Updated docs and added a redirection index for github pages

docs/html/analysis_8cpp.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/analysis.cpp File Reference</title>
+<title>RADSex: /home/romain/work/code/radsex/src/analysis.cpp File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/analysis_8cpp_source.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/analysis.cpp Source File</title>
+<title>RADSex: /home/romain/work/code/radsex/src/analysis.cpp Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/analysis_8h.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/analysis.h File Reference</title>
+<title>RADSex: /home/romain/work/code/radsex/src/analysis.h File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/analysis_8h_source.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/analysis.h Source File</title>
+<title>RADSex: /home/romain/work/code/radsex/src/analysis.h Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/arg__parser_8h.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/arg_parser.h File Reference</title>
+<title>RADSex: /home/romain/work/code/radsex/src/arg_parser.h File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/arg__parser_8h_source.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/arg_parser.h Source File</title>
+<title>RADSex: /home/romain/work/code/radsex/src/arg_parser.h Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/classAnalysis.html

@@ -481,8 +481,8 @@ Wait if queue is empty and update progress bar with processed markers. </p>
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="analysis_8h_source.html">analysis.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="analysis_8cpp_source.html">analysis.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="analysis_8h_source.html">analysis.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="analysis_8cpp_source.html">analysis.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classCustomFormatter.html

@@ -250,7 +250,7 @@ uint&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="clas
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="arg__parser_8h_source.html">arg_parser.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="arg__parser_8h_source.html">arg_parser.h</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classDepth.html

@@ -332,8 +332,8 @@ Individual | Group | Reads | Markers | Retained | Min_depth | Max_depth | Median
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="depth_8h_source.html">depth.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="depth_8cpp_source.html">depth.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="depth_8h_source.html">depth.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="depth_8cpp_source.html">depth.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classDistrib.html

@@ -339,8 +339,8 @@ Group1 | Group2 | Markers | P | P corrected | <a class="el" href="classSignif.ht
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="distrib_8h_source.html">distrib.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="distrib_8cpp_source.html">distrib.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="distrib_8h_source.html">distrib.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="distrib_8cpp_source.html">distrib.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classFreq.html

@@ -330,8 +330,8 @@ Frequency | Count </p>
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="freq_8h_source.html">freq.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="freq_8cpp_source.html">freq.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="freq_8h_source.html">freq.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="freq_8cpp_source.html">freq.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classHeader.html

@@ -158,8 +158,8 @@ std::vector&lt; std::string &gt;&#160;</td><td class="memItemRight" valign="bott
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="markers__table_8h_source.html">markers_table.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="markers__table_8cpp_source.html">markers_table.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="markers__table_8h_source.html">markers_table.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="markers__table_8cpp_source.html">markers_table.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classMap.html

@@ -485,8 +485,8 @@ Contig | Position | Length | Marker_id | Bias | P | <a class="el" href="classSig
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="map_8h_source.html">map.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="map_8cpp_source.html">map.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="map_8h_source.html">map.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="map_8cpp_source.html">map.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classMarker.html

@@ -283,8 +283,8 @@ float&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="cla
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="marker_8h_source.html">marker.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="marker_8cpp_source.html">marker.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="marker_8h_source.html">marker.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="marker_8cpp_source.html">marker.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classMarkersTable.html

@@ -340,8 +340,8 @@ Private Attributes</h2></td></tr>
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="markers__table_8h_source.html">markers_table.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="markers__table_8cpp_source.html">markers_table.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="markers__table_8h_source.html">markers_table.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="markers__table_8cpp_source.html">markers_table.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classPopmap.html

@@ -280,8 +280,8 @@ std::unordered_map&lt; std::string, uint &gt;&#160;</td><td class="memItemRight"
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="popmap_8h_source.html">popmap.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="popmap_8cpp_source.html">popmap.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="popmap_8h_source.html">popmap.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="popmap_8cpp_source.html">popmap.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classSignif.html

@@ -341,8 +341,8 @@ Export markers significantly associated with group to a file, either: <br  />
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="signif_8h_source.html">signif.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="signif_8cpp_source.html">signif.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="signif_8h_source.html">signif.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="signif_8cpp_source.html">signif.cpp</a></li>
 </ul>
 </div><!-- contents -->
 </div><!-- doc-content -->

docs/html/classSubset.html

@@ -345,8 +345,8 @@ Export markers verifying the conditions defined with CLI arguments, either: <br
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following files:<ul>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="subset_8h_source.html">subset.h</a></li>
-<li>/home/romain/work/code/RADSex/src/<a class="el" href="subset_8cpp_source.html">subset.cpp</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="subset_8h_source.html">subset.h</a></li>
+<li>/home/romain/work/code/radsex/src/<a class="el" href="subset_8cpp_source.html">subset.cpp</a></li>
 </ul>
 </div><!-- contents -->
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docs/html/depth_8cpp.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/depth.cpp File Reference</title>
+<title>RADSex: /home/romain/work/code/radsex/src/depth.cpp File Reference</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>

docs/html/depth_8cpp_source.html

@@ -5,7 +5,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen 1.8.17"/>
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
-<title>RADSex: /home/romain/work/code/RADSex/src/depth.cpp Source File</title>
+<title>RADSex: /home/romain/work/code/radsex/src/depth.cpp Source File</title>
 <link href="tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="jquery.js"></script>
 <script type="text/javascript" src="dynsections.js"></script>