b563fc216964e90e38f90aeecec5d7b9e4ca9 100644
Binary files a/doc/_build/doctrees/index.doctree and b/doc/_build/doctrees/index.doctree differ
diff --git a/doc/_build/html/.buildinfo b/doc/_build/html/.buildinfo
index 7973807d1c69071dd9427905d36f83acc0b30141..d4001700a5cc33291156a913bc4f82fc1f733f82 100644
--- a/doc/_build/html/.buildinfo
+++ b/doc/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4d7603fff8910e91226dddc14910dfe6
+config: 7890896c7cf0d3614ade393a5c103246
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/_autosummary/jass_preprocessing.html b/doc/_build/html/_autosummary/jass_preprocessing.html
index 875b0e9feb52089a9ac7c1559ccc57390f565637..573ab6b3f170548f62ad9a8f93e5098280342494 100644
--- a/doc/_build/html/_autosummary/jass_preprocessing.html
+++ b/doc/_build/html/_autosummary/jass_preprocessing.html
@@ -1,43 +1,83 @@
 
 
-<!doctype html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>jass_preprocessing package &#8212; jass_preprocessing 1.0 documentation</title>
-    <link rel="stylesheet" href="../_static/bizstyle.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <script type="text/javascript" src="../_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>jass_preprocessing package &mdash; jass_preprocessing 1.0 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
-    <meta name="viewport" content="width=device-width,initial-scale=1.0">
-    <!--[if lt IE 9]>
-    <script type="text/javascript" src="_static/css3-mediaqueries.js"></script>
-    <![endif]-->
-  </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <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">jass_preprocessing 1.0 documentation</a> &#187;</li> 
-      </ul>
-    </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper">
-  <h3><a href="../index.html">Table Of Contents</a></h3>
-  <ul>
+    <link rel="search" title="Search" href="../search.html" /> 
+
+  
+  <script src="../_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav">
+
+   
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search">
+          
+
+          
+            <a href="../index.html" class="icon icon-home"> jass_preprocessing
+          
+
+          
+          </a>
+
+          
+            
+            
+          
+
+          
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+          
+        </div>
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+          
+            
+            
+              
+            
+            
+              <!-- Local TOC -->
+              <div class="local-toc"><ul>
 <li><a class="reference internal" href="#">jass_preprocessing package</a><ul>
 <li><a class="reference internal" href="#submodules">Submodules</a></li>
 <li><a class="reference internal" href="#module-jass_preprocessing.compute_score">jass_preprocessing.compute_score module</a></li>
@@ -49,33 +89,68 @@
 </ul>
 </li>
 </ul>
-
-  <div role="note" aria-label="source link">
-    <h3>This Page</h3>
-    <ul class="this-page-menu">
-      <li><a href="../_sources/_autosummary/jass_preprocessing.rst.txt"
-            rel="nofollow">Show Source</a></li>
-    </ul>
-   </div>
-<div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    </div>
 </div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
+            
+          
         </div>
       </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" aria-label="top navigation">
+        
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">jass_preprocessing</a>
+        
+      </nav>
+
+
+      <div class="wy-nav-content">
+        
+        <div class="rst-content">
+        
+          
+
 
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body" role="main">
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="../index.html">Docs</a> &raquo;</li>
+        
+      <li>jass_preprocessing package</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+            
+            <a href="../_sources/_autosummary/jass_preprocessing.rst.txt" rel="nofollow"> View page source</a>
+          
+        
+      </li>
+    
+  </ul>
+
+  
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
             
   <div class="section" id="jass-preprocessing-package">
 <h1>jass_preprocessing package<a class="headerlink" href="#jass-preprocessing-package" title="Permalink to this headline">¶</a></h1>
@@ -336,26 +411,52 @@ Make sure that the same SNPs are in the reference panel and the gwas</p>
 </div>
 
 
+           </div>
+           
           </div>
+          <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2018, Hanna Julienne
+
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+</footer>
+
         </div>
       </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related" role="navigation" aria-label="related navigation">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             >index</a></li>
-        <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">jass_preprocessing 1.0 documentation</a> &#187;</li> 
-      </ul>
-    </div>
-    <div class="footer" role="contentinfo">
-        &#169; Copyright 2018, Hanna Julienne.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7.
-    </div>
-  </body>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    
+    
+      <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../_static/jquery.js"></script>
+        <script type="text/javascript" src="../_static/underscore.js"></script>
+        <script type="text/javascript" src="../_static/doctools.js"></script>
+    
+
+  
+
+  <script type="text/javascript" src="../_static/js/theme.js"></script>
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
 </html>
\ No newline at end of file
diff --git a/doc/_build/html/_autosummary/modules.html b/doc/_build/html/_autosummary/modules.html
index c7a9c3c1c7c2665e93f7a2fef06ba737f7259e25..889969b83af8690f63dda023cdc3bbc2880dcfa8 100644
--- a/doc/_build/html/_autosummary/modules.html
+++ b/doc/_build/html/_autosummary/modules.html
@@ -1,67 +1,147 @@
 
 
-<!doctype html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>jass_preprocessing &#8212; jass_preprocessing 1.0 documentation</title>
-    <link rel="stylesheet" href="../_static/bizstyle.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <script type="text/javascript" src="../_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>jass_preprocessing &mdash; jass_preprocessing 1.0 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
-    <link rel="search" title="Search" href="../search.html" />
-    <meta name="viewport" content="width=device-width,initial-scale=1.0">
-    <!--[if lt IE 9]>
-    <script type="text/javascript" src="_static/css3-mediaqueries.js"></script>
-    <![endif]-->
-  </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             accesskey="I">index</a></li>
-        <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">jass_preprocessing 1.0 documentation</a> &#187;</li> 
-      </ul>
-    </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper">
-  <div role="note" aria-label="source link">
-    <h3>This Page</h3>
-    <ul class="this-page-menu">
-      <li><a href="../_sources/_autosummary/modules.rst.txt"
-            rel="nofollow">Show Source</a></li>
-    </ul>
-   </div>
-<div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" />
-      <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
-    </form>
-    </div>
+    <link rel="search" title="Search" href="../search.html" /> 
+
+  
+  <script src="../_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav">
+
+   
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search">
+          
+
+          
+            <a href="../index.html" class="icon icon-home"> jass_preprocessing
+          
+
+          
+          </a>
+
+          
+            
+            
+          
+
+          
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
 </div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
+
+          
+        </div>
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+          
+            
+            
+              
+            
+            
+              <!-- Local TOC -->
+              <div class="local-toc"><ul>
+<li><a class="reference internal" href="#">jass_preprocessing</a></li>
+</ul>
+</div>
+            
+          
         </div>
       </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" aria-label="top navigation">
+        
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">jass_preprocessing</a>
+        
+      </nav>
+
+
+      <div class="wy-nav-content">
+        
+        <div class="rst-content">
+        
+          
+
 
-    <div class="document">
-      <div class="documentwrapper">
-        <div class="bodywrapper">
-          <div class="body" role="main">
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="../index.html">Docs</a> &raquo;</li>
+        
+      <li>jass_preprocessing</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+            
+            <a href="../_sources/_autosummary/modules.rst.txt" rel="nofollow"> View page source</a>
+          
+        
+      </li>
+    
+  </ul>
+
+  
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
             
   <div class="section" id="jass-preprocessing">
 <h1>jass_preprocessing<a class="headerlink" href="#jass-preprocessing" title="Permalink to this headline">¶</a></h1>
@@ -84,26 +164,52 @@
 </div>
 
 
+           </div>
+           
           </div>
+          <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2018, Hanna Julienne
+
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
+</footer>
+
         </div>
       </div>
-      <div class="clearer"></div>
-    </div>
-    <div class="related" role="navigation" aria-label="related navigation">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="../genindex.html" title="General Index"
-             >index</a></li>
-        <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">jass_preprocessing 1.0 documentation</a> &#187;</li> 
-      </ul>
-    </div>
-    <div class="footer" role="contentinfo">
-        &#169; Copyright 2018, Hanna Julienne.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7.
-    </div>
-  </body>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    
+    
+      <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../_static/jquery.js"></script>
+        <script type="text/javascript" src="../_static/underscore.js"></script>
+        <script type="text/javascript" src="../_static/doctools.js"></script>
+    
+
+  
+
+  <script type="text/javascript" src="../_static/js/theme.js"></script>
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
 </html>
\ No newline at end of file
diff --git a/doc/_build/html/_modules/index.html b/doc/_build/html/_modules/index.html
index 367ca793aba81ca00f79cd2820b95393a10d5bc4..e6e25eec70198b637d0b16d1d4adb236902341d7 100644
--- a/doc/_build/html/_modules/index.html
+++ b/doc/_build/html/_modules/index.html
@@ -1,60 +1,140 @@
 
 
-<!doctype html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Overview: module code &#8212; jass_preprocessing 1.0 documentation</title>
-    <link rel="stylesheet" href="../_static/bizstyle.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
-    <script type="text/javascript" src="../_static/jquery.js"></script>
-    <script type="text/javascript" src="../_static/underscore.js"></script>
-    <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <script type="text/javascript" src="../_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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   <h1>All modules for which code is available</h1>
 <ul><li><a href="jass_preprocessing/compute_score.html">jass_preprocessing.compute_score</a></li>
@@ -64,26 +144,52 @@
 <li><a href="jass_preprocessing/save_output.html">jass_preprocessing.save_output</a></li>
 </ul>
 
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diff --git a/doc/_build/html/_modules/jass_preprocessing/compute_score.html b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
index edd89e010c576de2bb0869af407d2461698b780f..98653d3f499163f7bb332b1efe50b191951cc632 100644
--- a/doc/_build/html/_modules/jass_preprocessing/compute_score.html
+++ b/doc/_build/html/_modules/jass_preprocessing/compute_score.html
@@ -1,61 +1,142 @@
 
 
-<!doctype html>
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+  <title>jass_preprocessing.compute_score &mdash; jass_preprocessing 1.0 documentation</title>
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+  
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+  
+
+  
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+  
+  
+    
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+  
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+  <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
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+
+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="../../index.html">Docs</a> &raquo;</li>
+        
+          <li><a href="../index.html">Module code</a> &raquo;</li>
+        
+      <li>jass_preprocessing.compute_score</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+      </li>
+    
+  </ul>
+
+  
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
             
   <h1>Source code for jass_preprocessing.compute_score</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
@@ -127,27 +208,52 @@
     <span class="k">return</span><span class="p">(</span><span class="n">mgwas</span><span class="p">)</span></div>
 </pre></div>
 
+           </div>
+           
           </div>
+          <footer>
+  
+
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+  <div role="contentinfo">
+    <p>
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-             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> &#187;</li>
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diff --git a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
index 9c9f6c83dabbf019566e5915c0fc8643a31bd957..c30ed3bd95e16da043b8cb7995d4e9210312c35c 100644
--- a/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
+++ b/doc/_build/html/_modules/jass_preprocessing/dna_utils.html
@@ -1,61 +1,142 @@
 
 
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+        
+      <li>jass_preprocessing.dna_utils</li>
+    
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+      <li class="wy-breadcrumbs-aside">
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   <h1>Source code for jass_preprocessing.dna_utils</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
@@ -75,27 +156,52 @@
     <span class="k">return</span><span class="p">([</span><span class="n">dna_complement_base</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="nb">input</span><span class="p">])</span></div>
 </pre></div>
 
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diff --git a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
index 3712dee7914b60ada2037e8981d1d61ddb524d3f..ec7b4140ecbad83c62ed14a47c3a91bc98dd442b 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_gwas.html
@@ -1,61 +1,142 @@
 
 
-<!doctype html>
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+          <li><a href="../index.html">Module code</a> &raquo;</li>
+        
+      <li>jass_preprocessing.map_gwas</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
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+           <div itemprop="articleBody">
             
   <h1>Source code for jass_preprocessing.map_gwas</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
@@ -206,27 +287,52 @@
     <span class="k">return</span> <span class="n">fullGWAS</span></div>
 </pre></div>
 
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           </div>
+          <footer>
+  
+
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-             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> &#187;</li>
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7.
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diff --git a/doc/_build/html/_modules/jass_preprocessing/map_reference.html b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
index 93f2563d2da8f234e7901800afb16e955d12e6e1..336b4d01f6c1864fbccce43fdeec165919dcf4ea 100644
--- a/doc/_build/html/_modules/jass_preprocessing/map_reference.html
+++ b/doc/_build/html/_modules/jass_preprocessing/map_reference.html
@@ -1,61 +1,142 @@
 
 
-<!doctype html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
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-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
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-    <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
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-    <script type="text/javascript" src="../../_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>jass_preprocessing.map_reference &mdash; jass_preprocessing 1.0 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
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+  
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+  <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
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+    
+      <li><a href="../../index.html">Docs</a> &raquo;</li>
+        
+          <li><a href="../index.html">Module code</a> &raquo;</li>
+        
+      <li>jass_preprocessing.map_reference</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+      </li>
+    
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+           <div itemprop="articleBody">
             
   <h1>Source code for jass_preprocessing.map_reference</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;</span>
@@ -186,27 +267,52 @@
     <span class="k">return</span><span class="p">(</span><span class="n">mgwas</span><span class="p">)</span></div>
 </pre></div>
 
+           </div>
+           
           </div>
+          <footer>
+  
+
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+
+  <div role="contentinfo">
+    <p>
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-        <li class="right" style="margin-right: 10px">
-          <a href="../../genindex.html" title="General Index"
-             >index</a></li>
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-          <a href="../../py-modindex.html" title="Python Module Index"
-             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> &#187;</li>
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-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7.
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diff --git a/doc/_build/html/_modules/jass_preprocessing/save_output.html b/doc/_build/html/_modules/jass_preprocessing/save_output.html
index 4eeb238ce9e9fbea0756066c96f4e7e7f56e8750..f9a906ee2fd0c0b6f3ed3d759fc0f70f5463714e 100644
--- a/doc/_build/html/_modules/jass_preprocessing/save_output.html
+++ b/doc/_build/html/_modules/jass_preprocessing/save_output.html
@@ -1,61 +1,142 @@
 
 
-<!doctype html>
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-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
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-    <link rel="stylesheet" href="../../_static/bizstyle.css" type="text/css" />
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-    <script type="text/javascript" src="../../_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>jass_preprocessing.save_output &mdash; jass_preprocessing 1.0 documentation</title>
+  
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+
+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="../../index.html">Docs</a> &raquo;</li>
+        
+          <li><a href="../index.html">Module code</a> &raquo;</li>
+        
+      <li>jass_preprocessing.save_output</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+      </li>
+    
+  </ul>
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+  
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
             
   <h1>Source code for jass_preprocessing.save_output</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
@@ -109,27 +190,52 @@
     <span class="n">mgwas_copy</span><span class="o">.</span><span class="n">sort_values</span><span class="p">([</span><span class="s1">&#39;chrom&#39;</span><span class="p">,</span><span class="s1">&#39;pos&#39;</span><span class="p">])</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">impg_output_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></div>
 </pre></div>
 
+           </div>
+           
           </div>
+          <footer>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2018, Hanna Julienne
+
+    </p>
+  </div>
+  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
+
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-      <ul>
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-             >index</a></li>
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-             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">jass_preprocessing 1.0 documentation</a> &#187;</li>
-          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li> 
-      </ul>
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-    <div class="footer" role="contentinfo">
-        &#169; Copyright 2018, Hanna Julienne.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.7.7.
-    </div>
-  </body>
+
+    </section>
+
+  </div>
+  
+
+
+  
+
+    
+    
+      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../../_static/jquery.js"></script>
+        <script type="text/javascript" src="../../_static/underscore.js"></script>
+        <script type="text/javascript" src="../../_static/doctools.js"></script>
+    
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
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 </html>
\ No newline at end of file
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
index e424cf390f160df460033869f157f95fa2c19b27..7136a4067686fa41a885c328bacf6133ea3bde08 100644
--- a/doc/_build/html/_sources/index.rst.txt
+++ b/doc/_build/html/_sources/index.rst.txt
@@ -24,6 +24,8 @@ The QC and preprocessing step goes as follow:
 * Select GWAS SNPs that are in the input reference panel
 * Align coded allele of the GWAS with the reference panel
 * Infer Number of sample by SNPs if not present in input data
+* Filter SNPs with a small sample size
+* Normalize the effect size by sample size to have Z-scores
 * Save the output by chromosome as the following example:
 
 +----------+-------+------+-----+--------+
@@ -93,11 +95,15 @@ Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)
 Command line usage example:
 ============================
 
-The file : "/JASS_Pre-processing/main_preprocessing.py" gives a complete example on how to use this package.
+It is possible to launch the complete preprocessing from the command line:
+
+.. argparse::
+  :ref: jass_preprocessing.__main__.add_preprocessing_argument
 
 Indices and tables
 ==================
 
+
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
diff --git a/doc/_build/html/_static/basic.css b/doc/_build/html/_static/basic.css
index 19ced1057aebf39d3dac6f6a5d864491231a3e33..104f076ae8ae5d6118dc13db6cb16e2ae9de1bda 100644
--- a/doc/_build/html/_static/basic.css
+++ b/doc/_build/html/_static/basic.css
@@ -81,6 +81,10 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
 div.sphinxsidebar #searchbox input[type="text"] {
     float: left;
     width: 80%;
@@ -427,6 +431,13 @@ table.field-list td, table.field-list th {
     hyphens: manual;
 }
 
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {
diff --git a/doc/_build/html/_static/doctools.js b/doc/_build/html/_static/doctools.js
index d8928926bf24bb081d91a12f7b92e1b2d8b142b6..ffadbec11f71c338696d5c014de9b64afe31a516 100644
--- a/doc/_build/html/_static/doctools.js
+++ b/doc/_build/html/_static/doctools.js
@@ -150,7 +150,9 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-    
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
   },
 
   /**
@@ -310,4 +312,4 @@ _ = Documentation.gettext;
 
 $(document).ready(function() {
   Documentation.init();
-});
\ No newline at end of file
+});
diff --git a/doc/_build/html/_static/documentation_options.js b/doc/_build/html/_static/documentation_options.js
index 9b69b42bcd98b555324995d9afee402ad1b09250..837eacf30de116b6aff70d9761453e9c93abb1b5 100644
--- a/doc/_build/html/_static/documentation_options.js
+++ b/doc/_build/html/_static/documentation_options.js
@@ -5,5 +5,292 @@ var DOCUMENTATION_OPTIONS = {
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',
     HAS_SOURCE: true,
-    SOURCELINK_SUFFIX: '.txt'
-};
\ No newline at end of file
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+    SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]
+};
+
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */ 
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+
+
+var splitChars = (function() {
+    var result = {};
+    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+    var i, j, start, end;
+    for (i = 0; i < singles.length; i++) {
+        result[singles[i]] = true;
+    }
+    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
+         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
+         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
+         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
+         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
+         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
+         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
+         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
+         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
+         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
+         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
+         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
+         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
+         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
+         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
+         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
+         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
+         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
+         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
+         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
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+         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
+         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
+         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
+         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
+         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
+         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
+         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
+         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
+         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
+         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
+         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
+         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
+         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
+         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
+         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
+         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
+         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
+         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
+         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
+         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
+         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
+         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
+         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
+         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+    for (i = 0; i < ranges.length; i++) {
+        start = ranges[i][0];
+        end = ranges[i][1];
+        for (j = start; j <= end; j++) {
+            result[j] = true;
+        }
+    }
+    return result;
+})();
+
+function splitQuery(query) {
+    var result = [];
+    var start = -1;
+    for (var i = 0; i < query.length; i++) {
+        if (splitChars[query.charCodeAt(i)]) {
+            if (start !== -1) {
+                result.push(query.slice(start, i));
+                start = -1;
+            }
+        } else if (start === -1) {
+            start = i;
+        }
+    }
+    if (start !== -1) {
+        result.push(query.slice(start));
+    }
+    return result;
+}
+
+
diff --git a/doc/_build/html/_static/searchtools.js b/doc/_build/html/_static/searchtools.js
index 41b8336776442fbc64332ffbd3d2c1ddd8b3b9c2..7473859b245fa63f5d8812e2249c8d1ae67425fd 100644
--- a/doc/_build/html/_static/searchtools.js
+++ b/doc/_build/html/_static/searchtools.js
@@ -1,5 +1,5 @@
 /*
- * searchtools.js_t
+ * searchtools.js
  * ~~~~~~~~~~~~~~~~
  *
  * Sphinx JavaScript utilities for the full-text search.
@@ -9,323 +9,44 @@
  *
  */
 
-
-/* Non-minified version JS is _stemmer.js if file is provided */ 
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
-  var step2list = {
-    ational: 'ate',
-    tional: 'tion',
-    enci: 'ence',
-    anci: 'ance',
-    izer: 'ize',
-    bli: 'ble',
-    alli: 'al',
-    entli: 'ent',
-    eli: 'e',
-    ousli: 'ous',
-    ization: 'ize',
-    ation: 'ate',
-    ator: 'ate',
-    alism: 'al',
-    iveness: 'ive',
-    fulness: 'ful',
-    ousness: 'ous',
-    aliti: 'al',
-    iviti: 'ive',
-    biliti: 'ble',
-    logi: 'log'
-  };
-
-  var step3list = {
-    icate: 'ic',
-    ative: '',
-    alize: 'al',
-    iciti: 'ic',
-    ical: 'ic',
-    ful: '',
-    ness: ''
+if (!Scorer) {
+  /**
+   * Simple result scoring code.
+   */
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [filename, title, anchor, descr, score]
+    // and returns the new score.
+    /*
+    score: function(result) {
+      return result[4];
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {0:  15,   // used to be importantResults
+              1:  5,   // used to be objectResults
+              2: -5},  // used to be unimportantResults
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    // query found in terms
+    term: 5
   };
-
-  var c = "[^aeiou]";          // consonant
-  var v = "[aeiouy]";          // vowel
-  var C = c + "[^aeiouy]*";    // consonant sequence
-  var V = v + "[aeiou]*";      // vowel sequence
-
-  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
-  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
-  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
-  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
-
-  this.stemWord = function (w) {
-    var stem;
-    var suffix;
-    var firstch;
-    var origword = w;
-
-    if (w.length < 3)
-      return w;
-
-    var re;
-    var re2;
-    var re3;
-    var re4;
-
-    firstch = w.substr(0,1);
-    if (firstch == "y")
-      w = firstch.toUpperCase() + w.substr(1);
-
-    // Step 1a
-    re = /^(.+?)(ss|i)es$/;
-    re2 = /^(.+?)([^s])s$/;
-
-    if (re.test(w))
-      w = w.replace(re,"$1$2");
-    else if (re2.test(w))
-      w = w.replace(re2,"$1$2");
-
-    // Step 1b
-    re = /^(.+?)eed$/;
-    re2 = /^(.+?)(ed|ing)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      re = new RegExp(mgr0);
-      if (re.test(fp[1])) {
-        re = /.$/;
-        w = w.replace(re,"");
-      }
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1];
-      re2 = new RegExp(s_v);
-      if (re2.test(stem)) {
-        w = stem;
-        re2 = /(at|bl|iz)$/;
-        re3 = new RegExp("([^aeiouylsz])\\1$");
-        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-        if (re2.test(w))
-          w = w + "e";
-        else if (re3.test(w)) {
-          re = /.$/;
-          w = w.replace(re,"");
-        }
-        else if (re4.test(w))
-          w = w + "e";
-      }
-    }
-
-    // Step 1c
-    re = /^(.+?)y$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(s_v);
-      if (re.test(stem))
-        w = stem + "i";
-    }
-
-    // Step 2
-    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step2list[suffix];
-    }
-
-    // Step 3
-    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step3list[suffix];
-    }
-
-    // Step 4
-    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
-    re2 = /^(.+?)(s|t)(ion)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      if (re.test(stem))
-        w = stem;
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1] + fp[2];
-      re2 = new RegExp(mgr1);
-      if (re2.test(stem))
-        w = stem;
-    }
-
-    // Step 5
-    re = /^(.+?)e$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      re2 = new RegExp(meq1);
-      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
-        w = stem;
-    }
-    re = /ll$/;
-    re2 = new RegExp(mgr1);
-    if (re.test(w) && re2.test(w)) {
-      re = /.$/;
-      w = w.replace(re,"");
-    }
-
-    // and turn initial Y back to y
-    if (firstch == "y")
-      w = firstch.toLowerCase() + w.substr(1);
-    return w;
-  }
 }
 
-
-
-/**
- * Simple result scoring code.
- */
-var Scorer = {
-  // Implement the following function to further tweak the score for each result
-  // The function takes a result array [filename, title, anchor, descr, score]
-  // and returns the new score.
-  /*
-  score: function(result) {
-    return result[4];
-  },
-  */
-
-  // query matches the full name of an object
-  objNameMatch: 11,
-  // or matches in the last dotted part of the object name
-  objPartialMatch: 6,
-  // Additive scores depending on the priority of the object
-  objPrio: {0:  15,   // used to be importantResults
-            1:  5,   // used to be objectResults
-            2: -5},  // used to be unimportantResults
-  //  Used when the priority is not in the mapping.
-  objPrioDefault: 0,
-
-  // query found in title
-  title: 15,
-  // query found in terms
-  term: 5
-};
-
-
-
-
-
-var splitChars = (function() {
-    var result = {};
-    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
-         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
-         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
-         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
-         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
-         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
-         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
-         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
-         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
-         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
-    var i, j, start, end;
-    for (i = 0; i < singles.length; i++) {
-        result[singles[i]] = true;
-    }
-    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
-         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
-         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
-         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
-         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
-         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
-         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
-         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
-         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
-         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
-         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
-         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
-         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
-         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
-         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
-         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
-         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
-         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
-         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
-         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
-         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
-         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
-         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
-         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
-         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
-         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
-         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
-         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
-         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
-         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
-         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
-         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
-         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
-         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
-         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
-         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
-         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
-         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
-         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
-         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
-         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
-         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
-         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
-         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
-         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
-         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
-         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
-         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
-         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
-    for (i = 0; i < ranges.length; i++) {
-        start = ranges[i][0];
-        end = ranges[i][1];
-        for (j = start; j <= end; j++) {
-            result[j] = true;
-        }
-    }
-    return result;
-})();
-
-function splitQuery(query) {
-    var result = [];
-    var start = -1;
-    for (var i = 0; i < query.length; i++) {
-        if (splitChars[query.charCodeAt(i)]) {
-            if (start !== -1) {
-                result.push(query.slice(start, i));
-                start = -1;
-            }
-        } else if (start === -1) {
-            start = i;
-        }
-    }
-    if (start !== -1) {
-        result.push(query.slice(start));
-    }
-    return result;
+if (!splitQuery) {
+  function splitQuery(query) {
+    return query.split(/\s+/);
+  }
 }
 
-
-
-
 /**
  * Search Module
  */
@@ -417,7 +138,7 @@ var Search = {
    */
   query : function(query) {
     var i;
-    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+    var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS;
 
     // stem the searchterms and add them to the correct list
     var stemmer = new Stemmer();
@@ -758,4 +479,4 @@ var Search = {
 
 $(document).ready(function() {
   Search.init();
-});
\ No newline at end of file
+});
diff --git a/doc/_build/html/genindex.html b/doc/_build/html/genindex.html
index 61624f3fb0c2325e247a74c62f4991b43835854b..d087160a11e743638e35b4cd4154d466406ea6ad 100644
--- a/doc/_build/html/genindex.html
+++ b/doc/_build/html/genindex.html
@@ -1,61 +1,143 @@
 
 
 
-<!doctype html>
-
-<html xmlns="http://www.w3.org/1999/xhtml">
-  <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Index &#8212; jass_preprocessing 1.0 documentation</title>
-    <link rel="stylesheet" href="_static/bizstyle.css" type="text/css" />
-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
-    <script type="text/javascript" src="_static/jquery.js"></script>
-    <script type="text/javascript" src="_static/underscore.js"></script>
-    <script type="text/javascript" src="_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <script type="text/javascript" src="_static/bizstyle.js"></script>
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>Index &mdash; jass_preprocessing 1.0 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="#" />
-    <link rel="search" title="Search" href="search.html" />
-    <meta name="viewport" content="width=device-width,initial-scale=1.0">
-    <!--[if lt IE 9]>
-    <script type="text/javascript" src="_static/css3-mediaqueries.js"></script>
-    <![endif]-->
-  </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
-      <h3>Navigation</h3>
-      <ul>
-        <li class="right" style="margin-right: 10px">
-          <a href="#" title="General Index"
-             accesskey="I">index</a></li>
-        <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">jass_preprocessing 1.0 documentation</a> &#187;</li> 
-      </ul>
-    </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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 <li><a class="reference internal" href="#">Welcome to jass_preprocessing’s documentation!</a></li>
 <li><a class="reference internal" href="#what-is-jass-preprocessing">What is jass preprocessing ?</a></li>
 <li><a class="reference internal" href="#overview">Overview</a></li>
 <li><a class="reference internal" href="#installation">Installation</a></li>
 <li><a class="reference internal" href="#input">Input</a></li>
-<li><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a></li>
+<li><a class="reference internal" href="#command-line-usage-example">Command line usage example:</a><ul>
+<li><a class="reference internal" href="#Named Arguments">Named Arguments</a></li>
+</ul>
+</li>
 <li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
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+           <div itemprop="articleBody">
             
   <div class="section" id="welcome-to-jass-preprocessing-s-documentation">
 <h1>Welcome to jass_preprocessing’s documentation!<a class="headerlink" href="#welcome-to-jass-preprocessing-s-documentation" title="Permalink to this headline">¶</a></h1>
@@ -92,6 +170,8 @@ heterogeneous GWAS summary statistics and performs standardization and quality c
 <li>Select GWAS SNPs that are in the input reference panel</li>
 <li>Align coded allele of the GWAS with the reference panel</li>
 <li>Infer Number of sample by SNPs if not present in input data</li>
+<li>Filter SNPs with a small sample size</li>
+<li>Normalize the effect size by sample size to have Z-scores</li>
 <li>Save the output by chromosome as the following example:</li>
 </ul>
 <table border="1" class="docutils">
@@ -221,7 +301,45 @@ execute the following lines:</p>
 </div>
 <div class="section" id="command-line-usage-example">
 <h1>Command line usage example:<a class="headerlink" href="#command-line-usage-example" title="Permalink to this headline">¶</a></h1>
-<p>The file : “/JASS_Pre-processing/main_preprocessing.py” gives a complete example on how to use this package.</p>
+<p>It is possible to launch the complete preprocessing from the command line:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">sphinx</span><span class="o">-</span><span class="n">build</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">percent</span><span class="o">-</span><span class="n">sample</span><span class="o">-</span><span class="n">size</span> <span class="n">PERCENT_SAMPLE_SIZE</span> <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">info</span>
+                    <span class="n">GWAS_INFO</span> <span class="o">--</span><span class="n">ref</span><span class="o">-</span><span class="n">folder</span> <span class="n">REF_FOLDER</span> <span class="o">--</span><span class="n">gwas</span><span class="o">-</span><span class="n">folder</span>
+                    <span class="n">GWAS_FOLDER</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span> <span class="n">OUTPUT_FOLDER</span>
+                    <span class="p">[</span><span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">folder</span><span class="o">-</span><span class="mi">1</span><span class="o">-</span><span class="n">file</span> <span class="n">OUTPUT_FOLDER_1_FILE</span><span class="p">]</span>
+</pre></div>
+</div>
+<div class="section" id="Named Arguments">
+<h2>Named Arguments<a class="headerlink" href="#Named Arguments" title="Permalink to this headline">¶</a></h2>
+<table class="docutils option-list" frame="void" rules="none">
+<col class="option" />
+<col class="description" />
+<tbody valign="top">
+<tr><td class="option-group" colspan="2">
+<kbd>--percent-sample-size</kbd></td>
+</tr>
+<tr><td>&#160;</td><td>the proportion of the 90th percentile of the sample size used to filter the SNPs</td></tr>
+<tr><td class="option-group">
+<kbd>--gwas-info</kbd></td>
+<td>Path to the file describing the format of the individual GWASs files</td></tr>
+<tr><td class="option-group">
+<kbd>--ref-folder</kbd></td>
+<td>reference panel location (used to determine which snp to impute)</td></tr>
+<tr><td class="option-group">
+<kbd>--gwas-folder</kbd></td>
+<td><blockquote class="first last">
+<div>Path to the folder containing the GWASs summ stat files, must end by ‘/’</div></blockquote>
+</td></tr>
+<tr><td class="option-group" colspan="2">
+<kbd>--output-folder</kbd></td>
+</tr>
+<tr><td>&#160;</td><td>Location of main ouput folder for preprocessed GWAS files (splitted by chromosome)</td></tr>
+<tr><td class="option-group" colspan="2">
+<kbd>--output-folder-1-file</kbd></td>
+</tr>
+<tr><td>&#160;</td><td>optional location to store the preprocessing in one tabular file with one chromosome columns</td></tr>
+</tbody>
+</table>
+</div>
 </div>
 <div class="section" id="indices-and-tables">
 <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
@@ -233,26 +351,52 @@ execute the following lines:</p>
 </div>
 
 
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diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
index 82a46b99e139cbf660b44a2c0de0fb5639805a65..744ac39d6336c598784b1426b95e4a81055a31b5 100644
Binary files a/doc/_build/html/objects.inv and b/doc/_build/html/objects.inv differ
diff --git a/doc/_build/html/py-modindex.html b/doc/_build/html/py-modindex.html
index 8f3e7593bd0c85b30221ca03cd11a16f195577c5..0bf1ea8b0ce87de824984e3a2ec94e25292d287b 100644
--- a/doc/_build/html/py-modindex.html
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diff --git a/doc/source/conf.py b/doc/source/conf.py
index 48e7f06a83dc70f2337709413fc2147a4769f674..cafa92a7493f3bc7953e721f57bf8e215557da0f 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -44,7 +44,8 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx.ext.todo',
-    'sphinx.ext.coverage'
+    'sphinx.ext.coverage',
+    'sphinxarg.ext'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -80,8 +81,8 @@ pygments_style = 'sphinx'
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'bizstyle'
-
+#html_theme = 'bizstyle'
+html_theme = 'sphinx_rtd_theme'
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
diff --git a/doc/source/index.rst b/doc/source/index.rst
index ac94d8f10cb7c99ea17b97c2ab2f8d7027b7264e..8a554cc7528d0462e33804feee04116856cd27b0 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -95,11 +95,17 @@ Hard coded path (l.20-29 of JASS_Pre-processing/main_preprocessing.py)
 Command line usage example:
 ============================
 
-The file : "/JASS_Pre-processing/main_preprocessing.py" gives a complete example on how to use this package.
+It is possible to launch the complete preprocessing (all steps described in section Overview section) from the command line:
+
+.. argparse::
+  :ref: jass_preprocessing.__main__.add_preprocessing_argument
 
 Indices and tables
 ==================
 
+
 * :ref:`genindex`
 * :ref:`modindex`
+.. automodule:: impute_jass
+   :members:
 * :ref:`search`
diff --git a/jass_preprocessing/__main__.py b/jass_preprocessing/__main__.py
index fe698cc57a2f26eb4f6542f3912dada4df7cf1e8..46943b83500480753a4898623f6e22447fe7fbe1 100644
--- a/jass_preprocessing/__main__.py
+++ b/jass_preprocessing/__main__.py
@@ -59,6 +59,7 @@ def launch_preprocessing(args):
 
 def add_preprocessing_argument():
 
+    parser = argparse.ArgumentParser()
     parser.add_argument('--percent-sample-size', required=True, help= "the proportion of the 90th percentile of the sample size used to filter the SNPs")
 
     parser.add_argument('--gwas-info', required=True, help= "Path to the file describing the format of the individual GWASs files")
@@ -70,11 +71,12 @@ def add_preprocessing_argument():
 
     parser.set_defaults(func=launch_preprocessing)
 
+    return parser
 
 def main():
 
-    parser = argparse.ArgumentParser()#prog='impute_jass')
-    parser = add_preprocessing_argument(parser)
+
+    parser = add_preprocessing_argument()
     args = parser.parse_args()
     args.func(args)
 
diff --git a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc
index 8061951fbd3e205cc5542110f65e84ea39a857f5..b2269fda3bde8364ba13e9146007998e0f9aa6cb 100644
Binary files a/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc and b/jass_preprocessing/__pycache__/compute_score.cpython-35.pyc differ