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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: b316255dee9ce301b8068bd695b9553d
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.nojekyll b/.nojekyll
diff --git a/_modules/baskerville/bed.html b/_modules/baskerville/bed.html
diff --git a/_modules/baskerville/blocks.html b/_modules/baskerville/blocks.html
diff --git a/_modules/baskerville/dataset.html b/_modules/baskerville/dataset.html
diff --git a/_modules/baskerville/dna.html b/_modules/baskerville/dna.html
diff --git a/_modules/baskerville/gene.html b/_modules/baskerville/gene.html
diff --git a/_modules/baskerville/layers.html b/_modules/baskerville/layers.html
diff --git a/_modules/baskerville/metrics.html b/_modules/baskerville/metrics.html
diff --git a/_modules/baskerville/seqnn.html b/_modules/baskerville/seqnn.html
diff --git a/_modules/baskerville/snps.html b/_modules/baskerville/snps.html
diff --git a/_modules/baskerville/trainer.html b/_modules/baskerville/trainer.html
diff --git a/_modules/baskerville/vcf.html b/_modules/baskerville/vcf.html
diff --git a/_modules/index.html b/_modules/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; baskerville 0.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <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=d45e8c67"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            baskerville
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../baskerville.html">baskerville package</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">baskerville</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="baskerville/bed.html">baskerville.bed</a></li>
+<li><a href="baskerville/blocks.html">baskerville.blocks</a></li>
+<li><a href="baskerville/dataset.html">baskerville.dataset</a></li>
+<li><a href="baskerville/dna.html">baskerville.dna</a></li>
+<li><a href="baskerville/gene.html">baskerville.gene</a></li>
+<li><a href="baskerville/layers.html">baskerville.layers</a></li>
+<li><a href="baskerville/metrics.html">baskerville.metrics</a></li>
+<li><a href="baskerville/seqnn.html">baskerville.seqnn</a></li>
+<li><a href="baskerville/snps.html">baskerville.snps</a></li>
+<li><a href="baskerville/trainer.html">baskerville.trainer</a></li>
+<li><a href="baskerville/vcf.html">baskerville.vcf</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, David Kelly.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
diff --git a/_sources/baskerville.rst.txt b/_sources/baskerville.rst.txt
@@ -0,0 +1,101 @@
+baskerville package
+===================
+
+Submodules
+----------
+
+baskerville.bed module
+----------------------
+
+.. automodule:: baskerville.bed
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.blocks module
+-------------------------
+
+.. automodule:: baskerville.blocks
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.dataset module
+--------------------------
+
+.. automodule:: baskerville.dataset
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.dna module
+----------------------
+
+.. automodule:: baskerville.dna
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.gene module
+-----------------------
+
+.. automodule:: baskerville.gene
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.layers module
+-------------------------
+
+.. automodule:: baskerville.layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.metrics module
+--------------------------
+
+.. automodule:: baskerville.metrics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.seqnn module
+------------------------
+
+.. automodule:: baskerville.seqnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.snps module
+-----------------------
+
+.. automodule:: baskerville.snps
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.trainer module
+--------------------------
+
+.. automodule:: baskerville.trainer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+baskerville.vcf module
+----------------------
+
+.. automodule:: baskerville.vcf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: baskerville
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,21 @@
+.. baskerville documentation master file, created by
+   sphinx-quickstart on Mon Dec 11 21:48:46 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to baskerville's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   baskerville
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js
@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
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+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}