cleanup

.gitignore

 *.o
+*.ai
+.DS_Store
 testingData
 *.pdf
 bin/*
 obj/*
 docs/_build/
+docs/content/images/
 src/utils/version/version_git.h
 .project
 .cproject

docs/_templates/page.html

-{% extends "!page.html" %}
-
-{# To customize for your project, search and replace 'labibi' stuff.
-   You might also want to replace the UA- string for google analytics.
-#}
-
-{% set disqus_shortname = 'bedtools' %}
-
-{# note, currently these must be set... #}
-{% set github_base_account = 'ar5qx' %}
-{% set github_project = 'bedtools2' %}
-
-{##################################################}
-{# for plone-derived "edit me" & Google analytics #}
-{##################################################}
-
-{% block footer %}
-{{ super() }}
-
-{# Add plone-derived 'edit me' sticky note #}
-<!-- <div id="editor-trap">
-      <h3>Edit this document!</h3>
-
-      <p>
-        This file can be edited directly through the Web. Anyone can
-        improve this document with few clicks --
-        no downloads needed.
-      <p>
-
-      <ol>
-
-        <li>
-          Go to
-        <a href="https://github.com/{{ github_base_account }}/{{ github_project }}/blob/master/{{ pagename }}.rst">
-          {{ title }}
-        </a> on GitHub.
-      </li>
-
-        <li>
-        <b>Edit</b> files using GitHub's text editor in your web browser.
-      </li>
-
-      <li>
-        Fill in the <b>Commit message</b> text box at the bottom of the page describing <i>why</i>
-        you made the changes.
-      </li>
-
-      <li>
-        Then click <b>Send a pull request</b>.
-      </li>
-
-      <li>
-        Your changes are now queued for review under the project's <a href="https://github.com/{{ github_base_account }}/{{ github_project }}/pulls">Pull requests</a> tab on GitHub!
-      </li>
-      </ol>
-
-      <p>
-        For an introduction to the documentation format please see <a href="http://docutils.sourceforge.net/docs/user/rst/quickstart.html">the reST primer</a>.
-      </p>
-
-  </div> -->
-
-
-{% endblock %}
-
-{#########################}
-{# for disqus commenting #}
-{#########################}
-
-{% macro comments() %}
-
-<div id="disqus_thread"></div>
-<script type="text/javascript">
-    /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
-    var disqus_shortname = '{{ disqus_shortname }}'; // required: replace example with your forum shortname
-
-    /* * * DON'T EDIT BELOW THIS LINE * * */
-    (function() {
-        var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
-        dsq.src = 'http://' + disqus_shortname + '.disqus.com/embed.js';
-        (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
-    })();
-</script>
-<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
-<a href="http://disqus.com" class="dsq-brlink">comments powered by <span class="logo-disqus">Disqus</span></a>
-
-{% endmacro %}
-
-{% block extrahead %}
-
-{% if github_base_account %}
-<script src="{{ pathto('_static/labibi.js', 1) }}"></script>
-{% else %}
-<style type="text/css">
-<!-- github-based editing disabled; set github_base_account
-     and github_project -->
-#editor-trap.toggled {
-  display: none;
-}
-</style>
-{% endif %}
-
-
-{% endblock %}
-
-{%- block body %}
-  {{ super() }}
-
-{% if disqus_shortname %}
-  {{ comments() }}
-{% else %}
-<!-- disqus commenting disabled; set disqus_shortname -->
-{% endif %}
-
-{%- endblock %}
-