diff --git a/_modules/index.html b/_modules/index.html
index a25c660..449ed24 100644
--- a/_modules/index.html
+++ b/_modules/index.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
diff --git a/_modules/trackhub/assembly.html b/_modules/trackhub/assembly.html
index 0c12472..442d6cf 100644
--- a/_modules/trackhub/assembly.html
+++ b/_modules/trackhub/assembly.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.assembly &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -154,12 +154,8 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="k">pass</span>
 
 
-<div class="viewcode-block" id="Assembly">
-<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly">[docs]</a>
-<span class="k">class</span> <span class="nc">Assembly</span><span class="p">(</span><span class="n">Genome</span><span class="p">):</span>
-<div class="viewcode-block" id="Assembly.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+<div class="viewcode-block" id="Assembly"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly">[docs]</a><span class="k">class</span> <span class="nc">Assembly</span><span class="p">(</span><span class="n">Genome</span><span class="p">):</span>
+<div class="viewcode-block" id="Assembly.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">genome</span><span class="p">,</span>
         <span class="n">twobit_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -204,7 +200,6 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">add_params</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="nf">add_twobit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">twobit</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">TwoBitFile</span><span class="p">)]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">twobit</span><span class="p">)</span>
@@ -229,9 +224,7 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;GenomesFile is level </span><span class="si">%s</span><span class="s2">, not -1&quot;</span> <span class="o">%</span> <span class="n">level</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">obj</span>
 
-<div class="viewcode-block" id="Assembly.add_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.add_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+<div class="viewcode-block" id="Assembly.add_params"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.add_params">[docs]</a>    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add [possibly many] parameters to the Assembly.</span>
 
@@ -250,10 +243,7 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kw</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
-<div class="viewcode-block" id="Assembly.remove_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.remove_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="Assembly.remove_params"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.remove_params">[docs]</a>    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Remove [possibly many] parameters from the Assembly.</span>
 
@@ -265,7 +255,6 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">_html</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">html_string</span><span class="p">:</span>
@@ -300,12 +289,8 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span>
 
-<div class="viewcode-block" id="Assembly.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="n">Genome</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
-</div>
-
+<div class="viewcode-block" id="Assembly.validate"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">Genome</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div></div>
         <span class="c1"># check for necessary params?</span>
 
 
diff --git a/_modules/trackhub/base.html b/_modules/trackhub/base.html
index cf0d019..3894110 100644
--- a/_modules/trackhub/base.html
+++ b/_modules/trackhub/base.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.base &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -117,21 +117,16 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">source</span><span class="p">,</span> <span class="n">filename</span>
 
 
-<div class="viewcode-block" id="HubComponent">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent">[docs]</a>
-<span class="k">class</span> <span class="nc">HubComponent</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent">[docs]</a><span class="k">class</span> <span class="nc">HubComponent</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Base class for various track hub components.  Several methods must be</span>
 <span class="sd">    overridden by subclasses.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-<div class="viewcode-block" id="HubComponent.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="kc">None</span></div>
 
-
     <span class="k">def</span> <span class="nf">_render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="s2">&quot;staging&quot;</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Renders the object to file.  Must be overridden by subclass.</span>
@@ -143,9 +138,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
             <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span>
         <span class="p">)</span>
 
-<div class="viewcode-block" id="HubComponent.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.validate"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Runs validation, raising exceptions as needed.  Must be overridden by</span>
 <span class="sd">        subclass.</span>
@@ -155,10 +148,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
             <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span>
         <span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="HubComponent.add_child">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.add_child">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_child</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">child</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.add_child"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.add_child">[docs]</a>    <span class="k">def</span> <span class="nf">add_child</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">child</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Adds self as parent to child, and then adds child.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -166,10 +156,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">child</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">child</span></div>
 
-
-<div class="viewcode-block" id="HubComponent.add_parent">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.add_parent">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_parent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.add_parent"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.add_parent">[docs]</a>    <span class="k">def</span> <span class="nf">add_parent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parent</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Adds self as child of parent, then adds parent.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -177,10 +164,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">parent</span> <span class="o">=</span> <span class="n">parent</span>
         <span class="k">return</span> <span class="n">parent</span></div>
 
-
-<div class="viewcode-block" id="HubComponent.root">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.root">[docs]</a>
-    <span class="k">def</span> <span class="nf">root</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.root"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.root">[docs]</a>    <span class="k">def</span> <span class="nf">root</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns the top-most HubComponent in the hierarchy.</span>
 
@@ -203,10 +187,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parent</span><span class="o">.</span><span class="n">root</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">level</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="HubComponent.leaves">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.leaves">[docs]</a>
-    <span class="k">def</span> <span class="nf">leaves</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">intermediate</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.leaves"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.leaves">[docs]</a>    <span class="k">def</span> <span class="nf">leaves</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="bp">cls</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">intermediate</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns an iterator of the HubComponent leaves that are of class `cls`.</span>
 
@@ -226,10 +207,7 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
             <span class="k">for</span> <span class="n">leaf</span><span class="p">,</span> <span class="n">_level</span> <span class="ow">in</span> <span class="n">child</span><span class="o">.</span><span class="n">leaves</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">level</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">intermediate</span><span class="o">=</span><span class="n">intermediate</span><span class="p">):</span>
                 <span class="k">yield</span> <span class="n">leaf</span><span class="p">,</span> <span class="n">_level</span></div>
 
-
-<div class="viewcode-block" id="HubComponent.render">
-<a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.render">[docs]</a>
-    <span class="k">def</span> <span class="nf">render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="HubComponent.render"><a class="viewcode-back" href="../../autodocs/trackhub.base.HubComponent.html#trackhub.base.HubComponent.render">[docs]</a>    <span class="k">def</span> <span class="nf">render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Renders the object to file, returning a list of created files.</span>
 
@@ -247,12 +225,10 @@ <h1>Source code for trackhub.base</h1><div class="highlight"><pre>
             <span class="n">created_files</span><span class="p">[</span><span class="nb">repr</span><span class="p">(</span><span class="n">child</span><span class="p">)]</span> <span class="o">=</span> <span class="n">child</span><span class="o">.</span><span class="n">render</span><span class="p">(</span><span class="n">staging</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">created_files</span></div>
 
-
     <span class="k">def</span> <span class="nf">makedirs</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">):</span>
         <span class="n">dirname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">fn</span><span class="p">)</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">dirname</span><span class="p">):</span>
             <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">dirname</span><span class="p">)</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/genome.html b/_modules/trackhub/genome.html
index f732c36..cf472f8 100644
--- a/_modules/trackhub/genome.html
+++ b/_modules/trackhub/genome.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.genome &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -92,12 +92,8 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">constants</span>
 
 
-<div class="viewcode-block" id="Genome">
-<a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome">[docs]</a>
-<span class="k">class</span> <span class="nc">Genome</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
-<div class="viewcode-block" id="Genome.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genome</span><span class="p">,</span> <span class="n">trackdb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">genome_file_obj</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="Genome"><a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome">[docs]</a><span class="k">class</span> <span class="nc">Genome</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="Genome.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genome</span><span class="p">,</span> <span class="n">trackdb</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">genome_file_obj</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a 2-line genome stanza within a &quot;genomes.txt&quot; file.</span>
 
@@ -129,7 +125,6 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">add_params</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">genome_file_obj</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">try</span><span class="p">:</span>
@@ -142,9 +137,7 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">trackdb</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">trackdb</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
 
-<div class="viewcode-block" id="Genome.add_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.add_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+<div class="viewcode-block" id="Genome.add_params"><a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.add_params">[docs]</a>    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add [possibly many] parameters to the Genome.</span>
 
@@ -162,10 +155,7 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kw</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
-<div class="viewcode-block" id="Genome.remove_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.remove_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="Genome.remove_params"><a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.remove_params">[docs]</a>    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Remove [possibly many] parameters from the Genome.</span>
 
@@ -177,7 +167,6 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">validate</span><span class="p">()</span>
@@ -202,22 +191,18 @@ <h1>Source code for trackhub.genome</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span>
 
-<div class="viewcode-block" id="Genome.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Genome.validate"><a class="viewcode-back" href="../../autodocs/trackhub.Genome.html#trackhub.Genome.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">ValidationError</span><span class="p">(</span><span class="s2">&quot;No TrackDb objects provided&quot;</span><span class="p">)</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">trackdb</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">ValidationError</span><span class="p">(</span><span class="s2">&quot;No TrackDb objects provided&quot;</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="nf">_render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="s2">&quot;staging&quot;</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        No file is created from a Genome object -- only from its parent</span>
 <span class="sd">        GenomesFile object.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">pass</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/genomes_file.html b/_modules/trackhub/genomes_file.html
index d859ca9..f1ba06b 100644
--- a/_modules/trackhub/genomes_file.html
+++ b/_modules/trackhub/genomes_file.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.genomes_file &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -91,12 +91,8 @@ <h1>Source code for trackhub.genomes_file</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.base</span> <span class="kn">import</span> <span class="n">HubComponent</span>
 
 
-<div class="viewcode-block" id="GenomesFile">
-<a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile">[docs]</a>
-<span class="k">class</span> <span class="nc">GenomesFile</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
-<div class="viewcode-block" id="GenomesFile.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genome</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="GenomesFile"><a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile">[docs]</a><span class="k">class</span> <span class="nc">GenomesFile</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="GenomesFile.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genome</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents the genomes file on disk.  Can contain multiple `Genome`</span>
 <span class="sd">        objects, each of which represent a stanza in this file.</span>
@@ -121,7 +117,6 @@ <h1>Source code for trackhub.genomes_file</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">filename</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
@@ -163,13 +158,9 @@ <h1>Source code for trackhub.genomes_file</h1><div class="highlight"><pre>
         <span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">fout</span><span class="o">.</span><span class="n">name</span>
 
-<div class="viewcode-block" id="GenomesFile.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="GenomesFile.validate"><a class="viewcode-back" href="../../autodocs/trackhub.GenomesFile.html#trackhub.GenomesFile.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No defined Genome objects to use&quot;</span><span class="p">)</span></div>
-</div>
-
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No defined Genome objects to use&quot;</span><span class="p">)</span></div></div>
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/groups.html b/_modules/trackhub/groups.html
index 77975ad..d3426c9 100644
--- a/_modules/trackhub/groups.html
+++ b/_modules/trackhub/groups.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.groups &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -93,12 +93,8 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.genomes_file</span> <span class="kn">import</span> <span class="n">GenomesFile</span>
 
 
-<div class="viewcode-block" id="GroupDefinition">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupDefinition.html#trackhub.GroupDefinition">[docs]</a>
-<span class="k">class</span> <span class="nc">GroupDefinition</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-<div class="viewcode-block" id="GroupDefinition.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupDefinition.html#trackhub.GroupDefinition.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">priority</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">default_is_closed</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupDefinition"><a class="viewcode-back" href="../../autodocs/trackhub.GroupDefinition.html#trackhub.GroupDefinition">[docs]</a><span class="k">class</span> <span class="nc">GroupDefinition</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupDefinition.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.GroupDefinition.html#trackhub.GroupDefinition.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">priority</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">default_is_closed</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a group of tracks in a trackhub.</span>
 
@@ -130,7 +126,6 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;default_is_closed must be 1 or 0&quot;</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">s</span> <span class="o">=</span> <span class="p">[</span>
             <span class="s2">&quot;name </span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
@@ -141,13 +136,8 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span></div>
 
 
-
-<div class="viewcode-block" id="GroupsFile">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile">[docs]</a>
-<span class="k">class</span> <span class="nc">GroupsFile</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
-<div class="viewcode-block" id="GroupsFile.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groups</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupsFile"><a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile">[docs]</a><span class="k">class</span> <span class="nc">GroupsFile</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupsFile.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groups</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents the groups file on disk, used for assembly hubs.</span>
 
@@ -165,10 +155,7 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_groups</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">filename</span></div>
 
-
-<div class="viewcode-block" id="GroupsFile.add_groups">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.add_groups">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_groups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groups</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupsFile.add_groups"><a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.add_groups">[docs]</a>    <span class="k">def</span> <span class="nf">add_groups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">groups</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a list of GroupDefinition objects.</span>
 
@@ -179,7 +166,6 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">groups</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">groups</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Render groups.txt file.</span>
@@ -226,9 +212,7 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">fn</span>
 
-<div class="viewcode-block" id="GroupsFile.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="GroupsFile.validate"><a class="viewcode-back" href="../../autodocs/trackhub.GroupsFile.html#trackhub.GroupsFile.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">genome</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">ValidationError</span><span class="p">(</span>
                 <span class="s2">&quot;GroupsFile object must be attached to an Genome instance &quot;</span>
@@ -236,7 +220,6 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
             <span class="p">)</span>
         <span class="k">pass</span></div>
 
-
     <span class="k">def</span> <span class="nf">_render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="s2">&quot;staging&quot;</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Renders the children GroupDefinition objects to file</span>
@@ -247,7 +230,6 @@ <h1>Source code for trackhub.groups</h1><div class="highlight"><pre>
         <span class="n">fout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span>
         <span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">fout</span><span class="o">.</span><span class="n">name</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/helpers.html b/_modules/trackhub/helpers.html
index cc2b155..b312b3a 100644
--- a/_modules/trackhub/helpers.html
+++ b/_modules/trackhub/helpers.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.helpers &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -95,9 +95,7 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
 <span class="n">_here</span> <span class="o">=</span> <span class="vm">__file__</span>
 
 
-<div class="viewcode-block" id="dimensions_from_subgroups">
-<a class="viewcode-back" href="../../autodocs/trackhub.helpers.dimensions_from_subgroups.html#trackhub.helpers.dimensions_from_subgroups">[docs]</a>
-<span class="k">def</span> <span class="nf">dimensions_from_subgroups</span><span class="p">(</span><span class="n">s</span><span class="p">):</span>
+<div class="viewcode-block" id="dimensions_from_subgroups"><a class="viewcode-back" href="../../autodocs/trackhub.helpers.dimensions_from_subgroups.html#trackhub.helpers.dimensions_from_subgroups">[docs]</a><span class="k">def</span> <span class="nf">dimensions_from_subgroups</span><span class="p">(</span><span class="n">s</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Given a sorted list of subgroups, return a string appropriate to provide as</span>
 <span class="sd">    a composite track&#39;s `dimensions` arg.</span>
@@ -110,10 +108,7 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s2">&quot;dim</span><span class="si">{0}</span><span class="s2">=</span><span class="si">{1}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">dim</span><span class="p">,</span> <span class="n">sg</span><span class="o">.</span><span class="n">name</span><span class="p">)</span> <span class="k">for</span> <span class="n">dim</span><span class="p">,</span> <span class="n">sg</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">letters</span><span class="p">,</span> <span class="n">s</span><span class="p">)])</span></div>
 
 
-
-<div class="viewcode-block" id="filter_composite_from_subgroups">
-<a class="viewcode-back" href="../../autodocs/trackhub.helpers.filter_composite_from_subgroups.html#trackhub.helpers.filter_composite_from_subgroups">[docs]</a>
-<span class="k">def</span> <span class="nf">filter_composite_from_subgroups</span><span class="p">(</span><span class="n">s</span><span class="p">):</span>
+<div class="viewcode-block" id="filter_composite_from_subgroups"><a class="viewcode-back" href="../../autodocs/trackhub.helpers.filter_composite_from_subgroups.html#trackhub.helpers.filter_composite_from_subgroups">[docs]</a><span class="k">def</span> <span class="nf">filter_composite_from_subgroups</span><span class="p">(</span><span class="n">s</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Given a sorted list of subgroups, return a string appropriate to provide as</span>
 <span class="sd">    the a composite track&#39;s `filterComposite` argument</span>
@@ -136,10 +131,7 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">dims</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="hex2rgb">
-<a class="viewcode-back" href="../../autodocs/trackhub.helpers.hex2rgb.html#trackhub.helpers.hex2rgb">[docs]</a>
-<span class="k">def</span> <span class="nf">hex2rgb</span><span class="p">(</span><span class="n">h</span><span class="p">):</span>
+<div class="viewcode-block" id="hex2rgb"><a class="viewcode-back" href="../../autodocs/trackhub.helpers.hex2rgb.html#trackhub.helpers.hex2rgb">[docs]</a><span class="k">def</span> <span class="nf">hex2rgb</span><span class="p">(</span><span class="n">h</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Convert hex colors to RGB tuples</span>
 
@@ -165,10 +157,7 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
     <span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="sanitize">
-<a class="viewcode-back" href="../../autodocs/trackhub.helpers.sanitize.html#trackhub.helpers.sanitize">[docs]</a>
-<span class="k">def</span> <span class="nf">sanitize</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<div class="viewcode-block" id="sanitize"><a class="viewcode-back" href="../../autodocs/trackhub.helpers.sanitize.html#trackhub.helpers.sanitize">[docs]</a><span class="k">def</span> <span class="nf">sanitize</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Sanitize a string.</span>
 
@@ -199,7 +188,6 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="s2">&quot;&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">s</span> <span class="k">if</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">allowed</span><span class="p">])</span></div>
 
 
-
 <span class="k">def</span> <span class="nf">auto_track_url</span><span class="p">(</span><span class="n">track</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Automatically sets the bigDataUrl for `track`.</span>
@@ -256,9 +244,7 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
         <span class="nb">print</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">rstrip</span><span class="p">())</span>
 
 
-<div class="viewcode-block" id="data_dir">
-<a class="viewcode-back" href="../../autodocs/trackhub.helpers.data_dir.html#trackhub.helpers.data_dir">[docs]</a>
-<span class="k">def</span> <span class="nf">data_dir</span><span class="p">():</span>
+<div class="viewcode-block" id="data_dir"><a class="viewcode-back" href="../../autodocs/trackhub.helpers.data_dir.html#trackhub.helpers.data_dir">[docs]</a><span class="k">def</span> <span class="nf">data_dir</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Returns the data directory that contains example files for tests and</span>
 <span class="sd">    documentation.</span>
@@ -266,7 +252,6 @@ <h1>Source code for trackhub.helpers</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">_here</span><span class="p">),</span> <span class="s2">&quot;test&quot;</span><span class="p">,</span> <span class="s2">&quot;data&quot;</span><span class="p">)</span></div>
 
 
-
 <span class="k">def</span> <span class="nf">example_bigbeds</span><span class="p">():</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Returns list of example bigBed files</span>
diff --git a/_modules/trackhub/hub.html b/_modules/trackhub/hub.html
index f53fe85..3a605ee 100644
--- a/_modules/trackhub/hub.html
+++ b/_modules/trackhub/hub.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.hub &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -92,15 +92,11 @@ <h1>Source code for trackhub.hub</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.base</span> <span class="kn">import</span> <span class="n">HubComponent</span>
 
 
-<div class="viewcode-block" id="Hub">
-<a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub">[docs]</a>
-<span class="k">class</span> <span class="nc">Hub</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="Hub"><a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub">[docs]</a><span class="k">class</span> <span class="nc">Hub</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
     <span class="c1"># map proper track hub stanza field names to pythonic attribute names in</span>
     <span class="c1"># this class.</span>
 
-<div class="viewcode-block" id="Hub.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+<div class="viewcode-block" id="Hub.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">hub</span><span class="p">,</span>
         <span class="n">short_label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -160,10 +156,7 @@ <h1>Source code for trackhub.hub</h1><div class="highlight"><pre>
             <span class="n">filename</span> <span class="o">=</span> <span class="n">hub</span> <span class="o">+</span> <span class="s2">&quot;.hub.txt&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="o">=</span> <span class="n">filename</span></div>
 
-
-<div class="viewcode-block" id="Hub.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="Hub.validate"><a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">genomes_file</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">raise</span> <span class="n">ValidationError</span><span class="p">(</span>
                 <span class="s2">&quot;No GenomesFile attached to Hub (use add_genomes_file())&quot;</span>
@@ -171,17 +164,13 @@ <h1>Source code for trackhub.hub</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">genomes_file</span><span class="o">.</span><span class="n">validate</span><span class="p">()</span>
         <span class="k">return</span> <span class="kc">True</span></div>
 
-
-<div class="viewcode-block" id="Hub.add_genomes_file">
-<a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.add_genomes_file">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_genomes_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genomes_file</span><span class="p">):</span>
+<div class="viewcode-block" id="Hub.add_genomes_file"><a class="viewcode-back" href="../../autodocs/trackhub.Hub.html#trackhub.Hub.add_genomes_file">[docs]</a>    <span class="k">def</span> <span class="nf">add_genomes_file</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">genomes_file</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        If a GenomesFile object was not provided upon instantiating this</span>
 <span class="sd">        object, attach one now</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">genomes_file</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">genomes_file</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">genomes_file</span> <span class="o">=</span> <span class="kc">None</span>
@@ -208,7 +197,6 @@ <h1>Source code for trackhub.hub</h1><div class="highlight"><pre>
         <span class="n">fout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span>
         <span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">fout</span><span class="o">.</span><span class="n">name</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/track.html b/_modules/trackhub/track.html
index 841aaf0..d3edcf9 100644
--- a/_modules/trackhub/track.html
+++ b/_modules/trackhub/track.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.track &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -151,12 +151,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">beginning</span> <span class="o">+</span> <span class="n">end</span>
 
 
-<div class="viewcode-block" id="SubGroupDefinition">
-<a class="viewcode-back" href="../../autodocs/trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition">[docs]</a>
-<span class="k">class</span> <span class="nc">SubGroupDefinition</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-<div class="viewcode-block" id="SubGroupDefinition.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">mapping</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;none&quot;</span><span class="p">):</span>
+<div class="viewcode-block" id="SubGroupDefinition"><a class="viewcode-back" href="../../autodocs/trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition">[docs]</a><span class="k">class</span> <span class="nc">SubGroupDefinition</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="SubGroupDefinition.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">label</span><span class="p">,</span> <span class="n">mapping</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="s2">&quot;none&quot;</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a subgroup line in a composite track.</span>
 
@@ -201,7 +197,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">mapping</span> <span class="o">=</span> <span class="n">mapping</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">default</span> <span class="o">=</span> <span class="n">default</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
@@ -210,13 +205,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="BaseTrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack">[docs]</a>
-<span class="k">class</span> <span class="nc">BaseTrack</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
-<div class="viewcode-block" id="BaseTrack.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+<div class="viewcode-block" id="BaseTrack"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack">[docs]</a><span class="k">class</span> <span class="nc">BaseTrack</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">name</span><span class="p">,</span>
         <span class="n">tracktype</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -332,7 +322,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">_html</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">html_string</span><span class="p">:</span>
@@ -405,18 +394,13 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="n">fields</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">constants</span><span class="o">.</span><span class="n">track_fields</span><span class="p">[</span><span class="n">base_tracktype</span><span class="p">])</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">track_field_order</span> <span class="o">=</span> <span class="n">update_list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">track_field_order</span><span class="p">,</span> <span class="n">fields</span><span class="p">)</span>
 
-<div class="viewcode-block" id="BaseTrack.add_trackdb">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_trackdb">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_trackdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trackdb</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.add_trackdb"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_trackdb">[docs]</a>    <span class="k">def</span> <span class="nf">add_trackdb</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trackdb</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Attach this track to a parent TrackDb object.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_parent</span><span class="p">(</span><span class="n">trackdb</span><span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="BaseTrack.add_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.add_params"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_params">[docs]</a>    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add [possibly many] parameters to the track.</span>
 
@@ -442,10 +426,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kw</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
-<div class="viewcode-block" id="BaseTrack.remove_params">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.remove_params">[docs]</a>
-    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.remove_params"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.remove_params">[docs]</a>    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Remove [possibly many] parameters from the track.</span>
 
@@ -457,10 +438,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-
-<div class="viewcode-block" id="BaseTrack.add_subgroups">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_subgroups">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_subgroups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subgroups</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.add_subgroups"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.add_subgroups">[docs]</a>    <span class="k">def</span> <span class="nf">add_subgroups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subgroups</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Update the subgroups for this track.</span>
 
@@ -483,7 +461,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">assert</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">subgroups</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">subgroups</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">subgroups</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
@@ -544,12 +521,9 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
             <span class="o">%</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="s2">&quot;</span><span class="si">%s</span><span class="s2">=</span><span class="si">%s</span><span class="s2">&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="k">for</span> <span class="p">(</span><span class="n">k</span><span class="p">,</span> <span class="n">v</span><span class="p">)</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">subgroups</span><span class="o">.</span><span class="n">items</span><span class="p">()])</span>
         <span class="p">]</span>
 
-<div class="viewcode-block" id="BaseTrack.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="BaseTrack.validate"><a class="viewcode-back" href="../../autodocs/trackhub.BaseTrack.html#trackhub.BaseTrack.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">pass</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">html_fn</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">trackdb</span><span class="p">:</span>
@@ -560,13 +534,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="Track">
-<a class="viewcode-back" href="../../autodocs/trackhub.Track.html#trackhub.Track">[docs]</a>
-<span class="k">class</span> <span class="nc">Track</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
-<div class="viewcode-block" id="Track.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.Track.html#trackhub.Track.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">url</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="Track"><a class="viewcode-back" href="../../autodocs/trackhub.Track.html#trackhub.Track">[docs]</a><span class="k">class</span> <span class="nc">Track</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
+<div class="viewcode-block" id="Track.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.Track.html#trackhub.Track.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">url</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a single track stanza along with the file it describes.</span>
 
@@ -593,7 +562,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="nb">super</span><span class="p">(</span><span class="n">Track</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_url</span> <span class="o">=</span> <span class="n">kwargs</span><span class="p">[</span><span class="s2">&quot;bigDataUrl&quot;</span><span class="p">]</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">url</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_url</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
@@ -609,13 +577,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_url</span> <span class="o">=</span> <span class="n">fn</span></div>
 
 
-
-<div class="viewcode-block" id="CompositeTrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack">[docs]</a>
-<span class="k">class</span> <span class="nc">CompositeTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
-<div class="viewcode-block" id="CompositeTrack.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack">[docs]</a><span class="k">class</span> <span class="nc">CompositeTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a composite track.  Subclasses :class:`BaseTrack`, and adds</span>
 <span class="sd">        some extras.</span>
@@ -644,10 +607,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">views</span> <span class="o">=</span> <span class="p">[]</span></div>
 
-
-<div class="viewcode-block" id="CompositeTrack.add_subgroups">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_subgroups">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_subgroups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subgroups</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack.add_subgroups"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_subgroups">[docs]</a>    <span class="k">def</span> <span class="nf">add_subgroups</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subgroups</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a list of SubGroupDefinition objects to this composite.</span>
 
@@ -667,10 +627,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
             <span class="n">_subgroups</span><span class="p">[</span><span class="n">sg</span><span class="o">.</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">sg</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">subgroups</span> <span class="o">=</span> <span class="n">_subgroups</span></div>
 
-
-<div class="viewcode-block" id="CompositeTrack.add_subtrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_subtrack">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_subtrack</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subtrack</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack.add_subtrack"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_subtrack">[docs]</a>    <span class="k">def</span> <span class="nf">add_subtrack</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subtrack</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a child :class:`Track`.</span>
 
@@ -679,10 +636,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_tracks</span><span class="p">(</span><span class="n">subtrack</span><span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="CompositeTrack.add_view">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_view">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_view</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">view</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack.add_view"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_view">[docs]</a>    <span class="k">def</span> <span class="nf">add_view</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">view</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a ViewTrack object to this composite.</span>
 
@@ -694,10 +648,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_tracks</span><span class="p">(</span><span class="n">view</span><span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="CompositeTrack.add_tracks">
-<a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_tracks">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="CompositeTrack.add_tracks"><a class="viewcode-back" href="../../autodocs/trackhub.CompositeTrack.html#trackhub.CompositeTrack.add_tracks">[docs]</a>    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        This method allows for both view and subtracks to be added to</span>
 <span class="sd">        a composite at the same time. `args` can be arbitrary BaseTrack objects</span>
@@ -722,7 +673,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
                     <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">track</span><span class="p">)</span>
                     <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">track</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="nf">_str_subgroups</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        renders subgroups to a list of strings</span>
@@ -765,13 +715,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="ViewTrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack">[docs]</a>
-<span class="k">class</span> <span class="nc">ViewTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
-<div class="viewcode-block" id="ViewTrack.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">view</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="ViewTrack"><a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack">[docs]</a><span class="k">class</span> <span class="nc">ViewTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
+<div class="viewcode-block" id="ViewTrack.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">view</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a View track.  Subclasses :class:`BaseTrack`, and adds some</span>
 <span class="sd">        extras.</span>
@@ -802,10 +747,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span> <span class="o">=</span> <span class="p">[]</span></div>
 
-
-<div class="viewcode-block" id="ViewTrack.add_tracks">
-<a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack.add_tracks">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="ViewTrack.add_tracks"><a class="viewcode-back" href="../../autodocs/trackhub.ViewTrack.html#trackhub.ViewTrack.add_tracks">[docs]</a>    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add one or more tracks to this view.</span>
 
@@ -823,7 +765,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
                 <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">track</span><span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">track</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">s</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">super</span><span class="p">(</span><span class="n">ViewTrack</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__str__</span><span class="p">())</span>
@@ -835,13 +776,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="SuperTrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack">[docs]</a>
-<span class="k">class</span> <span class="nc">SuperTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
-<div class="viewcode-block" id="SuperTrack.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="SuperTrack"><a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack">[docs]</a><span class="k">class</span> <span class="nc">SuperTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
+<div class="viewcode-block" id="SuperTrack.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents a Super track. Subclasses :class:`Track`, and adds some</span>
 <span class="sd">        extras.</span>
@@ -862,10 +798,7 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span> <span class="o">=</span> <span class="p">[]</span></div>
 
-
-<div class="viewcode-block" id="SuperTrack.add_tracks">
-<a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack.add_tracks">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="SuperTrack.add_tracks"><a class="viewcode-back" href="../../autodocs/trackhub.SuperTrack.html#trackhub.SuperTrack.add_tracks">[docs]</a>    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add one or more tracks.</span>
 
@@ -882,7 +815,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
                 <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">track</span><span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">track</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
@@ -897,13 +829,8 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span></div>
 
 
-
-<div class="viewcode-block" id="AggregateTrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack">[docs]</a>
-<span class="k">class</span> <span class="nc">AggregateTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
-<div class="viewcode-block" id="AggregateTrack.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aggregate</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<div class="viewcode-block" id="AggregateTrack"><a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack">[docs]</a><span class="k">class</span> <span class="nc">AggregateTrack</span><span class="p">(</span><span class="n">BaseTrack</span><span class="p">):</span>
+<div class="viewcode-block" id="AggregateTrack.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">aggregate</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents an Aggregate or Overlay track. Subclasses :class:`Track`,</span>
 <span class="sd">        adds some extras.</span>
@@ -936,19 +863,13 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span> <span class="o">=</span> <span class="p">[]</span></div>
 
-
-<div class="viewcode-block" id="AggregateTrack.add_subtrack">
-<a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.add_subtrack">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_subtrack</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subtrack</span><span class="p">):</span>
+<div class="viewcode-block" id="AggregateTrack.add_subtrack"><a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.add_subtrack">[docs]</a>    <span class="k">def</span> <span class="nf">add_subtrack</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">subtrack</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a child :class:`SubTrack` to this aggregate.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_tracks</span><span class="p">(</span><span class="n">subtrack</span><span class="p">)</span></div>
 
-
-<div class="viewcode-block" id="AggregateTrack.add_tracks">
-<a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.add_tracks">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+<div class="viewcode-block" id="AggregateTrack.add_tracks"><a class="viewcode-back" href="../../autodocs/trackhub.AggregateTrack.html#trackhub.AggregateTrack.add_tracks">[docs]</a>    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add one or more tracks.</span>
 
@@ -966,7 +887,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
                 <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">track</span><span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">subtracks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">track</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 
         <span class="n">s</span> <span class="o">=</span> <span class="p">[]</span>
@@ -981,7 +901,6 @@ <h1>Source code for trackhub.track</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span></div>
 
 
-
 <span class="k">class</span> <span class="nc">HTMLDoc</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">contents</span><span class="p">,</span> <span class="n">html_string_format</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
diff --git a/_modules/trackhub/trackdb.html b/_modules/trackhub/trackdb.html
index 7af786e..567b027 100644
--- a/_modules/trackhub/trackdb.html
+++ b/_modules/trackhub/trackdb.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.trackdb &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -93,12 +93,8 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">.genome</span> <span class="kn">import</span> <span class="n">Genome</span>
 
 
-<div class="viewcode-block" id="TrackDb">
-<a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb">[docs]</a>
-<span class="k">class</span> <span class="nc">TrackDb</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
-<div class="viewcode-block" id="TrackDb.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tracks</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="TrackDb"><a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb">[docs]</a><span class="k">class</span> <span class="nc">TrackDb</span><span class="p">(</span><span class="n">HubComponent</span><span class="p">):</span>
+<div class="viewcode-block" id="TrackDb.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tracks</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Represents the file containing one or more Track objects (which each</span>
 <span class="sd">        represent a stanza).</span>
@@ -121,7 +117,6 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">filename</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">hub</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">(</span><span class="bp">cls</span><span class="o">=</span><span class="n">Hub</span><span class="p">)</span>
@@ -166,9 +161,7 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">filename</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fn</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_filename</span> <span class="o">=</span> <span class="n">fn</span>
 
-<div class="viewcode-block" id="TrackDb.add_tracks">
-<a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.add_tracks">[docs]</a>
-    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">track</span><span class="p">):</span>
+<div class="viewcode-block" id="TrackDb.add_tracks"><a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.add_tracks">[docs]</a>    <span class="k">def</span> <span class="nf">add_tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">track</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add a track or iterable of tracks.</span>
 
@@ -189,7 +182,6 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
                 <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">t</span><span class="p">)</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">_tracks</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">t</span><span class="p">)</span></div>
 
-
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">tracks</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="kn">from</span> <span class="nn">trackhub</span> <span class="kn">import</span> <span class="n">Track</span>
@@ -210,13 +202,10 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
 
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
 
-<div class="viewcode-block" id="TrackDb.validate">
-<a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.validate">[docs]</a>
-    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="TrackDb.validate"><a class="viewcode-back" href="../../autodocs/trackhub.TrackDb.html#trackhub.TrackDb.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">children</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No Track objects specified&quot;</span><span class="p">)</span></div>
 
-
     <span class="k">def</span> <span class="nf">_render</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="s2">&quot;staging&quot;</span><span class="p">):</span>
         <span class="n">rendered_filename</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">staging</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">filename</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">rendered_filename</span><span class="p">)</span>
@@ -224,7 +213,6 @@ <h1>Source code for trackhub.trackdb</h1><div class="highlight"><pre>
         <span class="n">fout</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span>
         <span class="n">fout</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
         <span class="k">return</span> <span class="n">fout</span><span class="o">.</span><span class="n">name</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/upload.html b/_modules/trackhub/upload.html
index b4983c3..99b768a 100644
--- a/_modules/trackhub/upload.html
+++ b/_modules/trackhub/upload.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.upload &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -287,9 +287,7 @@ <h1>Source code for trackhub.upload</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">linknames</span>
 
 
-<div class="viewcode-block" id="stage_hub">
-<a class="viewcode-back" href="../../autodocs/trackhub.upload.stage_hub.html#trackhub.upload.stage_hub">[docs]</a>
-<span class="k">def</span> <span class="nf">stage_hub</span><span class="p">(</span><span class="n">hub</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="stage_hub"><a class="viewcode-back" href="../../autodocs/trackhub.upload.stage_hub.html#trackhub.upload.stage_hub">[docs]</a><span class="k">def</span> <span class="nf">stage_hub</span><span class="p">(</span><span class="n">hub</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Stage a hub by symlinking all its connected files to a local directory.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -302,10 +300,7 @@ <h1>Source code for trackhub.upload</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">staging</span><span class="p">,</span> <span class="n">linknames</span></div>
 
 
-
-<div class="viewcode-block" id="upload_hub">
-<a class="viewcode-back" href="../../autodocs/trackhub.upload.upload_hub.html#trackhub.upload.upload_hub">[docs]</a>
-<span class="k">def</span> <span class="nf">upload_hub</span><span class="p">(</span>
+<div class="viewcode-block" id="upload_hub"><a class="viewcode-back" href="../../autodocs/trackhub.upload.upload_hub.html#trackhub.upload.upload_hub">[docs]</a><span class="k">def</span> <span class="nf">upload_hub</span><span class="p">(</span>
     <span class="n">hub</span><span class="p">,</span> <span class="n">host</span><span class="p">,</span> <span class="n">remote_dir</span><span class="p">,</span> <span class="n">user</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">port</span><span class="o">=</span><span class="mi">22</span><span class="p">,</span> <span class="n">rsync_options</span><span class="o">=</span><span class="n">RSYNC_OPTIONS</span><span class="p">,</span> <span class="n">staging</span><span class="o">=</span><span class="kc">None</span>
 <span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
@@ -324,7 +319,6 @@ <h1>Source code for trackhub.upload</h1><div class="highlight"><pre>
         <span class="n">rsync_options</span><span class="o">=</span><span class="n">rsync_options</span><span class="p">,</span>
     <span class="p">)</span>
     <span class="k">return</span> <span class="n">linknames</span></div>
-
 </pre></div>
 
            </div>
diff --git a/_modules/trackhub/validate.html b/_modules/trackhub/validate.html
index de5a37c..84bd7ea 100644
--- a/_modules/trackhub/validate.html
+++ b/_modules/trackhub/validate.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.validate &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -162,12 +162,8 @@ <h1>Source code for trackhub.validate</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="n">wrapper</span>
 
 
-<div class="viewcode-block" id="Param">
-<a class="viewcode-back" href="../../autodocs/trackhub.parsed_params.Param.html#trackhub.parsed_params.Param">[docs]</a>
-<span class="k">class</span> <span class="nc">Param</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-<div class="viewcode-block" id="Param.__init__">
-<a class="viewcode-back" href="../../autodocs/trackhub.parsed_params.Param.html#trackhub.parsed_params.Param.__init__">[docs]</a>
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">fmt</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">required</span><span class="p">,</span> <span class="n">validator</span><span class="p">,</span> <span class="n">min_bed_fields</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="Param"><a class="viewcode-back" href="../../autodocs/trackhub.parsed_params.Param.html#trackhub.parsed_params.Param">[docs]</a><span class="k">class</span> <span class="nc">Param</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="Param.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.parsed_params.Param.html#trackhub.parsed_params.Param.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">,</span> <span class="n">fmt</span><span class="p">,</span> <span class="n">types</span><span class="p">,</span> <span class="n">required</span><span class="p">,</span> <span class="n">validator</span><span class="p">,</span> <span class="n">min_bed_fields</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Parameters</span>
 <span class="sd">        ----------</span>
@@ -213,7 +209,6 @@ <h1>Source code for trackhub.validate</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">required</span> <span class="o">=</span> <span class="n">required</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">validator</span> <span class="o">=</span> <span class="n">validator</span></div>
 
-
     <span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">return</span> <span class="s1">&#39;&lt;</span><span class="si">%s</span><span class="s1"> &quot;</span><span class="si">%s</span><span class="s1">&quot; at </span><span class="si">%s</span><span class="s1">&gt;&#39;</span> <span class="o">%</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="nb">id</span><span class="p">(</span><span class="bp">self</span><span class="p">))</span>
 
@@ -239,7 +234,6 @@ <h1>Source code for trackhub.validate</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="kc">False</span></div>
 
 
-
 <span class="nd">@validator</span><span class="p">(</span><span class="s2">&quot;tag=value&quot;</span><span class="p">,</span> <span class="s2">&quot;tag1=val1 tag2=val2&quot;</span><span class="p">)</span>
 <span class="k">def</span> <span class="nf">key_val</span><span class="p">(</span><span class="n">v</span><span class="p">):</span>
     <span class="k">try</span><span class="p">:</span>
diff --git a/_static/basic.css b/_static/basic.css
index f316efc..cfc60b8 100644
--- a/_static/basic.css
+++ b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -237,10 +237,6 @@ a.headerlink {
     visibility: hidden;
 }
 
-a:visited {
-    color: #551A8B;
-}
-
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
diff --git a/_static/doctools.js b/_static/doctools.js
index 4d67807..d06a71d 100644
--- a/_static/doctools.js
+++ b/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index 529239f..a7f754b 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,4 +1,5 @@
-const DOCUMENTATION_OPTIONS = {
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
     VERSION: '1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
diff --git a/_static/graphviz.css b/_static/graphviz.css
index 027576e..8d81c02 100644
--- a/_static/graphviz.css
+++ b/_static/graphviz.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- graphviz extension.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
diff --git a/_static/language_data.js b/_static/language_data.js
index 367b8ed..250f566 100644
--- a/_static/language_data.js
+++ b/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -13,7 +13,7 @@
 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"];
 
 
-/* Non-minified version is copied as a separate JS file, if available */
+/* Non-minified version is copied as a separate JS file, is available */
 
 /**
  * Porter Stemmer
diff --git a/_static/searchtools.js b/_static/searchtools.js
index 92da3f8..97d56a7 100644
--- a/_static/searchtools.js
+++ b/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms, highlightTerms) => {
+const _displayItem = (item, searchTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
+  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
-  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,35 +75,28 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = contentRoot + dirname;
+    requestUrl = docUrlRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = contentRoot + docName + docFileSuffix;
+    requestUrl = docUrlRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr) {
+  if (descr)
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
-    // highlight search terms in the description
-    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
-      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
-  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
       .then((data) => {
         if (data)
           listItem.appendChild(
-            Search.makeSearchSummary(data, searchTerms, anchor)
+            Search.makeSearchSummary(data, searchTerms)
           );
-        // highlight search terms in the summary
-        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
-          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -116,43 +109,26 @@ const _finishSearch = (resultCount) => {
     );
   else
     Search.status.innerText = _(
-      "Search finished, found ${resultCount} page(s) matching the search query."
-    ).replace('${resultCount}', resultCount);
+      `Search finished, found ${resultCount} page(s) matching the search query.`
+    );
 };
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms,
-  highlightTerms,
+  searchTerms
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms, highlightTerms);
+    _displayItem(results.pop(), searchTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
+      () => _displayNextItem(results, resultCount, searchTerms),
       5
     );
   }
   // search finished, update title and status message
   else _finishSearch(resultCount);
 };
-// Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
-// Order the results by score (in opposite order of appearance, since the
-// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
-const _orderResultsByScoreThenName = (a, b) => {
-  const leftScore = a[4];
-  const rightScore = b[4];
-  if (leftScore === rightScore) {
-    // same score: sort alphabetically
-    const leftTitle = a[1].toLowerCase();
-    const rightTitle = b[1].toLowerCase();
-    if (leftTitle === rightTitle) return 0;
-    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
-  }
-  return leftScore > rightScore ? 1 : -1;
-};
 
 /**
  * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -176,26 +152,13 @@ const Search = {
   _queued_query: null,
   _pulse_status: -1,
 
-  htmlToText: (htmlString, anchor) => {
+  htmlToText: (htmlString) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
-      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
-    }
-    if (anchor) {
-      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
-      if (anchorContent) return anchorContent.textContent;
-
-      console.warn(
-        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
-      );
-    }
-
-    // if anchor not specified or not found, fall back to main content
+    htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
     const docContent = htmlElement.querySelector('[role="main"]');
-    if (docContent) return docContent.textContent;
-
+    if (docContent !== undefined) return docContent.textContent;
     console.warn(
-      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
+      "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
     );
     return "";
   },
@@ -268,7 +231,16 @@ const Search = {
     else Search.deferQuery(query);
   },
 
-  _parseQuery: (query) => {
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  query: (query) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
     // stem the search terms and add them to the correct list
     const stemmer = new Stemmer();
     const searchTerms = new Set();
@@ -304,32 +276,16 @@ const Search = {
     // console.info("required: ", [...searchTerms]);
     // console.info("excluded: ", [...excludedTerms]);
 
-    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
-  },
-
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
-    const filenames = Search._index.filenames;
-    const docNames = Search._index.docnames;
-    const titles = Search._index.titles;
-    const allTitles = Search._index.alltitles;
-    const indexEntries = Search._index.indexentries;
-
-    // Collect multiple result groups to be sorted separately and then ordered.
-    // Each is an array of [docname, title, anchor, descr, score, filename].
-    const normalResults = [];
-    const nonMainIndexResults = [];
-
+    // array of [docname, title, anchor, descr, score, filename]
+    let results = [];
     _removeChildren(document.getElementById("search-progress"));
 
-    const queryLower = query.toLowerCase().trim();
+    const queryLower = query.toLowerCase();
     for (const [title, foundTitles] of Object.entries(allTitles)) {
-      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
+      if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
           let score = Math.round(100 * queryLower.length / title.length)
-          normalResults.push([
+          results.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
@@ -344,47 +300,46 @@ const Search = {
     // search for explicit entries in index directives
     for (const [entry, foundEntries] of Object.entries(indexEntries)) {
       if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
-        for (const [file, id, isMain] of foundEntries) {
-          const score = Math.round(100 * queryLower.length / entry.length);
-          const result = [
+        for (const [file, id] of foundEntries) {
+          let score = Math.round(100 * queryLower.length / entry.length)
+          results.push([
             docNames[file],
             titles[file],
             id ? "#" + id : "",
             null,
             score,
             filenames[file],
-          ];
-          if (isMain) {
-            normalResults.push(result);
-          } else {
-            nonMainIndexResults.push(result);
-          }
+          ]);
         }
       }
     }
 
     // lookup as object
     objectTerms.forEach((term) =>
-      normalResults.push(...Search.performObjectSearch(term, objectTerms))
+      results.push(...Search.performObjectSearch(term, objectTerms))
     );
 
     // lookup as search terms in fulltext
-    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+    results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
 
     // let the scorer override scores with a custom scoring function
-    if (Scorer.score) {
-      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
-      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
-    }
-
-    // Sort each group of results by score and then alphabetically by name.
-    normalResults.sort(_orderResultsByScoreThenName);
-    nonMainIndexResults.sort(_orderResultsByScoreThenName);
-
-    // Combine the result groups in (reverse) order.
-    // Non-main index entries are typically arbitrary cross-references,
-    // so display them after other results.
-    let results = [...nonMainIndexResults, ...normalResults];
+    if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
+
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort((a, b) => {
+      const leftScore = a[4];
+      const rightScore = b[4];
+      if (leftScore === rightScore) {
+        // same score: sort alphabetically
+        const leftTitle = a[1].toLowerCase();
+        const rightTitle = b[1].toLowerCase();
+        if (leftTitle === rightTitle) return 0;
+        return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+      }
+      return leftScore > rightScore ? 1 : -1;
+    });
 
     // remove duplicate search results
     // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
@@ -398,19 +353,14 @@ const Search = {
       return acc;
     }, []);
 
-    return results.reverse();
-  },
-
-  query: (query) => {
-    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
-    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
+    results = results.reverse();
 
     // for debugging
     //Search.lastresults = results.slice();  // a copy
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms, highlightTerms);
+    _displayNextItem(results, results.length, searchTerms);
   },
 
   /**
@@ -508,18 +458,14 @@ const Search = {
       // add support for partial matches
       if (word.length > 2) {
         const escapedWord = _escapeRegExp(word);
-        if (!terms.hasOwnProperty(word)) {
-          Object.keys(terms).forEach((term) => {
-            if (term.match(escapedWord))
-              arr.push({ files: terms[term], score: Scorer.partialTerm });
-          });
-        }
-        if (!titleTerms.hasOwnProperty(word)) {
-          Object.keys(titleTerms).forEach((term) => {
-            if (term.match(escapedWord))
-              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
-          });
-        }
+        Object.keys(terms).forEach((term) => {
+          if (term.match(escapedWord) && !terms[word])
+            arr.push({ files: terms[term], score: Scorer.partialTerm });
+        });
+        Object.keys(titleTerms).forEach((term) => {
+          if (term.match(escapedWord) && !titleTerms[word])
+            arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
+        });
       }
 
       // no match but word was a required one
@@ -542,8 +488,9 @@ const Search = {
 
       // create the mapping
       files.forEach((file) => {
-        if (!fileMap.has(file)) fileMap.set(file, [word]);
-        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
+        if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
+          fileMap.get(file).push(word);
+        else fileMap.set(file, [word]);
       });
     });
 
@@ -594,8 +541,8 @@ const Search = {
    * search summary for a given text. keywords is a list
    * of stemmed words.
    */
-  makeSearchSummary: (htmlText, keywords, anchor) => {
-    const text = Search.htmlToText(htmlText, anchor);
+  makeSearchSummary: (htmlText, keywords) => {
+    const text = Search.htmlToText(htmlText);
     if (text === "") return null;
 
     const textLower = text.toLowerCase();
diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js
index 8a96c69..aae669d 100644
--- a/_static/sphinx_highlight.js
+++ b/_static/sphinx_highlight.js
@@ -29,19 +29,14 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
-      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          rest,
+          document.createTextNode(val.substr(pos + text.length)),
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
-      /* There may be more occurrences of search term in this node. So call this
-       * function recursively on the remaining fragment.
-       */
-      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -145,10 +140,5 @@ const SphinxHighlight = {
   },
 };
 
-_ready(() => {
-  /* Do not call highlightSearchWords() when we are on the search page.
-   * It will highlight words from the *previous* search query.
-   */
-  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
-  SphinxHighlight.initEscapeListener();
-});
+_ready(SphinxHighlight.highlightSearchWords);
+_ready(SphinxHighlight.initEscapeListener);
diff --git a/assembly_example.html b/assembly_example.html
index 032efac..2260606 100644
--- a/assembly_example.html
+++ b/assembly_example.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Assembly example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -87,7 +87,7 @@
            <div itemprop="articleBody">
              
   <section id="assembly-example">
-<span id="id1"></span><h1>Assembly example<a class="headerlink" href="#assembly-example" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1>Assembly example<a class="headerlink" href="#assembly-example" title="Permalink to this heading"></a></h1>
 <p>The following example shows how to generate an <a class="reference external" href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs">Assembly Hub</a>, which is a way of
 supporting an assembly that is not already supported on UCSC.</p>
 <p>It requires a <code class="docutils literal notranslate"><span class="pre">.2bit</span></code> file, which is created from a FASTA file using UCSC’s
diff --git a/autodocs.html b/autodocs.html
index 3476114..c188843 100644
--- a/autodocs.html
+++ b/autodocs.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>API documentation &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -112,7 +112,7 @@
            <div itemprop="articleBody">
              
   <section id="api-documentation">
-<span id="autodoc"></span><h1>API documentation<a class="headerlink" href="#api-documentation" title="Link to this heading"></a></h1>
+<span id="autodoc"></span><h1>API documentation<a class="headerlink" href="#api-documentation" title="Permalink to this heading"></a></h1>
 <p class="rubric">Classes:</p>
 <table class="autosummary longtable docutils align-default">
 <tbody>
diff --git a/autodocs/trackhub.AggregateTrack.html b/autodocs/trackhub.AggregateTrack.html
index 859d925..5a41f58 100644
--- a/autodocs/trackhub.AggregateTrack.html
+++ b/autodocs/trackhub.AggregateTrack.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.AggregateTrack &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -131,7 +131,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-aggregatetrack">
-<h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack" title="Link to this heading"></a></h1>
+<h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack" title="Permalink to this heading"></a></h1>
 digraph inheritance9cb2cd4622 {
 bgcolor=transparent;
 rankdir=LR;
@@ -144,7 +144,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">AggregateTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">aggregate</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">AggregateTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">aggregate</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.track.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a></p>
 <p>Represents an Aggregate or Overlay track. Subclasses <a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code></a>,
 adds some extras.</p>
@@ -211,7 +211,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">aggregate</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">aggregate</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents an Aggregate or Overlay track. Subclasses <a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code></a>,
 adds some extras.</p>
 <p>Aggregate tracks allow closley related tracks to be viewed as a single
@@ -232,13 +232,13 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -250,13 +250,13 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Update the subgroups for this track.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.CompositeTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CompositeTrack()</span></code></a>, which takes a list of
 <a class="reference internal" href="trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition" title="trackhub.SubGroupDefinition"><code class="xref py py-class docutils literal notranslate"><span class="pre">SubGroupDefinition</span></code></a> objects representing the allowed subgroups,
@@ -274,30 +274,30 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_subtrack">
-<span class="sig-name descname"><span class="pre">add_subtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subtrack</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.add_subtrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.add_subtrack" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subtrack</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.add_subtrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.add_subtrack" title="Permalink to this definition"></a></dt>
 <dd><p>Add a child <code class="xref py py-class docutils literal notranslate"><span class="pre">SubTrack</span></code> to this aggregate.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.add_tracks">
-<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.add_tracks" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#AggregateTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.AggregateTrack.add_tracks" title="Permalink to this definition"></a></dt>
 <dd><p>Add one or more tracks.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>)</p>
+<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>) – </p>
 </dd>
 </dl>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -305,7 +305,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -315,7 +315,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -323,7 +323,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -333,7 +333,7 @@ <h1>trackhub.AggregateTrack<a class="headerlink" href="#trackhub-aggregatetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.AggregateTrack.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.AggregateTrack.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.Assembly.html b/autodocs/trackhub.Assembly.html
index 59ec182..e856df6 100644
--- a/autodocs/trackhub.Assembly.html
+++ b/autodocs/trackhub.Assembly.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.Assembly &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -127,7 +127,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-assembly">
-<h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link to this heading"></a></h1>
+<h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Permalink to this heading"></a></h1>
 digraph inheritance6fc99b999d {
 bgcolor=transparent;
 rankdir=LR;
@@ -140,7 +140,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.Assembly">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Assembly</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">twobit_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Assembly</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">twobit_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.Genome.html#trackhub.Genome" title="trackhub.genome.Genome"><code class="xref py py-class docutils literal notranslate"><span class="pre">Genome</span></code></a></p>
 <p>Represents a genome stanza within a “genomes.txt” file for a non-UCSC genome.</p>
 <p>The file itself is represented by a <a class="reference internal" href="trackhub.GenomesFile.html#trackhub.GenomesFile" title="trackhub.GenomesFile"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenomesFile</span></code></a> object.</p>
@@ -198,7 +198,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">twobit_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">twobit_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a genome stanza within a “genomes.txt” file for a non-UCSC genome.</p>
 <p>The file itself is represented by a <a class="reference internal" href="trackhub.GenomesFile.html#trackhub.GenomesFile" title="trackhub.GenomesFile"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenomesFile</span></code></a> object.</p>
 <dl class="field-list simple">
@@ -213,13 +213,13 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the Assembly.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -227,13 +227,13 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -241,7 +241,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the Assembly.</p>
 <p>E.g.,</p>
 <p>remove_params(‘color’, ‘visibility’)</p>
@@ -249,7 +249,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -257,7 +257,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Assembly.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -267,7 +267,7 @@ <h1>trackhub.Assembly<a class="headerlink" href="#trackhub-assembly" title="Link
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Assembly.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/assembly.html#Assembly.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Assembly.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.BaseTrack.html b/autodocs/trackhub.BaseTrack.html
index dcc31a6..3c36a0c 100644
--- a/autodocs/trackhub.BaseTrack.html
+++ b/autodocs/trackhub.BaseTrack.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.BaseTrack &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -129,7 +129,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-basetrack">
-<h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Link to this heading"></a></h1>
+<h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Permalink to this heading"></a></h1>
 digraph inheritance5d138bf573 {
 bgcolor=transparent;
 rankdir=LR;
@@ -140,7 +140,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.BaseTrack">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">BaseTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tracktype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subgroups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">BaseTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tracktype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subgroups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents a single track stanza, base class for other track types.</p>
 <dl class="field-list simple">
@@ -228,7 +228,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tracktype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subgroups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tracktype</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subgroups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">source</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">html_string_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'rst'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a single track stanza, base class for other track types.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -276,13 +276,13 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -294,13 +294,13 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Update the subgroups for this track.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.CompositeTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CompositeTrack()</span></code></a>, which takes a list of
 <a class="reference internal" href="trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition" title="trackhub.SubGroupDefinition"><code class="xref py py-class docutils literal notranslate"><span class="pre">SubGroupDefinition</span></code></a> objects representing the allowed subgroups,
@@ -318,13 +318,13 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_trackdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.add_trackdb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -332,7 +332,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -342,7 +342,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -350,7 +350,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.BaseTrack.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -360,7 +360,7 @@ <h1>trackhub.BaseTrack<a class="headerlink" href="#trackhub-basetrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.BaseTrack.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#BaseTrack.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.BaseTrack.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.CompositeTrack.html b/autodocs/trackhub.CompositeTrack.html
index 4df7dd6..41d5eda 100644
--- a/autodocs/trackhub.CompositeTrack.html
+++ b/autodocs/trackhub.CompositeTrack.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.CompositeTrack &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -132,7 +132,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-compositetrack">
-<h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack" title="Link to this heading"></a></h1>
+<h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack" title="Permalink to this heading"></a></h1>
 digraph inheritance3eb64a83f5 {
 bgcolor=transparent;
 rankdir=LR;
@@ -145,7 +145,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">CompositeTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">CompositeTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.track.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a></p>
 <p>Represents a composite track.  Subclasses <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a>, and adds
 some extras.</p>
@@ -208,7 +208,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a composite track.  Subclasses <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a>, and adds
 some extras.</p>
 <p>Add a view or subtrack to this composite with <a class="reference internal" href="#trackhub.CompositeTrack.add_tracks" title="trackhub.CompositeTrack.add_tracks"><code class="xref py py-meth docutils literal notranslate"><span class="pre">add_tracks()</span></code></a>.</p>
@@ -222,13 +222,13 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -240,13 +240,13 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Add a list of SubGroupDefinition objects to this composite.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BaseTrack()</span></code></a>, which takes a single
 dictionary indicating the particular subgroups for the track, this
@@ -261,7 +261,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_subtrack">
-<span class="sig-name descname"><span class="pre">add_subtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subtrack</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_subtrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_subtrack" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subtrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subtrack</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_subtrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_subtrack" title="Permalink to this definition"></a></dt>
 <dd><p>Add a child <a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code></a>.</p>
 <p>Deprecated in favor of the more generic <cite>add_tracks</cite> method, but
 maintained for backwards compatibility.</p>
@@ -269,13 +269,13 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_tracks">
-<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_tracks" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_tracks" title="Permalink to this definition"></a></dt>
 <dd><p>This method allows for both view and subtracks to be added to
 a composite at the same time. <cite>args</cite> can be arbitrary BaseTrack objects
 (typically Track or View objects), either singly or as a list. For
@@ -291,7 +291,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.add_view">
-<span class="sig-name descname"><span class="pre">add_view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_view"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_view" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_view</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#CompositeTrack.add_view"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.CompositeTrack.add_view" title="Permalink to this definition"></a></dt>
 <dd><p>Add a ViewTrack object to this composite.</p>
 <p>Deprecated in favor of the more generic <cite>add_tracks</cite> method, but
 maintained for backwards compatibility.</p>
@@ -304,7 +304,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -312,7 +312,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -322,7 +322,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -330,7 +330,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -340,7 +340,7 @@ <h1>trackhub.CompositeTrack<a class="headerlink" href="#trackhub-compositetrack"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.CompositeTrack.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.CompositeTrack.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.Genome.html b/autodocs/trackhub.Genome.html
index 4a1639b..81a553e 100644
--- a/autodocs/trackhub.Genome.html
+++ b/autodocs/trackhub.Genome.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.Genome &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -127,7 +127,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-genome">
-<h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to this heading"></a></h1>
+<h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Permalink to this heading"></a></h1>
 digraph inheritance30c3775cc1 {
 bgcolor=transparent;
 rankdir=LR;
@@ -138,7 +138,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.Genome">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Genome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Genome</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents a 2-line genome stanza within a “genomes.txt” file.</p>
 <p>The file itself is represented by a <a class="reference internal" href="trackhub.GenomesFile.html#trackhub.GenomesFile" title="trackhub.GenomesFile"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenomesFile</span></code></a> object.</p>
@@ -191,7 +191,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trackdb</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genome_file_obj</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a 2-line genome stanza within a “genomes.txt” file.</p>
 <p>The file itself is represented by a <a class="reference internal" href="trackhub.GenomesFile.html#trackhub.GenomesFile" title="trackhub.GenomesFile"><code class="xref py py-class docutils literal notranslate"><span class="pre">GenomesFile</span></code></a> object.</p>
 <dl class="field-list simple">
@@ -207,13 +207,13 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.add_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the Genome.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -221,13 +221,13 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -235,7 +235,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.remove_params"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the Genome.</p>
 <p>E.g.,</p>
 <p>remove_params(‘color’, ‘visibility’)</p>
@@ -243,7 +243,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -251,7 +251,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Genome.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -261,7 +261,7 @@ <h1>trackhub.Genome<a class="headerlink" href="#trackhub-genome" title="Link to
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Genome.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genome.html#Genome.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Genome.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.GenomesFile.html b/autodocs/trackhub.GenomesFile.html
index d8bcdc6..22450a9 100644
--- a/autodocs/trackhub.GenomesFile.html
+++ b/autodocs/trackhub.GenomesFile.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.GenomesFile &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -125,7 +125,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-genomesfile">
-<h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title="Link to this heading"></a></h1>
+<h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title="Permalink to this heading"></a></h1>
 digraph inheritance41de0a9936 {
 bgcolor=transparent;
 rankdir=LR;
@@ -136,7 +136,7 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.GenomesFile">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GenomesFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GenomesFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents the genomes file on disk.  Can contain multiple <cite>Genome</cite>
 objects, each of which represent a stanza in this file.</p>
@@ -183,7 +183,7 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genome</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents the genomes file on disk.  Can contain multiple <cite>Genome</cite>
 objects, each of which represent a stanza in this file.</p>
 <dl class="field-list simple">
@@ -199,19 +199,19 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -219,7 +219,7 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -227,7 +227,7 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GenomesFile.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -237,7 +237,7 @@ <h1>trackhub.GenomesFile<a class="headerlink" href="#trackhub-genomesfile" title
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GenomesFile.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/genomes_file.html#GenomesFile.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GenomesFile.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.GroupDefinition.html b/autodocs/trackhub.GroupDefinition.html
index 677d785..3dda68b 100644
--- a/autodocs/trackhub.GroupDefinition.html
+++ b/autodocs/trackhub.GroupDefinition.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.GroupDefinition &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -119,7 +119,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-groupdefinition">
-<h1>trackhub.GroupDefinition<a class="headerlink" href="#trackhub-groupdefinition" title="Link to this heading"></a></h1>
+<h1>trackhub.GroupDefinition<a class="headerlink" href="#trackhub-groupdefinition" title="Permalink to this heading"></a></h1>
 digraph inheritance415fc95d1e {
 bgcolor=transparent;
 rankdir=LR;
@@ -128,7 +128,7 @@ <h1>trackhub.GroupDefinition<a class="headerlink" href="#trackhub-groupdefinitio
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.GroupDefinition">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GroupDefinition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_is_closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupDefinition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupDefinition" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GroupDefinition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_is_closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupDefinition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupDefinition" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Represents a group of tracks in a trackhub.</p>
 <p>Instances of this class are provided to an assembly.</p>
@@ -153,7 +153,7 @@ <h1>trackhub.GroupDefinition<a class="headerlink" href="#trackhub-groupdefinitio
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupDefinition.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_is_closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupDefinition.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupDefinition.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_is_closed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupDefinition.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupDefinition.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a group of tracks in a trackhub.</p>
 <p>Instances of this class are provided to an assembly.</p>
 <dl class="field-list simple">
diff --git a/autodocs/trackhub.GroupsFile.html b/autodocs/trackhub.GroupsFile.html
index 6fb793e..9190a4c 100644
--- a/autodocs/trackhub.GroupsFile.html
+++ b/autodocs/trackhub.GroupsFile.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.GroupsFile &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -126,7 +126,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-groupsfile">
-<h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="Link to this heading"></a></h1>
+<h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="Permalink to this heading"></a></h1>
 digraph inheritanced2db589814 {
 bgcolor=transparent;
 rankdir=LR;
@@ -137,7 +137,7 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.GroupsFile">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GroupsFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">GroupsFile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents the groups file on disk, used for assembly hubs.</p>
 <dl class="field-list simple">
@@ -183,7 +183,7 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents the groups file on disk, used for assembly hubs.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -198,13 +198,13 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.add_groups">
-<span class="sig-name descname"><span class="pre">add_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.add_groups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.add_groups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.add_groups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.add_groups" title="Permalink to this definition"></a></dt>
 <dd><p>Add a list of GroupDefinition objects.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -215,13 +215,13 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -229,7 +229,7 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -237,7 +237,7 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.GroupsFile.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -247,7 +247,7 @@ <h1>trackhub.GroupsFile<a class="headerlink" href="#trackhub-groupsfile" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.GroupsFile.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/groups.html#GroupsFile.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.GroupsFile.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.Hub.html b/autodocs/trackhub.Hub.html
index 1c69dd9..ae935bf 100644
--- a/autodocs/trackhub.Hub.html
+++ b/autodocs/trackhub.Hub.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.Hub &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -126,7 +126,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-hub">
-<h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this heading"></a></h1>
+<h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Permalink to this heading"></a></h1>
 digraph inheritance88b4433c18 {
 bgcolor=transparent;
 rankdir=LR;
@@ -137,7 +137,7 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.Hub">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents a top-level track hub container.</p>
 <dl class="simple">
@@ -194,7 +194,7 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">short_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">long_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genomes_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">email</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a top-level track hub container.</p>
 <dl class="simple">
 <dt>hub<span class="classifier">str</span></dt><dd><p>Top-level name of the hub.</p>
@@ -220,26 +220,26 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.add_genomes_file">
-<span class="sig-name descname"><span class="pre">add_genomes_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.add_genomes_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.add_genomes_file" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_genomes_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">genomes_file</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.add_genomes_file"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.add_genomes_file" title="Permalink to this definition"></a></dt>
 <dd><p>If a GenomesFile object was not provided upon instantiating this
 object, attach one now</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -247,7 +247,7 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -255,7 +255,7 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Hub.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -265,7 +265,7 @@ <h1>trackhub.Hub<a class="headerlink" href="#trackhub-hub" title="Link to this h
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Hub.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/hub.html#Hub.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Hub.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.SubGroupDefinition.html b/autodocs/trackhub.SubGroupDefinition.html
index fd47d2f..5193ff4 100644
--- a/autodocs/trackhub.SubGroupDefinition.html
+++ b/autodocs/trackhub.SubGroupDefinition.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.SubGroupDefinition &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -119,7 +119,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-subgroupdefinition">
-<h1>trackhub.SubGroupDefinition<a class="headerlink" href="#trackhub-subgroupdefinition" title="Link to this heading"></a></h1>
+<h1>trackhub.SubGroupDefinition<a class="headerlink" href="#trackhub-subgroupdefinition" title="Permalink to this heading"></a></h1>
 digraph inheritance11992ac205 {
 bgcolor=transparent;
 rankdir=LR;
@@ -128,7 +128,7 @@ <h1>trackhub.SubGroupDefinition<a class="headerlink" href="#trackhub-subgroupdef
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.SubGroupDefinition">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">SubGroupDefinition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mapping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SubGroupDefinition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SubGroupDefinition" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">SubGroupDefinition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mapping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SubGroupDefinition"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SubGroupDefinition" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Represents a subgroup line in a composite track.</p>
 <p>Instances of this class are provided to a composite track in order to
@@ -171,7 +171,7 @@ <h1>trackhub.SubGroupDefinition<a class="headerlink" href="#trackhub-subgroupdef
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SubGroupDefinition.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mapping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SubGroupDefinition.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SubGroupDefinition.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mapping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'none'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SubGroupDefinition.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SubGroupDefinition.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a subgroup line in a composite track.</p>
 <p>Instances of this class are provided to a composite track in order to
 define options for the subtracks’ groups.</p>
diff --git a/autodocs/trackhub.SuperTrack.html b/autodocs/trackhub.SuperTrack.html
index 04cbb05..be2492e 100644
--- a/autodocs/trackhub.SuperTrack.html
+++ b/autodocs/trackhub.SuperTrack.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.SuperTrack &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -130,7 +130,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-supertrack">
-<h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="Link to this heading"></a></h1>
+<h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="Permalink to this heading"></a></h1>
 digraph inheritance45a2de254f {
 bgcolor=transparent;
 rankdir=LR;
@@ -143,7 +143,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.SuperTrack">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">SuperTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">SuperTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.track.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a></p>
 <p>Represents a Super track. Subclasses <a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code></a>, and adds some
 extras.</p>
@@ -199,7 +199,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a Super track. Subclasses <a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code></a>, and adds some
 extras.</p>
 <p>Super tracks are container tracks (folders) that group tracks. They are
@@ -212,13 +212,13 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -230,13 +230,13 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Update the subgroups for this track.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.CompositeTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CompositeTrack()</span></code></a>, which takes a list of
 <a class="reference internal" href="trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition" title="trackhub.SubGroupDefinition"><code class="xref py py-class docutils literal notranslate"><span class="pre">SubGroupDefinition</span></code></a> objects representing the allowed subgroups,
@@ -254,24 +254,24 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.add_tracks">
-<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack.add_tracks" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#SuperTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.SuperTrack.add_tracks" title="Permalink to this definition"></a></dt>
 <dd><p>Add one or more tracks.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>)</p>
+<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>) – </p>
 </dd>
 </dl>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -279,7 +279,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -289,7 +289,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -297,7 +297,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -307,7 +307,7 @@ <h1>trackhub.SuperTrack<a class="headerlink" href="#trackhub-supertrack" title="
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.SuperTrack.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.SuperTrack.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.Track.html b/autodocs/trackhub.Track.html
index f193689..e00e7c3 100644
--- a/autodocs/trackhub.Track.html
+++ b/autodocs/trackhub.Track.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.Track &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -129,7 +129,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-track">
-<h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to this heading"></a></h1>
+<h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Permalink to this heading"></a></h1>
 digraph inheritancef595ae0a64 {
 bgcolor=transparent;
 rankdir=LR;
@@ -142,7 +142,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.Track">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Track</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#Track"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Track" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">Track</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#Track"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Track" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.track.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a></p>
 <p>Represents a single track stanza along with the file it describes.</p>
 <p>See <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a> for details on arguments. Additional arguments
@@ -199,7 +199,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#Track.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Track.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">url</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#Track.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.Track.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a single track stanza along with the file it describes.</p>
 <p>See <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a> for details on arguments. Additional arguments
 supported by this class:</p>
@@ -216,13 +216,13 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -234,13 +234,13 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Update the subgroups for this track.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.CompositeTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CompositeTrack()</span></code></a>, which takes a list of
 <a class="reference internal" href="trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition" title="trackhub.SubGroupDefinition"><code class="xref py py-class docutils literal notranslate"><span class="pre">SubGroupDefinition</span></code></a> objects representing the allowed subgroups,
@@ -258,13 +258,13 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -272,7 +272,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -282,7 +282,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -290,7 +290,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -300,7 +300,7 @@ <h1>trackhub.Track<a class="headerlink" href="#trackhub-track" title="Link to th
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.Track.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.Track.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.TrackDb.html b/autodocs/trackhub.TrackDb.html
index e1c5bdb..aef925b 100644
--- a/autodocs/trackhub.TrackDb.html
+++ b/autodocs/trackhub.TrackDb.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.TrackDb &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -126,7 +126,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-trackdb">
-<h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link to this heading"></a></h1>
+<h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Permalink to this heading"></a></h1>
 digraph inheritancee8eb7d8e37 {
 bgcolor=transparent;
 rankdir=LR;
@@ -137,7 +137,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.TrackDb">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">TrackDb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tracks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">TrackDb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tracks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.base.HubComponent.html#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a></p>
 <p>Represents the file containing one or more Track objects (which each
 represent a stanza).</p>
@@ -185,7 +185,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tracks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tracks</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents the file containing one or more Track objects (which each
 represent a stanza).</p>
 <dl class="simple">
@@ -199,19 +199,19 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.add_tracks">
-<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">track</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.add_tracks" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">track</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.add_tracks" title="Permalink to this definition"></a></dt>
 <dd><p>Add a track or iterable of tracks.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -223,7 +223,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -231,7 +231,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -239,7 +239,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.TrackDb.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -249,7 +249,7 @@ <h1>trackhub.TrackDb<a class="headerlink" href="#trackhub-trackdb" title="Link t
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.TrackDb.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/trackdb.html#TrackDb.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.TrackDb.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.ViewTrack.html b/autodocs/trackhub.ViewTrack.html
index d5bdafa..17545c7 100644
--- a/autodocs/trackhub.ViewTrack.html
+++ b/autodocs/trackhub.ViewTrack.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.ViewTrack &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -130,7 +130,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-viewtrack">
-<h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Link to this heading"></a></h1>
+<h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Permalink to this heading"></a></h1>
 digraph inheritance4be2653339 {
 bgcolor=transparent;
 rankdir=LR;
@@ -143,7 +143,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.ViewTrack">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">ViewTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.</span></span><span class="sig-name descname"><span class="pre">ViewTrack</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.track.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a></p>
 <p>Represents a View track.  Subclasses <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a>, and adds some
 extras.</p>
@@ -204,7 +204,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack.__init__" title="Permalink to this definition"></a></dt>
 <dd><p>Represents a View track.  Subclasses <a class="reference internal" href="trackhub.BaseTrack.html#trackhub.BaseTrack" title="trackhub.BaseTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">BaseTrack</span></code></a>, and adds some
 extras.</p>
 <p>This will need to be added to a <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.track.CompositeTrack"><code class="xref py py-class docutils literal notranslate"><span class="pre">track.CompositeTrack</span></code></a> with
@@ -222,13 +222,13 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_params">
-<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kw</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_params" title="Permalink to this definition"></a></dt>
 <dd><p>Add [possibly many] parameters to the track.</p>
 <p>Parameters will be checked against known UCSC parameters and their
 supported formats.</p>
@@ -240,13 +240,13 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_subgroups">
-<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">subgroups</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Update the subgroups for this track.</p>
 <p>Note that in contrast to <a class="reference internal" href="trackhub.CompositeTrack.html#trackhub.CompositeTrack" title="trackhub.CompositeTrack"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CompositeTrack()</span></code></a>, which takes a list of
 <a class="reference internal" href="trackhub.SubGroupDefinition.html#trackhub.SubGroupDefinition" title="trackhub.SubGroupDefinition"><code class="xref py py-class docutils literal notranslate"><span class="pre">SubGroupDefinition</span></code></a> objects representing the allowed subgroups,
@@ -264,24 +264,24 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_trackdb">
-<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_trackdb" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_trackdb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trackdb</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.add_trackdb" title="Permalink to this definition"></a></dt>
 <dd><p>Attach this track to a parent TrackDb object.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.add_tracks">
-<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack.add_tracks" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_tracks</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/track.html#ViewTrack.add_tracks"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.ViewTrack.add_tracks" title="Permalink to this definition"></a></dt>
 <dd><p>Add one or more tracks to this view.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>)</p>
+<dd class="field-odd"><p><strong>args</strong> (<a class="reference internal" href="trackhub.Track.html#trackhub.Track" title="trackhub.Track"><em>Track</em></a><em> or </em><em>iterable</em><em> of </em><em>Tracks</em>) – </p>
 </dd>
 </dl>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -289,7 +289,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.remove_params">
-<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.remove_params" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">remove_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.remove_params" title="Permalink to this definition"></a></dt>
 <dd><p>Remove [possibly many] parameters from the track.</p>
 <p>E.g.:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">remove_params</span><span class="p">(</span><span class="s1">&#39;color&#39;</span><span class="p">,</span> <span class="s1">&#39;visibility&#39;</span><span class="p">)</span>
@@ -299,7 +299,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code>, the rendering is recursive.</p>
@@ -307,7 +307,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -317,7 +317,7 @@ <h1>trackhub.ViewTrack<a class="headerlink" href="#trackhub-viewtrack" title="Li
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.ViewTrack.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#trackhub.ViewTrack.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.base.HubComponent.html b/autodocs/trackhub.base.HubComponent.html
index 02f9f19..8ac53a6 100644
--- a/autodocs/trackhub.base.HubComponent.html
+++ b/autodocs/trackhub.base.HubComponent.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.base.HubComponent &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -125,7 +125,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-base-hubcomponent">
-<h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomponent" title="Link to this heading"></a></h1>
+<h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomponent" title="Permalink to this heading"></a></h1>
 digraph inheritancef245ed092d {
 bgcolor=transparent;
 rankdir=LR;
@@ -134,7 +134,7 @@ <h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomp
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.base.</span></span><span class="sig-name descname"><span class="pre">HubComponent</span></span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.base.</span></span><span class="sig-name descname"><span class="pre">HubComponent</span></span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Base class for various track hub components.  Several methods must be
 overridden by subclasses.</p>
@@ -169,24 +169,24 @@ <h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomp
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.__init__" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.add_child">
-<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.add_child"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.add_child" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_child</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">child</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.add_child"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.add_child" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as parent to child, and then adds child.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.add_parent">
-<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.add_parent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.add_parent" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">add_parent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parent</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.add_parent"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.add_parent" title="Permalink to this definition"></a></dt>
 <dd><p>Adds self as child of parent, then adds parent.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.leaves">
-<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.leaves"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.leaves" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">leaves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intermediate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.leaves"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.leaves" title="Permalink to this definition"></a></dt>
 <dd><p>Returns an iterator of the HubComponent leaves that are of class <cite>cls</cite>.</p>
 <p>If <cite>intermediate</cite> is True, then return any intermediate classes as
 well.</p>
@@ -194,7 +194,7 @@ <h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomp
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.render">
-<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.render"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.render" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">render</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.render"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.render" title="Permalink to this definition"></a></dt>
 <dd><p>Renders the object to file, returning a list of created files.</p>
 <p>Calls validation code, and, as long as each child is also a subclass of
 <a class="reference internal" href="#trackhub.base.HubComponent" title="trackhub.base.HubComponent"><code class="xref py py-class docutils literal notranslate"><span class="pre">HubComponent</span></code></a>, the rendering is recursive.</p>
@@ -202,7 +202,7 @@ <h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomp
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.root">
-<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.root"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.root" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">root</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cls</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.root"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.root" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the top-most HubComponent in the hierarchy.</p>
 <p>If <cite>cls</cite> is not None, then return the top-most attribute HubComponent
 that is an instance of class <cite>cls</cite>.</p>
@@ -212,7 +212,7 @@ <h1>trackhub.base.HubComponent<a class="headerlink" href="#trackhub-base-hubcomp
 
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.base.HubComponent.validate">
-<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.validate" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">validate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/base.html#HubComponent.validate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.base.HubComponent.validate" title="Permalink to this definition"></a></dt>
 <dd><p>Runs validation, raising exceptions as needed.  Must be overridden by
 subclass.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.helpers.data_dir.html b/autodocs/trackhub.helpers.data_dir.html
index 45eb35f..195c442 100644
--- a/autodocs/trackhub.helpers.data_dir.html
+++ b/autodocs/trackhub.helpers.data_dir.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.helpers.data_dir &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,10 +116,10 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-helpers-data-dir">
-<h1>trackhub.helpers.data_dir<a class="headerlink" href="#trackhub-helpers-data-dir" title="Link to this heading"></a></h1>
+<h1>trackhub.helpers.data_dir<a class="headerlink" href="#trackhub-helpers-data-dir" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.helpers.data_dir">
-<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">data_dir</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#data_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.data_dir" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">data_dir</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#data_dir"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.data_dir" title="Permalink to this definition"></a></dt>
 <dd><p>Returns the data directory that contains example files for tests and
 documentation.</p>
 </dd></dl>
diff --git a/autodocs/trackhub.helpers.dimensions_from_subgroups.html b/autodocs/trackhub.helpers.dimensions_from_subgroups.html
index 608e122..96f2ae0 100644
--- a/autodocs/trackhub.helpers.dimensions_from_subgroups.html
+++ b/autodocs/trackhub.helpers.dimensions_from_subgroups.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.helpers.dimensions_from_subgroups &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,15 +116,15 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-helpers-dimensions-from-subgroups">
-<h1>trackhub.helpers.dimensions_from_subgroups<a class="headerlink" href="#trackhub-helpers-dimensions-from-subgroups" title="Link to this heading"></a></h1>
+<h1>trackhub.helpers.dimensions_from_subgroups<a class="headerlink" href="#trackhub-helpers-dimensions-from-subgroups" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.helpers.dimensions_from_subgroups">
-<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">dimensions_from_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#dimensions_from_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.dimensions_from_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">dimensions_from_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#dimensions_from_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.dimensions_from_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Given a sorted list of subgroups, return a string appropriate to provide as
 a composite track’s <cite>dimensions</cite> arg.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>s</strong> (list of SubGroup objects (or anything with a <cite>name</cite> attribute))</p>
+<dd class="field-odd"><p><strong>s</strong> (list of SubGroup objects (or anything with a <cite>name</cite> attribute)) – </p>
 </dd>
 </dl>
 </dd></dl>
diff --git a/autodocs/trackhub.helpers.filter_composite_from_subgroups.html b/autodocs/trackhub.helpers.filter_composite_from_subgroups.html
index 4412a12..7dbe0cb 100644
--- a/autodocs/trackhub.helpers.filter_composite_from_subgroups.html
+++ b/autodocs/trackhub.helpers.filter_composite_from_subgroups.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.helpers.filter_composite_from_subgroups &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,10 +116,10 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-helpers-filter-composite-from-subgroups">
-<h1>trackhub.helpers.filter_composite_from_subgroups<a class="headerlink" href="#trackhub-helpers-filter-composite-from-subgroups" title="Link to this heading"></a></h1>
+<h1>trackhub.helpers.filter_composite_from_subgroups<a class="headerlink" href="#trackhub-helpers-filter-composite-from-subgroups" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.helpers.filter_composite_from_subgroups">
-<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">filter_composite_from_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#filter_composite_from_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.filter_composite_from_subgroups" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">filter_composite_from_subgroups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#filter_composite_from_subgroups"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.filter_composite_from_subgroups" title="Permalink to this definition"></a></dt>
 <dd><p>Given a sorted list of subgroups, return a string appropriate to provide as
 the a composite track’s <cite>filterComposite</cite> argument</p>
 <div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">trackhub</span>
diff --git a/autodocs/trackhub.helpers.hex2rgb.html b/autodocs/trackhub.helpers.hex2rgb.html
index 856ce2d..7e61ae3 100644
--- a/autodocs/trackhub.helpers.hex2rgb.html
+++ b/autodocs/trackhub.helpers.hex2rgb.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.helpers.hex2rgb &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,19 +116,19 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-helpers-hex2rgb">
-<h1>trackhub.helpers.hex2rgb<a class="headerlink" href="#trackhub-helpers-hex2rgb" title="Link to this heading"></a></h1>
+<h1>trackhub.helpers.hex2rgb<a class="headerlink" href="#trackhub-helpers-hex2rgb" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.helpers.hex2rgb">
-<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">hex2rgb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">h</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#hex2rgb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.hex2rgb" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">hex2rgb</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">h</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#hex2rgb"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.hex2rgb" title="Permalink to this definition"></a></dt>
 <dd><p>Convert hex colors to RGB tuples</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>h</strong> (<em>str</em>) – String hex color value</p></li>
-<li><p><strong>hex2rgb</strong><strong>(</strong><strong>&quot;#ff0033&quot;</strong><strong>)</strong> (<em>&gt;&gt;&gt;</em>)</p></li>
-<li><p><strong>'255</strong></p></li>
-<li><p><strong>0</strong></p></li>
-<li><p><strong>51'</strong></p></li>
+<li><p><strong>hex2rgb</strong><strong>(</strong><strong>&quot;#ff0033&quot;</strong><strong>)</strong> (<em>&gt;&gt;&gt;</em>) – </p></li>
+<li><p><strong>'255</strong> – </p></li>
+<li><p><strong>0</strong> – </p></li>
+<li><p><strong>51'</strong> – </p></li>
 </ul>
 </dd>
 </dl>
diff --git a/autodocs/trackhub.helpers.sanitize.html b/autodocs/trackhub.helpers.sanitize.html
index f99952d..a3e8543 100644
--- a/autodocs/trackhub.helpers.sanitize.html
+++ b/autodocs/trackhub.helpers.sanitize.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.helpers.sanitize &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,10 +116,10 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-helpers-sanitize">
-<h1>trackhub.helpers.sanitize<a class="headerlink" href="#trackhub-helpers-sanitize" title="Link to this heading"></a></h1>
+<h1>trackhub.helpers.sanitize<a class="headerlink" href="#trackhub-helpers-sanitize" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.helpers.sanitize">
-<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">sanitize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#sanitize"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.sanitize" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.helpers.</span></span><span class="sig-name descname"><span class="pre">sanitize</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/helpers.html#sanitize"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.helpers.sanitize" title="Permalink to this definition"></a></dt>
 <dd><p>Sanitize a string.</p>
 <p>Spaces are converted to underscore; if strict=True they are then removed.</p>
 <dl class="field-list simple">
diff --git a/autodocs/trackhub.parsed_params.Param.html b/autodocs/trackhub.parsed_params.Param.html
index 062a690..fa31d9a 100644
--- a/autodocs/trackhub.parsed_params.Param.html
+++ b/autodocs/trackhub.parsed_params.Param.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.parsed_params.Param &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -119,7 +119,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-parsed-params-param">
-<h1>trackhub.parsed_params.Param<a class="headerlink" href="#trackhub-parsed-params-param" title="Link to this heading"></a></h1>
+<h1>trackhub.parsed_params.Param<a class="headerlink" href="#trackhub-parsed-params-param" title="Permalink to this heading"></a></h1>
 digraph inheritancecc27fbbc05 {
 bgcolor=transparent;
 rankdir=LR;
@@ -128,7 +128,7 @@ <h1>trackhub.parsed_params.Param<a class="headerlink" href="#trackhub-parsed-par
 }
 <dl class="py class">
 <dt class="sig sig-object py" id="trackhub.parsed_params.Param">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.parsed_params.</span></span><span class="sig-name descname"><span class="pre">Param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_bed_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/validate.html#Param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.parsed_params.Param" title="Link to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">trackhub.parsed_params.</span></span><span class="sig-name descname"><span class="pre">Param</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_bed_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/validate.html#Param"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.parsed_params.Param" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -178,7 +178,7 @@ <h1>trackhub.parsed_params.Param<a class="headerlink" href="#trackhub-parsed-par
 </table>
 <dl class="py method">
 <dt class="sig sig-object py" id="trackhub.parsed_params.Param.__init__">
-<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_bed_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/validate.html#Param.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.parsed_params.Param.__init__" title="Link to this definition"></a></dt>
+<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">types</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">required</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_bed_fields</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/validate.html#Param.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.parsed_params.Param.__init__" title="Permalink to this definition"></a></dt>
 <dd><dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
diff --git a/autodocs/trackhub.upload.stage_hub.html b/autodocs/trackhub.upload.stage_hub.html
index 27fa34b..cb49972 100644
--- a/autodocs/trackhub.upload.stage_hub.html
+++ b/autodocs/trackhub.upload.stage_hub.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.upload.stage_hub &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,10 +116,10 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-upload-stage-hub">
-<h1>trackhub.upload.stage_hub<a class="headerlink" href="#trackhub-upload-stage-hub" title="Link to this heading"></a></h1>
+<h1>trackhub.upload.stage_hub<a class="headerlink" href="#trackhub-upload-stage-hub" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.upload.stage_hub">
-<span class="sig-prename descclassname"><span class="pre">trackhub.upload.</span></span><span class="sig-name descname"><span class="pre">stage_hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/upload.html#stage_hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.upload.stage_hub" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.upload.</span></span><span class="sig-name descname"><span class="pre">stage_hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/upload.html#stage_hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.upload.stage_hub" title="Permalink to this definition"></a></dt>
 <dd><p>Stage a hub by symlinking all its connected files to a local directory.</p>
 </dd></dl>
 
diff --git a/autodocs/trackhub.upload.upload_hub.html b/autodocs/trackhub.upload.upload_hub.html
index 1ea96fe..6057369 100644
--- a/autodocs/trackhub.upload.upload_hub.html
+++ b/autodocs/trackhub.upload.upload_hub.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub.upload.upload_hub &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -116,10 +116,10 @@
            <div itemprop="articleBody">
              
   <section id="trackhub-upload-upload-hub">
-<h1>trackhub.upload.upload_hub<a class="headerlink" href="#trackhub-upload-upload-hub" title="Link to this heading"></a></h1>
+<h1>trackhub.upload.upload_hub<a class="headerlink" href="#trackhub-upload-upload-hub" title="Permalink to this heading"></a></h1>
 <dl class="py function">
 <dt class="sig sig-object py" id="trackhub.upload.upload_hub">
-<span class="sig-prename descclassname"><span class="pre">trackhub.upload.</span></span><span class="sig-name descname"><span class="pre">upload_hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">host</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remote_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">user</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">port</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">22</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rsync_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'--progress</span> <span class="pre">-rvL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/upload.html#upload_hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.upload.upload_hub" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">trackhub.upload.</span></span><span class="sig-name descname"><span class="pre">upload_hub</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hub</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">host</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remote_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">user</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">port</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">22</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rsync_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'--progress</span> <span class="pre">-rvL'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">staging</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/trackhub/upload.html#upload_hub"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#trackhub.upload.upload_hub" title="Permalink to this definition"></a></dt>
 <dd><p>Renders, stages, and uploads a hub.</p>
 </dd></dl>
 
diff --git a/changelog.html b/changelog.html
index 74577f4..d1e64e1 100644
--- a/changelog.html
+++ b/changelog.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Changelog &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -106,19 +106,19 @@
            <div itemprop="articleBody">
              
   <section id="changelog">
-<h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading"></a></h1>
+<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this heading"></a></h1>
 <section id="version-1-0-april-2024">
-<h2>Version 1.0 (April 2024)<a class="headerlink" href="#version-1-0-april-2024" title="Link to this heading"></a></h2>
+<h2>Version 1.0 (April 2024)<a class="headerlink" href="#version-1-0-april-2024" title="Permalink to this heading"></a></h2>
 <p>This major release is backwards-compatible but adds many new features and tests.</p>
 <section id="testing-infrastructure-overhaul">
-<h3>Testing infrastructure overhaul<a class="headerlink" href="#testing-infrastructure-overhaul" title="Link to this heading"></a></h3>
+<h3>Testing infrastructure overhaul<a class="headerlink" href="#testing-infrastructure-overhaul" title="Permalink to this heading"></a></h3>
 <p>Extensive example hubs that demonstrate the various track types and
 configuration options. These use data provided by UCSC and are built as part of
 the testing framework. Thanks to Eva Jason (&#64;evajason).</p>
 <p>See <a class="reference internal" href="tests.html#tests"><span class="std std-ref">Testing infrastructure</span></a> and <a class="reference internal" href="tracktypes.html#tracktypes"><span class="std std-ref">Examples of hubs using various supported track types</span></a> for details.</p>
 </section>
 <section id="build-a-trackhub-configured-in-excel">
-<h3>Build a trackhub configured in Excel<a class="headerlink" href="#build-a-trackhub-configured-in-excel" title="Link to this heading"></a></h3>
+<h3>Build a trackhub configured in Excel<a class="headerlink" href="#build-a-trackhub-configured-in-excel" title="Permalink to this heading"></a></h3>
 <p>Build a trackhub using only a command-line tool and configuration in Excel.
 This new tool, <code class="docutils literal notranslate"><span class="pre">trackhub_from_excel</span></code>, can write out a template you can use to
 fill in details on what tracks should be included, how to organize them, and
@@ -128,7 +128,7 @@ <h3>Build a trackhub configured in Excel<a class="headerlink" href="#build-a-tra
 <p>Thanks Eva Jason (&#64;evajason) for this new feature.</p>
 </section>
 <section id="semi-automated-updating-of-validated-parameters">
-<h3>Semi-automated updating of validated parameters<a class="headerlink" href="#semi-automated-updating-of-validated-parameters" title="Link to this heading"></a></h3>
+<h3>Semi-automated updating of validated parameters<a class="headerlink" href="#semi-automated-updating-of-validated-parameters" title="Permalink to this heading"></a></h3>
 <p>Dramatically improved semi-automatic updating mechanism for making sure
 parameters are up-to-date with the main UCSC instance (see
 <code class="docutils literal notranslate"><span class="pre">trackhub/parse.py</span></code> and <code class="docutils literal notranslate"><span class="pre">trackhub/parsed_params.py</span></code>). These scrape the UCSC
@@ -138,7 +138,7 @@ <h3>Semi-automated updating of validated parameters<a class="headerlink" href="#
 Genome Browser since the last trackhub Python package update.</p>
 </section>
 <section id="other-changes">
-<h3>Other changes<a class="headerlink" href="#other-changes" title="Link to this heading"></a></h3>
+<h3>Other changes<a class="headerlink" href="#other-changes" title="Permalink to this heading"></a></h3>
 <ul class="simple">
 <li><p>New section that details how validation works (see <a class="reference internal" href="validation.html#validation"><span class="std std-ref">Validation</span></a>).</p></li>
 <li><p><cite>defaultPos</cite> can now be set when using the <cite>default_hub</cite> helper function</p></li>
@@ -158,9 +158,9 @@ <h3>Other changes<a class="headerlink" href="#other-changes" title="Link to this
 </section>
 </section>
 <section id="version-0-2-4-dec-2017">
-<h2>Version 0.2.4 (Dec 2017)<a class="headerlink" href="#version-0-2-4-dec-2017" title="Link to this heading"></a></h2>
+<h2>Version 0.2.4 (Dec 2017)<a class="headerlink" href="#version-0-2-4-dec-2017" title="Permalink to this heading"></a></h2>
 <section id="improved-file-uploading">
-<h3>Improved file uploading<a class="headerlink" href="#improved-file-uploading" title="Link to this heading"></a></h3>
+<h3>Improved file uploading<a class="headerlink" href="#improved-file-uploading" title="Permalink to this heading"></a></h3>
 <p>Instead of uploading files one-by-one, first the hub is rendered to a local
 “staging” directory and tracks are symlinked over to this directory. BAM and
 VCF indexes are also symlinked if needed, and any HTML documentation is also
@@ -170,7 +170,7 @@ <h3>Improved file uploading<a class="headerlink" href="#improved-file-uploading"
 <figure class="align-default" id="id1">
 <img alt="_images/upload_strategy.png" src="_images/upload_strategy.png" />
 <figcaption>
-<p><span class="caption-text">Diagram illustrating the changes in uploading strategies.</span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
+<p><span class="caption-text">Diagram illustrating the changes in uploading strategies.</span><a class="headerlink" href="#id1" title="Permalink to this image"></a></p>
 <div class="legend">
 <p><em>Using the old method, the hub, genomes, and trackdb files were rendered in
 the working directory, cluttering it. Each file was then individually
@@ -183,7 +183,7 @@ <h3>Improved file uploading<a class="headerlink" href="#improved-file-uploading"
 </figure>
 </section>
 <section id="local-fn-argument-is-now-replaced-by-source">
-<h3><cite>local_fn</cite> argument is now replaced by <cite>source</cite><a class="headerlink" href="#local-fn-argument-is-now-replaced-by-source" title="Link to this heading"></a></h3>
+<h3><cite>local_fn</cite> argument is now replaced by <cite>source</cite><a class="headerlink" href="#local-fn-argument-is-now-replaced-by-source" title="Permalink to this heading"></a></h3>
 <p>To better align the semantics of keyword arguments with this new uploading
 strategy, <cite>local_fn</cite> and <cite>remote_fn</cite> are deprecated as arguments to
 <code class="xref py py-class docutils literal notranslate"><span class="pre">Track</span></code> objects. With the new uploading strategy described aboved,
@@ -204,7 +204,7 @@ <h3><cite>local_fn</cite> argument is now replaced by <cite>source</cite><a clas
 <cite>source</cite>, <cite>filename</cite>, and <cite>url</cite>.</p>
 </section>
 <section id="improved-documentation">
-<h3>Improved documentation<a class="headerlink" href="#improved-documentation" title="Link to this heading"></a></h3>
+<h3>Improved documentation<a class="headerlink" href="#improved-documentation" title="Permalink to this heading"></a></h3>
 <p>The documentation at <a class="reference external" href="https://daler.github.io/trackhub">https://daler.github.io/trackhub</a> has been rewritten, and
 now includes example code for progressively more complex trackhubs that
 demonstrate different features of the package and track hubs in general.</p>
@@ -226,14 +226,14 @@ <h3>Improved documentation<a class="headerlink" href="#improved-documentation" t
 <p>Or the hub can be loaded directly into UCSC with the following URL: <a class="reference external" href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&amp;hubUrl=https://raw.githubusercontent.com/daler/trackhub-demo/master/quickstart/quickstart.hub.txt&amp;position=chr1%3A1-5000">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&amp;hubUrl=https://raw.githubusercontent.com/daler/trackhub-demo/master/quickstart/quickstart.hub.txt&amp;position=chr1%3A1-5000</a></p>
 </section>
 <section id="python-2-and-3-support">
-<h3>Python 2 and 3 support<a class="headerlink" href="#python-2-and-3-support" title="Link to this heading"></a></h3>
+<h3>Python 2 and 3 support<a class="headerlink" href="#python-2-and-3-support" title="Permalink to this heading"></a></h3>
 <p>Since we are no longer using <cite>fabric</cite> as a dependency (which is only available
 under Python 2), <cite>trackhub</cite> now supports Python 2 and Python 3 and is tested on
 both versions.</p>
 </section>
 </section>
 <section id="version-0-1-3-nov-2015">
-<h2>Version 0.1.3 (Nov 2015)<a class="headerlink" href="#version-0-1-3-nov-2015" title="Link to this heading"></a></h2>
+<h2>Version 0.1.3 (Nov 2015)<a class="headerlink" href="#version-0-1-3-nov-2015" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>fixed bug where local rsync operations were not using the provided rsync options</p></li>
 <li><p>docs now at <a class="reference external" href="https://daler.github.io/trackhub">https://daler.github.io/trackhub</a></p></li>
@@ -241,7 +241,7 @@ <h2>Version 0.1.3 (Nov 2015)<a class="headerlink" href="#version-0-1-3-nov-2015"
 </ul>
 </section>
 <section id="version-0-1-2-jan-2-2015">
-<h2>Version 0.1.2 (Jan 2 2015)<a class="headerlink" href="#version-0-1-2-jan-2-2015" title="Link to this heading"></a></h2>
+<h2>Version 0.1.2 (Jan 2 2015)<a class="headerlink" href="#version-0-1-2-jan-2-2015" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>always use the remote filename of a BAM when uploading the corresponding .bai</p></li>
 <li><p>add support for BAM parameters <cite>baseColorUseSequence</cite>, <cite>baseColorDefault</cite>,
@@ -253,7 +253,7 @@ <h2>Version 0.1.2 (Jan 2 2015)<a class="headerlink" href="#version-0-1-2-jan-2-2
 </ul>
 </section>
 <section id="version-0-1-1-dec-19-2012">
-<h2>Version 0.1.1 (Dec 19 2012)<a class="headerlink" href="#version-0-1-1-dec-19-2012" title="Link to this heading"></a></h2>
+<h2>Version 0.1.1 (Dec 19 2012)<a class="headerlink" href="#version-0-1-1-dec-19-2012" title="Permalink to this heading"></a></h2>
 <ul class="simple">
 <li><p>Initial support for SuperTracks (Venkat Malladi)</p></li>
 <li><p>Support for vcfTabix format (Venkat Malladi)</p></li>
@@ -269,7 +269,7 @@ <h2>Version 0.1.1 (Dec 19 2012)<a class="headerlink" href="#version-0-1-1-dec-19
 </ul>
 </section>
 <section id="version-0-1-oct-30-2012">
-<h2>Version 0.1 (Oct 30 2012)<a class="headerlink" href="#version-0-1-oct-30-2012" title="Link to this heading"></a></h2>
+<h2>Version 0.1 (Oct 30 2012)<a class="headerlink" href="#version-0-1-oct-30-2012" title="Permalink to this heading"></a></h2>
 <p>Initial release</p>
 </section>
 </section>
diff --git a/excelinstructions.html b/excelinstructions.html
index 92556c6..0f460f7 100644
--- a/excelinstructions.html
+++ b/excelinstructions.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Track hub from Excel &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -108,7 +108,7 @@
            <div itemprop="articleBody">
              
   <section id="track-hub-from-excel">
-<span id="excelinstructions"></span><h1>Track hub from Excel<a class="headerlink" href="#track-hub-from-excel" title="Link to this heading"></a></h1>
+<span id="excelinstructions"></span><h1>Track hub from Excel<a class="headerlink" href="#track-hub-from-excel" title="Permalink to this heading"></a></h1>
 <p>If you are an avid user of the UCSC Genome Browser and the <em>trackhub</em> package,
 you might find it tedious to write a script for every single hub you create.
 The command-line tool uses this package to further automate the trak hub making
@@ -117,7 +117,7 @@
 and how to fill out an Excel workbook to make any simple or complex
 visualization on the UCSC Genome Browser.</p>
 <section id="create-a-template">
-<h2>1. Create a template<a class="headerlink" href="#create-a-template" title="Link to this heading"></a></h2>
+<h2>1. Create a template<a class="headerlink" href="#create-a-template" title="Permalink to this heading"></a></h2>
 <p>The Excel file must have a specific format to be parsed correctly.</p>
 <p>To create a template, run:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">trackhub_from_excel</span> <span class="o">--</span><span class="n">template</span>
@@ -131,11 +131,11 @@ <h2>1. Create a template<a class="headerlink" href="#create-a-template" title="L
 </div>
 </section>
 <section id="fill-out-the-excel-workbook">
-<h2>2. Fill out the Excel workbook<a class="headerlink" href="#fill-out-the-excel-workbook" title="Link to this heading"></a></h2>
+<h2>2. Fill out the Excel workbook<a class="headerlink" href="#fill-out-the-excel-workbook" title="Permalink to this heading"></a></h2>
 <p>Using the template just created, fill out the sheets with the data you’d like
 to visualize.</p>
 <section id="hub-and-genome-sheets">
-<h3>hub and genome sheets<a class="headerlink" href="#hub-and-genome-sheets" title="Link to this heading"></a></h3>
+<h3>hub and genome sheets<a class="headerlink" href="#hub-and-genome-sheets" title="Permalink to this heading"></a></h3>
 <p>The following special sheet names are used for configuring the hub and the
 genome (for assembly tracks):</p>
 <p><code class="docutils literal notranslate"><span class="pre">hub</span></code> – This sheet is necessary for all track hubs. It
@@ -143,7 +143,7 @@ <h3>hub and genome sheets<a class="headerlink" href="#hub-and-genome-sheets" tit
 <p><code class="docutils literal notranslate"><span class="pre">genome</span></code> – This sheet is only necessary when using a genome assembly. It
 points to the 2bit file and gives the genome a name and label.</p>
 <section id="example-hub-sheet">
-<h4>Example <code class="docutils literal notranslate"><span class="pre">hub</span></code> sheet<a class="headerlink" href="#example-hub-sheet" title="Link to this heading"></a></h4>
+<h4>Example <code class="docutils literal notranslate"><span class="pre">hub</span></code> sheet<a class="headerlink" href="#example-hub-sheet" title="Permalink to this heading"></a></h4>
 <table class="docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p>hub</p></td>
@@ -166,7 +166,7 @@ <h4>Example <code class="docutils literal notranslate"><span class="pre">hub</sp
 </section>
 </section>
 <section id="container-track-sheets">
-<h3>Container track sheets<a class="headerlink" href="#container-track-sheets" title="Link to this heading"></a></h3>
+<h3>Container track sheets<a class="headerlink" href="#container-track-sheets" title="Permalink to this heading"></a></h3>
 <p>Container tracks must be configured in their own sheet.</p>
 <p>The following special sheet names are required when using the corresponding
 container track. These sheets are created in the template:
@@ -198,7 +198,7 @@ <h3>Container track sheets<a class="headerlink" href="#container-track-sheets" t
 section below for details.</p>
 </div>
 <section id="example-view-config-sheet">
-<h4>Example <code class="docutils literal notranslate"><span class="pre">view_config</span></code> sheet<a class="headerlink" href="#example-view-config-sheet" title="Link to this heading"></a></h4>
+<h4>Example <code class="docutils literal notranslate"><span class="pre">view_config</span></code> sheet<a class="headerlink" href="#example-view-config-sheet" title="Permalink to this heading"></a></h4>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>name</p></th>
@@ -231,7 +231,7 @@ <h4>Example <code class="docutils literal notranslate"><span class="pre">view_co
 </table>
 </section>
 <section id="example-composite-config-sheet">
-<h4>Example <code class="docutils literal notranslate"><span class="pre">composite_config</span></code> sheet<a class="headerlink" href="#example-composite-config-sheet" title="Link to this heading"></a></h4>
+<h4>Example <code class="docutils literal notranslate"><span class="pre">composite_config</span></code> sheet<a class="headerlink" href="#example-composite-config-sheet" title="Permalink to this heading"></a></h4>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>name</p></th>
@@ -258,7 +258,7 @@ <h4>Example <code class="docutils literal notranslate"><span class="pre">composi
 </table>
 </section>
 <section id="example-super-config-sheet">
-<h4>Example <code class="docutils literal notranslate"><span class="pre">super_config</span></code> sheet<a class="headerlink" href="#example-super-config-sheet" title="Link to this heading"></a></h4>
+<h4>Example <code class="docutils literal notranslate"><span class="pre">super_config</span></code> sheet<a class="headerlink" href="#example-super-config-sheet" title="Permalink to this heading"></a></h4>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>name</p></th>
@@ -276,7 +276,7 @@ <h4>Example <code class="docutils literal notranslate"><span class="pre">super_c
 </section>
 </section>
 <section id="tracks">
-<h3>Tracks<a class="headerlink" href="#tracks" title="Link to this heading"></a></h3>
+<h3>Tracks<a class="headerlink" href="#tracks" title="Permalink to this heading"></a></h3>
 <p>All other sheets that do not have the special names indicated above are assumed
 to configure tracks.</p>
 <p>Each row defines a track and must have values in the <code class="docutils literal notranslate"><span class="pre">name</span></code>, <code class="docutils literal notranslate"><span class="pre">tracktype</span></code>,
@@ -304,7 +304,7 @@ <h3>Tracks<a class="headerlink" href="#tracks" title="Link to this heading"><
 <code class="docutils literal notranslate"><span class="pre">subgroup_genotype</span></code> and fill in the rows with “WT” or “KO”. You can make
 as many subgroups as you need.</p>
 <section id="example-tracks-sheet">
-<h4>Example <code class="docutils literal notranslate"><span class="pre">tracks</span></code> sheet<a class="headerlink" href="#example-tracks-sheet" title="Link to this heading"></a></h4>
+<h4>Example <code class="docutils literal notranslate"><span class="pre">tracks</span></code> sheet<a class="headerlink" href="#example-tracks-sheet" title="Permalink to this heading"></a></h4>
 <table class="docutils align-default">
 <thead>
 <tr class="row-odd"><th class="head"><p>name</p></th>
@@ -354,7 +354,7 @@ <h4>Example <code class="docutils literal notranslate"><span class="pre">tracks<
 </section>
 </section>
 <section id="run-the-script">
-<h2>3. Run the script<a class="headerlink" href="#run-the-script" title="Link to this heading"></a></h2>
+<h2>3. Run the script<a class="headerlink" href="#run-the-script" title="Permalink to this heading"></a></h2>
 <p>This will default to naming the track hub directory as “staging”</p>
 <p><code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">trackhub_from_excel.py</span> <span class="pre">--excel_file</span> <span class="pre">experiment.xlsx</span></code></p>
 <p>You can run it with the <code class="docutils literal notranslate"><span class="pre">--staging</span></code> flag to specify the name</p>
diff --git a/genindex.html b/genindex.html
index d0eac79..8a4f350 100644
--- a/genindex.html
+++ b/genindex.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 
diff --git a/groupAutoScale.html b/groupAutoScale.html
index 82e4389..ad6da42 100644
--- a/groupAutoScale.html
+++ b/groupAutoScale.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>groupAutoScale example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -87,7 +87,7 @@
            <div itemprop="articleBody">
              
   <section id="groupautoscale-example">
-<span id="groupautoscale"></span><h1>groupAutoScale example<a class="headerlink" href="#groupautoscale-example" title="Link to this heading"></a></h1>
+<span id="groupautoscale"></span><h1>groupAutoScale example<a class="headerlink" href="#groupautoscale-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a track that auto scales as a group
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/hgWiggleTrackHelp.html">UCSC’s Configuring graph based-tracks help page</a>.</p>
 <p>This code is automatically run and the built trackhub is uploaded to the
diff --git a/grouping.html b/grouping.html
index b6db6fa..aca9372 100644
--- a/grouping.html
+++ b/grouping.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Organizing larger track hubs &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -87,7 +87,7 @@
            <div itemprop="articleBody">
              
   <section id="organizing-larger-track-hubs">
-<span id="grouping-example"></span><h1>Organizing larger track hubs<a class="headerlink" href="#organizing-larger-track-hubs" title="Link to this heading"></a></h1>
+<span id="grouping-example"></span><h1>Organizing larger track hubs<a class="headerlink" href="#organizing-larger-track-hubs" title="Permalink to this heading"></a></h1>
 <p>This is a modified version of the example in the README which shows how to
 organize the data into multiple kinds of containers – multiWig,
 compositeTracks, and superTracks. See UCSC’s <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/hubQuickStartGroups.html">grouping quick start</a> for some
@@ -101,13 +101,13 @@
 <figure class="align-default" id="id1">
 <a class="reference internal image-reference" href="_images/screenshot.png"><img alt="_images/screenshot.png" src="_images/screenshot.png" style="width: 500px;" /></a>
 <figcaption>
-<p><span class="caption-text">Screenshot of the hub generated from <a class="reference internal" href="#grouping-example"><span class="std std-ref">Organizing larger track hubs</span></a></span><a class="headerlink" href="#id1" title="Link to this image"></a></p>
+<p><span class="caption-text">Screenshot of the hub generated from <a class="reference internal" href="#grouping-example"><span class="std std-ref">Organizing larger track hubs</span></a></span><a class="headerlink" href="#id1" title="Permalink to this image"></a></p>
 </figcaption>
 </figure>
 <figure class="align-default" id="id2">
 <a class="reference internal image-reference" href="_images/config-screenshot.png"><img alt="_images/config-screenshot.png" src="_images/config-screenshot.png" style="width: 500px;" /></a>
 <figcaption>
-<p><span class="caption-text">Screenshot of the configuration page generated by <a class="reference internal" href="#grouping-example"><span class="std std-ref">Organizing larger track hubs</span></a></span><a class="headerlink" href="#id2" title="Link to this image"></a></p>
+<p><span class="caption-text">Screenshot of the configuration page generated by <a class="reference internal" href="#grouping-example"><span class="std std-ref">Organizing larger track hubs</span></a></span><a class="headerlink" href="#id2" title="Permalink to this image"></a></p>
 </figcaption>
 </figure>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">glob</span><span class="o">,</span> <span class="nn">os</span>
diff --git a/html_doc.html b/html_doc.html
index 3a56041..df7ea08 100644
--- a/html_doc.html
+++ b/html_doc.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Documenting tracks in hubs &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -87,7 +87,7 @@
            <div itemprop="articleBody">
              
   <section id="documenting-tracks-in-hubs">
-<span id="htmldoc-example"></span><h1>Documenting tracks in hubs<a class="headerlink" href="#documenting-tracks-in-hubs" title="Link to this heading"></a></h1>
+<span id="htmldoc-example"></span><h1>Documenting tracks in hubs<a class="headerlink" href="#documenting-tracks-in-hubs" title="Permalink to this heading"></a></h1>
 <p><cite>trackhub</cite> supports documentation written in <a class="reference external" href="http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">ReStructured Text</a> that is
 automatically converted to HTML. Here we show examples of how this works.</p>
 <ul class="simple">
diff --git a/index.html b/index.html
index 4596901..12f9d94 100644
--- a/index.html
+++ b/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>trackhub &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -86,7 +86,7 @@
            <div itemprop="articleBody">
              
   <section id="trackhub">
-<h1>trackhub<a class="headerlink" href="#trackhub" title="Link to this heading"></a></h1>
+<h1>trackhub<a class="headerlink" href="#trackhub" title="Permalink to this heading"></a></h1>
 <a class="reference external image-reference" href="https://github.com/daler/trackhub/actions?query=workflow%3Amain"><img alt="https://github.com/daler/trackhub/workflows/main/badge.svg" src="https://github.com/daler/trackhub/workflows/main/badge.svg" /></a>
 <p>See the documentation at <a class="reference external" href="https://daler.github.io/trackhub">https://daler.github.io/trackhub</a> for more details.</p>
 <p>Data visualization is critical at all steps of genomic data analysis, from QC
@@ -107,19 +107,19 @@ <h1>trackhub<a class="headerlink" href="#trackhub" title="Link to this heading">
 availabe on PyPI, bioconda, and GitHub; an automated test suite and tested
 documentation ensure high-quality code and help.</p>
 <section id="installation">
-<h2>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h2>
+<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h2>
 <p>Using pip: <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">trackhub</span></code></p>
 <p>Using <a class="reference external" href="https://bioconda.github.io">bioconda</a>: <code class="docutils literal notranslate"><span class="pre">conda</span> <span class="pre">install</span> <span class="pre">trackhub</span></code></p>
 </section>
 <section id="features">
-<h2>Features<a class="headerlink" href="#features" title="Link to this heading"></a></h2>
+<h2>Features<a class="headerlink" href="#features" title="Permalink to this heading"></a></h2>
 <section id="validation">
-<h3>Validation<a class="headerlink" href="#validation" title="Link to this heading"></a></h3>
+<h3>Validation<a class="headerlink" href="#validation" title="Permalink to this heading"></a></h3>
 <p><cite>trackhub</cite> validates parameters against UCSC’s documented options, so errors
 are caught early and less time is spent debugging in the Genome Browser.</p>
 </section>
 <section id="filename-handling">
-<h3>Filename handling<a class="headerlink" href="#filename-handling" title="Link to this heading"></a></h3>
+<h3>Filename handling<a class="headerlink" href="#filename-handling" title="Permalink to this heading"></a></h3>
 <p>The directory structure of an analysis rarely matches the organization you want
 for a track hub.  <cite>trackhub</cite> symlinks track files to a staging area so the hub
 can be inspected locally before being uploaded, e.g., with <code class="docutils literal notranslate"><span class="pre">rsync</span></code>. Staging
@@ -127,7 +127,7 @@ <h3>Filename handling<a class="headerlink" href="#filename-handling" title="Link
 will be uploaded on subsequent calls.</p>
 </section>
 <section id="flexibility">
-<h3>Flexibility<a class="headerlink" href="#flexibility" title="Link to this heading"></a></h3>
+<h3>Flexibility<a class="headerlink" href="#flexibility" title="Permalink to this heading"></a></h3>
 <p>Sensible defaults make it easy to build a functioning track hub. However, these
 defaults can always be overridden for complex configurations or when more
 precise control is needed. For example, by default a track’s <cite>name</cite> also
@@ -135,14 +135,14 @@ <h3>Flexibility<a class="headerlink" href="#flexibility" title="Link to this hea
 unless any of these are overridden by the user.</p>
 </section>
 <section id="easy-track-documentation">
-<h3>Easy track documentation<a class="headerlink" href="#easy-track-documentation" title="Link to this heading"></a></h3>
+<h3>Easy track documentation<a class="headerlink" href="#easy-track-documentation" title="Permalink to this heading"></a></h3>
 <p>Write track hub documentation in ReStructured Text, and it is converted to
 HTML, connected to the track and uploaded with the rest of the hub. This allows
 for programmatically including content without the tedium of writing HTML by
 hand.</p>
 </section>
 <section id="extensible">
-<h3>Extensible<a class="headerlink" href="#extensible" title="Link to this heading"></a></h3>
+<h3>Extensible<a class="headerlink" href="#extensible" title="Permalink to this heading"></a></h3>
 <p>The framework provided by <cite>trackhub</cite> can be extended as new hub functionality is
 added to the UCSC Genome Browser.</p>
 <p>Full documentation can be found at <a class="reference external" href="https://daler.github.io/trackhub">https://daler.github.io/trackhub</a>. The code
@@ -150,7 +150,7 @@ <h3>Extensible<a class="headerlink" href="#extensible" title="Link to this headi
 </section>
 </section>
 <section id="basic-example">
-<span id="id1"></span><h2>Basic example<a class="headerlink" href="#basic-example" title="Link to this heading"></a></h2>
+<span id="id1"></span><h2>Basic example<a class="headerlink" href="#basic-example" title="Permalink to this heading"></a></h2>
 <p>The following code demonstrates a track hub built out of all bigWig files found
 in a directory. It is relatively simple; see these other examples from the
 documentation for complex usage.</p>
diff --git a/quickstart.html b/quickstart.html
index 3fba9c2..7a19ae1 100644
--- a/quickstart.html
+++ b/quickstart.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Quickstart &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -93,9 +93,9 @@
            <div itemprop="articleBody">
              
   <section id="quickstart">
-<span id="id1"></span><h1>Quickstart<a class="headerlink" href="#quickstart" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1>Quickstart<a class="headerlink" href="#quickstart" title="Permalink to this heading"></a></h1>
 <section id="preliminaries">
-<h2>Preliminaries<a class="headerlink" href="#preliminaries" title="Link to this heading"></a></h2>
+<h2>Preliminaries<a class="headerlink" href="#preliminaries" title="Permalink to this heading"></a></h2>
 <p>If you’ve never created a track hub before, it’s important to read the <a class="reference external" href="http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html">track
 hub help</a> so you
 know some of the terminology.</p>
@@ -115,7 +115,7 @@ <h2>Preliminaries<a class="headerlink" href="#preliminaries" title="Link to this
 </ul>
 </section>
 <section id="create-hub-components">
-<h2>Create hub components<a class="headerlink" href="#create-hub-components" title="Link to this heading"></a></h2>
+<h2>Create hub components<a class="headerlink" href="#create-hub-components" title="Permalink to this heading"></a></h2>
 <p>A track hub consists of connected components of files that point to each other.
 The hub file points to a genomes file, which points to a trackDb file, which
 points to the various data tracks.</p>
@@ -165,7 +165,7 @@ <h2>Create hub components<a class="headerlink" href="#create-hub-components" tit
 </div>
 </section>
 <section id="adding-tracks">
-<h2>Adding tracks<a class="headerlink" href="#adding-tracks" title="Link to this heading"></a></h2>
+<h2>Adding tracks<a class="headerlink" href="#adding-tracks" title="Permalink to this heading"></a></h2>
 <p>In this example, we are adding tracks one at a time. This is not much easier
 than just writing the trackDb file in a text editor. However, creating tracks
 in Python makes it easy to scale up to hundreds of tracks and unlocks all of
@@ -234,7 +234,7 @@ <h2>Adding tracks<a class="headerlink" href="#adding-tracks" title="Link to this
 </div>
 </section>
 <section id="render-stage-the-hub">
-<h2>Render (stage) the hub<a class="headerlink" href="#render-stage-the-hub" title="Link to this heading"></a></h2>
+<h2>Render (stage) the hub<a class="headerlink" href="#render-stage-the-hub" title="Permalink to this heading"></a></h2>
 <p>To get ready for uploading, <cite>trackhub</cite> renders the hub files and symlinks all
 the track source files into a local directory. This allows us to inspect the
 hub before uploading.</p>
diff --git a/search.html b/search.html
index aadb59a..2b63bdd 100644
--- a/search.html
+++ b/search.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Search &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
     
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <script src="_static/searchtools.js"></script>
     <script src="_static/language_data.js"></script>
diff --git a/searchindex.js b/searchindex.js
index be5a48c..fbd6e4a 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1. Create a template": [[26, "create-a-template"]], "2. Fill out the Excel workbook": [[26, "fill-out-the-excel-workbook"]], "3. Run the script": [[26, "run-the-script"]], "API documentation": [[1, "api-documentation"]], "Adding tracks": [[31, "adding-tracks"]], "Assembly example": [[0, "assembly-example"]], "Basic example": [[30, "basic-example"]], "Build a trackhub configured in Excel": [[25, "build-a-trackhub-configured-in-excel"]], "Changelog": [[25, "changelog"]], "Container track sheets": [[26, "container-track-sheets"]], "Create hub components": [[31, "create-hub-components"]], "Documenting tracks in hubs": [[29, "documenting-tracks-in-hubs"]], "Easy track documentation": [[30, "easy-track-documentation"]], "Example composite_config sheet": [[26, "example-composite-config-sheet"]], "Example hub sheet": [[26, "example-hub-sheet"]], "Example super_config sheet": [[26, "example-super-config-sheet"]], "Example tracks sheet": [[26, "example-tracks-sheet"]], "Example view_config sheet": [[26, "example-view-config-sheet"]], "Examples of hubs using various supported track types": [[33, "examples-of-hubs-using-various-supported-track-types"]], "Extensible": [[30, "extensible"]], "Features": [[30, "features"]], "Filename handling": [[30, "filename-handling"]], "Flexibility": [[30, "flexibility"]], "Hi-C example": [[44, "hi-c-example"]], "Improved documentation": [[25, "improved-documentation"]], "Improved file uploading": [[25, "improved-file-uploading"]], "Installation": [[30, "installation"]], "Organizing larger track hubs": [[28, "organizing-larger-track-hubs"]], "Other changes": [[25, "other-changes"]], "Preliminaries": [[31, "preliminaries"]], "Python 2 and 3 support": [[25, "python-2-and-3-support"]], "Quickstart": [[31, "quickstart"]], "Render (stage) the hub": [[31, "render-stage-the-hub"]], "Semi-automated updating of validated parameters": [[25, "semi-automated-updating-of-validated-parameters"]], "Testing infrastructure": [[32, "testing-infrastructure"]], "Testing infrastructure overhaul": [[25, "testing-infrastructure-overhaul"]], "Track hub from Excel": [[26, "track-hub-from-excel"]], "Tracks": [[26, "tracks"]], "Updating parameters": [[46, "updating-parameters"]], "Validation": [[30, "validation"], [46, "validation"]], "Version 0.1 (Oct 30 2012)": [[25, "version-0-1-oct-30-2012"]], "Version 0.1.1 (Dec 19 2012)": [[25, "version-0-1-1-dec-19-2012"]], "Version 0.1.2 (Jan 2 2015)": [[25, "version-0-1-2-jan-2-2015"]], "Version 0.1.3 (Nov 2015)": [[25, "version-0-1-3-nov-2015"]], "Version 0.2.4 (Dec 2017)": [[25, "version-0-2-4-dec-2017"]], "Version 1.0 (April 2024)": [[25, "version-1-0-april-2024"]], "bam example": [[34, "bam-example"]], "bigBarChart example": [[35, "bigbarchart-example"]], "bigChain example": [[36, "bigchain-example"]], "bigGenePred example": [[37, "biggenepred-example"]], "bigInteract example": [[38, "biginteract-example"]], "bigLolly example": [[39, "biglolly-example"]], "bigMaf example": [[40, "bigmaf-example"]], "bigNarrowPeak example": [[41, "bignarrowpeak-example"]], "bigPsl example": [[42, "bigpsl-example"]], "bigWig example": [[43, "bigwig-example"]], "groupAutoScale example": [[27, "groupautoscale-example"]], "hub and genome sheets": [[26, "hub-and-genome-sheets"]], "local_fn argument is now replaced by source": [[25, "local-fn-argument-is-now-replaced-by-source"]], "trackhub": [[30, "trackhub"]], "trackhub.AggregateTrack": [[2, "trackhub-aggregatetrack"]], "trackhub.Assembly": [[3, "trackhub-assembly"]], "trackhub.BaseTrack": [[4, "trackhub-basetrack"]], "trackhub.CompositeTrack": [[5, "trackhub-compositetrack"]], "trackhub.Genome": [[6, "trackhub-genome"]], "trackhub.GenomesFile": [[7, "trackhub-genomesfile"]], "trackhub.GroupDefinition": [[8, "trackhub-groupdefinition"]], "trackhub.GroupsFile": [[9, "trackhub-groupsfile"]], "trackhub.Hub": [[10, "trackhub-hub"]], "trackhub.SubGroupDefinition": [[11, "trackhub-subgroupdefinition"]], "trackhub.SuperTrack": [[12, "trackhub-supertrack"]], "trackhub.Track": [[13, "trackhub-track"]], "trackhub.TrackDb": [[14, "trackhub-trackdb"]], "trackhub.ViewTrack": [[15, "trackhub-viewtrack"]], "trackhub.base.HubComponent": [[16, "trackhub-base-hubcomponent"]], "trackhub.helpers.data_dir": [[17, "trackhub-helpers-data-dir"]], "trackhub.helpers.dimensions_from_subgroups": [[18, "trackhub-helpers-dimensions-from-subgroups"]], "trackhub.helpers.filter_composite_from_subgroups": [[19, "trackhub-helpers-filter-composite-from-subgroups"]], "trackhub.helpers.hex2rgb": [[20, "trackhub-helpers-hex2rgb"]], "trackhub.helpers.sanitize": [[21, "trackhub-helpers-sanitize"]], "trackhub.parsed_params.Param": [[22, "trackhub-parsed-params-param"]], "trackhub.upload.stage_hub": [[23, "trackhub-upload-stage-hub"]], "trackhub.upload.upload_hub": [[24, "trackhub-upload-upload-hub"]], "vcfTabix example": [[45, "vcftabix-example"]]}, "docnames": ["assembly_example", "autodocs", "autodocs/trackhub.AggregateTrack", "autodocs/trackhub.Assembly", "autodocs/trackhub.BaseTrack", "autodocs/trackhub.CompositeTrack", "autodocs/trackhub.Genome", "autodocs/trackhub.GenomesFile", "autodocs/trackhub.GroupDefinition", "autodocs/trackhub.GroupsFile", "autodocs/trackhub.Hub", "autodocs/trackhub.SubGroupDefinition", "autodocs/trackhub.SuperTrack", "autodocs/trackhub.Track", "autodocs/trackhub.TrackDb", "autodocs/trackhub.ViewTrack", "autodocs/trackhub.base.HubComponent", "autodocs/trackhub.helpers.data_dir", "autodocs/trackhub.helpers.dimensions_from_subgroups", "autodocs/trackhub.helpers.filter_composite_from_subgroups", "autodocs/trackhub.helpers.hex2rgb", "autodocs/trackhub.helpers.sanitize", "autodocs/trackhub.parsed_params.Param", "autodocs/trackhub.upload.stage_hub", "autodocs/trackhub.upload.upload_hub", "changelog", "excelinstructions", "groupAutoScale", "grouping", "html_doc", "index", "quickstart", "tests", "tracktypes", "tracktypes/bam", "tracktypes/bigBarChart", "tracktypes/bigChain", "tracktypes/bigGenePred", "tracktypes/bigInteract", "tracktypes/bigLolly", "tracktypes/bigMaf", "tracktypes/bigNarrowPeak", "tracktypes/bigPsl", "tracktypes/bigWig", "tracktypes/hic", "tracktypes/vcfTabix", "validation"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1}, "filenames": ["assembly_example.rst", "autodocs.rst", "autodocs/trackhub.AggregateTrack.rst", "autodocs/trackhub.Assembly.rst", "autodocs/trackhub.BaseTrack.rst", "autodocs/trackhub.CompositeTrack.rst", "autodocs/trackhub.Genome.rst", "autodocs/trackhub.GenomesFile.rst", "autodocs/trackhub.GroupDefinition.rst", "autodocs/trackhub.GroupsFile.rst", "autodocs/trackhub.Hub.rst", "autodocs/trackhub.SubGroupDefinition.rst", "autodocs/trackhub.SuperTrack.rst", "autodocs/trackhub.Track.rst", "autodocs/trackhub.TrackDb.rst", "autodocs/trackhub.ViewTrack.rst", 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Create a template": [[26, "create-a-template"]], "2. Fill out the Excel workbook": [[26, "fill-out-the-excel-workbook"]], "hub and genome sheets": [[26, "hub-and-genome-sheets"]], "Example hub sheet": [[26, "example-hub-sheet"]], "Container track sheets": [[26, "container-track-sheets"]], "Example view_config sheet": [[26, "example-view-config-sheet"]], "Example composite_config sheet": [[26, "example-composite-config-sheet"]], "Example super_config sheet": [[26, "example-super-config-sheet"]], "Tracks": [[26, "tracks"]], "Example tracks sheet": [[26, "example-tracks-sheet"]], "3. Run the script": [[26, "run-the-script"]], "groupAutoScale example": [[27, "groupautoscale-example"]], "Organizing larger track hubs": [[28, "organizing-larger-track-hubs"]], "Documenting tracks in hubs": [[29, "documenting-tracks-in-hubs"]], "trackhub": [[30, "trackhub"]], "Installation": [[30, "installation"]], "Features": [[30, "features"]], "Validation": [[30, "validation"], [46, "validation"]], "Filename handling": [[30, "filename-handling"]], "Flexibility": [[30, "flexibility"]], "Easy track documentation": [[30, "easy-track-documentation"]], "Extensible": [[30, "extensible"]], "Basic example": [[30, "basic-example"]], "Quickstart": [[31, "quickstart"]], "Preliminaries": [[31, "preliminaries"]], "Create hub components": [[31, "create-hub-components"]], "Adding tracks": [[31, "adding-tracks"]], "Render (stage) the hub": [[31, "render-stage-the-hub"]], "Testing infrastructure": [[32, "testing-infrastructure"]], "Examples of hubs using various supported track types": [[33, "examples-of-hubs-using-various-supported-track-types"]], "bam example": [[34, "bam-example"]], "bigBarChart example": [[35, "bigbarchart-example"]], "bigChain example": [[36, "bigchain-example"]], "bigGenePred example": [[37, "biggenepred-example"]], "bigInteract example": [[38, "biginteract-example"]], "bigLolly example": [[39, "biglolly-example"]], "bigMaf example": [[40, "bigmaf-example"]], "bigNarrowPeak example": [[41, "bignarrowpeak-example"]], "bigPsl example": [[42, "bigpsl-example"]], "bigWig example": [[43, "bigwig-example"]], "Hi-C example": [[44, "hi-c-example"]], "vcfTabix example": [[45, "vcftabix-example"]], "Updating parameters": [[46, "updating-parameters"]]}, "indexentries": {"aggregatetrack (class in trackhub)": [[2, "trackhub.AggregateTrack"]], "__init__() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.__init__"]], "add_child() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_child"]], "add_params() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_params"]], "add_parent() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_parent"]], "add_subgroups() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_subgroups"]], "add_subtrack() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_subtrack"]], "add_trackdb() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_trackdb"]], "add_tracks() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.add_tracks"]], "leaves() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.leaves"]], "remove_params() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.remove_params"]], "render() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.render"]], "root() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.root"]], "validate() (trackhub.aggregatetrack method)": [[2, "trackhub.AggregateTrack.validate"]], "assembly (class in trackhub)": [[3, "trackhub.Assembly"]], "__init__() (trackhub.assembly method)": [[3, "trackhub.Assembly.__init__"]], "add_child() (trackhub.assembly method)": [[3, "trackhub.Assembly.add_child"]], "add_params() (trackhub.assembly method)": [[3, "trackhub.Assembly.add_params"]], "add_parent() (trackhub.assembly method)": [[3, "trackhub.Assembly.add_parent"]], "leaves() (trackhub.assembly method)": [[3, "trackhub.Assembly.leaves"]], "remove_params() (trackhub.assembly method)": [[3, "trackhub.Assembly.remove_params"]], "render() (trackhub.assembly method)": [[3, "trackhub.Assembly.render"]], "root() (trackhub.assembly method)": [[3, "trackhub.Assembly.root"]], "validate() (trackhub.assembly method)": [[3, "trackhub.Assembly.validate"]], "basetrack (class in trackhub)": [[4, "trackhub.BaseTrack"]], "__init__() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.__init__"]], "add_child() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.add_child"]], "add_params() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.add_params"]], "add_parent() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.add_parent"]], "add_subgroups() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.add_subgroups"]], "add_trackdb() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.add_trackdb"]], "leaves() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.leaves"]], "remove_params() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.remove_params"]], "render() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.render"]], "root() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.root"]], "validate() (trackhub.basetrack method)": [[4, "trackhub.BaseTrack.validate"]], "compositetrack (class in trackhub)": [[5, "trackhub.CompositeTrack"]], "__init__() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.__init__"]], "add_child() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_child"]], "add_params() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_params"]], "add_parent() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_parent"]], "add_subgroups() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_subgroups"]], "add_subtrack() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_subtrack"]], "add_trackdb() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_trackdb"]], "add_tracks() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_tracks"]], "add_view() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.add_view"]], "leaves() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.leaves"]], "remove_params() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.remove_params"]], "render() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.render"]], "root() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.root"]], "validate() (trackhub.compositetrack method)": [[5, "trackhub.CompositeTrack.validate"]], "genome (class in trackhub)": [[6, "trackhub.Genome"]], "__init__() (trackhub.genome method)": [[6, "trackhub.Genome.__init__"]], "add_child() (trackhub.genome method)": [[6, "trackhub.Genome.add_child"]], "add_params() (trackhub.genome method)": [[6, "trackhub.Genome.add_params"]], "add_parent() (trackhub.genome method)": [[6, "trackhub.Genome.add_parent"]], "leaves() (trackhub.genome method)": [[6, "trackhub.Genome.leaves"]], "remove_params() (trackhub.genome method)": [[6, "trackhub.Genome.remove_params"]], "render() (trackhub.genome method)": [[6, "trackhub.Genome.render"]], "root() (trackhub.genome method)": [[6, "trackhub.Genome.root"]], "validate() (trackhub.genome method)": [[6, "trackhub.Genome.validate"]], "genomesfile (class in trackhub)": [[7, "trackhub.GenomesFile"]], "__init__() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.__init__"]], "add_child() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.add_child"]], "add_parent() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.add_parent"]], "leaves() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.leaves"]], "render() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.render"]], "root() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.root"]], "validate() (trackhub.genomesfile method)": [[7, "trackhub.GenomesFile.validate"]], "groupdefinition (class in trackhub)": [[8, "trackhub.GroupDefinition"]], "__init__() (trackhub.groupdefinition method)": [[8, "trackhub.GroupDefinition.__init__"]], "groupsfile (class in trackhub)": [[9, "trackhub.GroupsFile"]], "__init__() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.__init__"]], "add_child() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.add_child"]], "add_groups() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.add_groups"]], "add_parent() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.add_parent"]], "leaves() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.leaves"]], "render() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.render"]], "root() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.root"]], "validate() (trackhub.groupsfile method)": [[9, "trackhub.GroupsFile.validate"]], "hub (class in trackhub)": [[10, "trackhub.Hub"]], "__init__() (trackhub.hub method)": [[10, "trackhub.Hub.__init__"]], "add_child() (trackhub.hub method)": [[10, "trackhub.Hub.add_child"]], "add_genomes_file() (trackhub.hub method)": [[10, "trackhub.Hub.add_genomes_file"]], "add_parent() (trackhub.hub method)": [[10, "trackhub.Hub.add_parent"]], "leaves() (trackhub.hub method)": [[10, "trackhub.Hub.leaves"]], "render() (trackhub.hub method)": [[10, "trackhub.Hub.render"]], "root() (trackhub.hub method)": [[10, "trackhub.Hub.root"]], "validate() (trackhub.hub method)": [[10, "trackhub.Hub.validate"]], "subgroupdefinition (class in trackhub)": [[11, "trackhub.SubGroupDefinition"]], "__init__() (trackhub.subgroupdefinition method)": [[11, "trackhub.SubGroupDefinition.__init__"]], "supertrack (class in trackhub)": [[12, "trackhub.SuperTrack"]], "__init__() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.__init__"]], "add_child() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_child"]], "add_params() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_params"]], "add_parent() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_parent"]], "add_subgroups() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_subgroups"]], "add_trackdb() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_trackdb"]], "add_tracks() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.add_tracks"]], "leaves() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.leaves"]], "remove_params() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.remove_params"]], "render() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.render"]], "root() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.root"]], "validate() (trackhub.supertrack method)": [[12, "trackhub.SuperTrack.validate"]], "track (class in trackhub)": [[13, "trackhub.Track"]], "__init__() (trackhub.track method)": [[13, "trackhub.Track.__init__"]], "add_child() (trackhub.track method)": [[13, "trackhub.Track.add_child"]], "add_params() (trackhub.track method)": [[13, "trackhub.Track.add_params"]], "add_parent() (trackhub.track method)": [[13, "trackhub.Track.add_parent"]], "add_subgroups() (trackhub.track method)": [[13, "trackhub.Track.add_subgroups"]], "add_trackdb() (trackhub.track method)": [[13, "trackhub.Track.add_trackdb"]], "leaves() (trackhub.track method)": [[13, "trackhub.Track.leaves"]], "remove_params() (trackhub.track method)": [[13, "trackhub.Track.remove_params"]], "render() (trackhub.track method)": [[13, "trackhub.Track.render"]], "root() (trackhub.track method)": [[13, "trackhub.Track.root"]], "validate() (trackhub.track method)": [[13, "trackhub.Track.validate"]], "trackdb (class in trackhub)": [[14, "trackhub.TrackDb"]], "__init__() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.__init__"]], "add_child() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.add_child"]], "add_parent() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.add_parent"]], "add_tracks() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.add_tracks"]], "leaves() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.leaves"]], "render() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.render"]], "root() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.root"]], "validate() (trackhub.trackdb method)": [[14, "trackhub.TrackDb.validate"]], "viewtrack (class in trackhub)": [[15, "trackhub.ViewTrack"]], "__init__() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.__init__"]], "add_child() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_child"]], "add_params() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_params"]], "add_parent() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_parent"]], "add_subgroups() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_subgroups"]], "add_trackdb() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_trackdb"]], "add_tracks() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.add_tracks"]], "leaves() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.leaves"]], "remove_params() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.remove_params"]], "render() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.render"]], "root() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.root"]], "validate() (trackhub.viewtrack method)": [[15, "trackhub.ViewTrack.validate"]], "hubcomponent (class in trackhub.base)": [[16, "trackhub.base.HubComponent"]], "__init__() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.__init__"]], "add_child() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.add_child"]], "add_parent() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.add_parent"]], "leaves() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.leaves"]], "render() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.render"]], "root() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.root"]], "validate() (trackhub.base.hubcomponent method)": [[16, "trackhub.base.HubComponent.validate"]], "data_dir() (in module trackhub.helpers)": [[17, "trackhub.helpers.data_dir"]], "dimensions_from_subgroups() (in module trackhub.helpers)": [[18, "trackhub.helpers.dimensions_from_subgroups"]], "filter_composite_from_subgroups() (in module trackhub.helpers)": [[19, "trackhub.helpers.filter_composite_from_subgroups"]], "hex2rgb() (in module trackhub.helpers)": [[20, "trackhub.helpers.hex2rgb"]], "sanitize() (in module trackhub.helpers)": [[21, "trackhub.helpers.sanitize"]], "param (class in trackhub.parsed_params)": [[22, "trackhub.parsed_params.Param"]], "__init__() (trackhub.parsed_params.param method)": [[22, "trackhub.parsed_params.Param.__init__"]], "stage_hub() (in module trackhub.upload)": [[23, "trackhub.upload.stage_hub"]], "upload_hub() (in module trackhub.upload)": [[24, "trackhub.upload.upload_hub"]]}})
\ No newline at end of file
diff --git a/tests.html b/tests.html
index 49f7116..45789f3 100644
--- a/tests.html
+++ b/tests.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Testing infrastructure &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -87,7 +87,7 @@
            <div itemprop="articleBody">
              
   <section id="testing-infrastructure">
-<span id="tests"></span><h1>Testing infrastructure<a class="headerlink" href="#testing-infrastructure" title="Link to this heading"></a></h1>
+<span id="tests"></span><h1>Testing infrastructure<a class="headerlink" href="#testing-infrastructure" title="Permalink to this heading"></a></h1>
 <p>Tests are run on GitHub Actions, configured in <code class="docutils literal notranslate"><span class="pre">.github/workflows/main.yml</span></code>.</p>
 <p>In addition to unit tests, now any code in the documentation that shows how to
 build example track hubs is handled like this:</p>
diff --git a/tracktypes.html b/tracktypes.html
index 2ceefea..c73aa9c 100644
--- a/tracktypes.html
+++ b/tracktypes.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Examples of hubs using various supported track types &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -101,7 +101,7 @@
            <div itemprop="articleBody">
              
   <section id="examples-of-hubs-using-various-supported-track-types">
-<span id="tracktypes"></span><h1>Examples of hubs using various supported track types<a class="headerlink" href="#examples-of-hubs-using-various-supported-track-types" title="Link to this heading"></a></h1>
+<span id="tracktypes"></span><h1>Examples of hubs using various supported track types<a class="headerlink" href="#examples-of-hubs-using-various-supported-track-types" title="Permalink to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="tracktypes/bigWig.html">bigWig example</a></li>
diff --git a/tracktypes/bam.html b/tracktypes/bam.html
index d9ef7a9..1b430e2 100644
--- a/tracktypes/bam.html
+++ b/tracktypes/bam.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bam example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bam-example">
-<span id="id1"></span><h1>bam example<a class="headerlink" href="#bam-example" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1>bam example<a class="headerlink" href="#bam-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bam track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bam.html">UCSC’s bam help page</a>. The following code uses the example files provided by UCSC.</p>
 <p>This code is automatically run and the built trackhub is uploaded to the
diff --git a/tracktypes/bigBarChart.html b/tracktypes/bigBarChart.html
index 684672f..e13af19 100644
--- a/tracktypes/bigBarChart.html
+++ b/tracktypes/bigBarChart.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigBarChart example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bigbarchart-example">
-<span id="id1"></span><h1>bigBarChart example<a class="headerlink" href="#bigbarchart-example" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1>bigBarChart example<a class="headerlink" href="#bigbarchart-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigBarChart track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/barChart.html">UCSC’s bigBarChart help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigChain.html b/tracktypes/bigChain.html
index 1c54a42..64c9c1c 100644
--- a/tracktypes/bigChain.html
+++ b/tracktypes/bigChain.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigChain example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bigchain-example">
-<span id="bigchain"></span><h1>bigChain example<a class="headerlink" href="#bigchain-example" title="Link to this heading"></a></h1>
+<span id="bigchain"></span><h1>bigChain example<a class="headerlink" href="#bigchain-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigChain track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigChain.html">UCSC’s bigChain help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigGenePred.html b/tracktypes/bigGenePred.html
index 2fc5eba..4124254 100644
--- a/tracktypes/bigGenePred.html
+++ b/tracktypes/bigGenePred.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigGenePred example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="biggenepred-example">
-<span id="biggenepred"></span><h1>bigGenePred example<a class="headerlink" href="#biggenepred-example" title="Link to this heading"></a></h1>
+<span id="biggenepred"></span><h1>bigGenePred example<a class="headerlink" href="#biggenepred-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigGenePred track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigGenePred.html">UCSC”s bigBarChart help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigInteract.html b/tracktypes/bigInteract.html
index 7c973a9..8169f1d 100644
--- a/tracktypes/bigInteract.html
+++ b/tracktypes/bigInteract.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigInteract example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="biginteract-example">
-<span id="biginteract"></span><h1>bigInteract example<a class="headerlink" href="#biginteract-example" title="Link to this heading"></a></h1>
+<span id="biginteract"></span><h1>bigInteract example<a class="headerlink" href="#biginteract-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigInteract track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigInteract.html">UCSC’s bigInteract help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigLolly.html b/tracktypes/bigLolly.html
index 5f3bc6d..482e535 100644
--- a/tracktypes/bigLolly.html
+++ b/tracktypes/bigLolly.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigLolly example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="biglolly-example">
-<span id="biglolly"></span><h1>bigLolly example<a class="headerlink" href="#biglolly-example" title="Link to this heading"></a></h1>
+<span id="biglolly"></span><h1>bigLolly example<a class="headerlink" href="#biglolly-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigLolly track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigLolly.html">UCSC’s bigLolly help page</a>. The following code uses the example files provided by UCSC.
 This track type uses non-standard names for some parameters. These paramters can be added as a dictionary and setting
diff --git a/tracktypes/bigMaf.html b/tracktypes/bigMaf.html
index 4be399c..f14880a 100644
--- a/tracktypes/bigMaf.html
+++ b/tracktypes/bigMaf.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigMaf example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bigmaf-example">
-<span id="bigmaf"></span><h1>bigMaf example<a class="headerlink" href="#bigmaf-example" title="Link to this heading"></a></h1>
+<span id="bigmaf"></span><h1>bigMaf example<a class="headerlink" href="#bigmaf-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigMaf track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigMaf.html">UCSC’s bigMaf help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigNarrowPeak.html b/tracktypes/bigNarrowPeak.html
index 4bb6291..5397520 100644
--- a/tracktypes/bigNarrowPeak.html
+++ b/tracktypes/bigNarrowPeak.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigNarrowPeak example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bignarrowpeak-example">
-<span id="bignarrowpeak"></span><h1>bigNarrowPeak example<a class="headerlink" href="#bignarrowpeak-example" title="Link to this heading"></a></h1>
+<span id="bignarrowpeak"></span><h1>bigNarrowPeak example<a class="headerlink" href="#bignarrowpeak-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigNarrowPeak track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigNarrowPeak.html">UCSC’s bigNarrowPeak help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigPsl.html b/tracktypes/bigPsl.html
index b7f6bea..2c99f4b 100644
--- a/tracktypes/bigPsl.html
+++ b/tracktypes/bigPsl.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigPsl example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bigpsl-example">
-<span id="bigpsl"></span><h1>bigPsl example<a class="headerlink" href="#bigpsl-example" title="Link to this heading"></a></h1>
+<span id="bigpsl"></span><h1>bigPsl example<a class="headerlink" href="#bigpsl-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigPsl track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigPsl.html">UCSC’s bigPsl help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/bigWig.html b/tracktypes/bigWig.html
index c70b6f0..4e6bd80 100644
--- a/tracktypes/bigWig.html
+++ b/tracktypes/bigWig.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>bigWig example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="bigwig-example">
-<span id="bigwig"></span><h1>bigWig example<a class="headerlink" href="#bigwig-example" title="Link to this heading"></a></h1>
+<span id="bigwig"></span><h1>bigWig example<a class="headerlink" href="#bigwig-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a bigWig track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/bigWig.html">UCSC’s bigWig help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/hic.html b/tracktypes/hic.html
index f304bfb..121c23e 100644
--- a/tracktypes/hic.html
+++ b/tracktypes/hic.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Hi-C example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="hi-c-example">
-<span id="hic-example"></span><h1>Hi-C example<a class="headerlink" href="#hi-c-example" title="Link to this heading"></a></h1>
+<span id="hic-example"></span><h1>Hi-C example<a class="headerlink" href="#hi-c-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a Hi-C track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/hic.html">UCSC’s hic help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/tracktypes/vcfTabix.html b/tracktypes/vcfTabix.html
index e3461b7..a838752 100644
--- a/tracktypes/vcfTabix.html
+++ b/tracktypes/vcfTabix.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>vcfTabix example &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="../_static/doctools.js?v=9a2dae69"></script>
-        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -102,7 +102,7 @@
            <div itemprop="articleBody">
              
   <section id="vcftabix-example">
-<span id="vcftabix"></span><h1>vcfTabix example<a class="headerlink" href="#vcftabix-example" title="Link to this heading"></a></h1>
+<span id="vcftabix"></span><h1>vcfTabix example<a class="headerlink" href="#vcftabix-example" title="Permalink to this heading"></a></h1>
 <p>You can read more about preparing the files necessary for a vcfTabix track
 on <a class="reference external" href="https://genome.ucsc.edu/goldenPath/help/vcf.html">UCSC’s bigInteract help page</a>. The following code
 uses the example files provided by UCSC.</p>
diff --git a/validation.html b/validation.html
index b851851..f66c679 100644
--- a/validation.html
+++ b/validation.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="./">
+<html class="writer-html5" lang="en">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -7,7 +7,7 @@
   <title>Validation &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="_static/graphviz.css?v=eafc0fe6" />
 
   
   <!--[if lt IE 9]>
@@ -16,9 +16,9 @@
   
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=f2a433a1"></script>
-        <script src="_static/doctools.js?v=9a2dae69"></script>
-        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=359c27e9"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -90,7 +90,7 @@
            <div itemprop="articleBody">
              
   <section id="validation">
-<span id="id1"></span><h1>Validation<a class="headerlink" href="#validation" title="Link to this heading"></a></h1>
+<span id="id1"></span><h1>Validation<a class="headerlink" href="#validation" title="Permalink to this heading"></a></h1>
 <p>By default, parameters for tracks are validated to catch errors at creation
 time rather than upload time.</p>
 <p>In this example, we set <cite>fake_param</cite>. Note that track object is created with no
@@ -162,7 +162,7 @@
 </pre></div>
 </div>
 <section id="updating-parameters">
-<h2>Updating parameters<a class="headerlink" href="#updating-parameters" title="Link to this heading"></a></h2>
+<h2>Updating parameters<a class="headerlink" href="#updating-parameters" title="Permalink to this heading"></a></h2>
 <p>The track hub specification changes. In order to stay up-to-date with these
 changes, the <cite>trackhub.parse</cite> module can be used to parse the HTML of the Track
 Database Definition page and create the corresponding <cite>Param</cite> objects.</p>
