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betteridiot · Mar 19, 2019 · 6e00862 · 6e00862
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diff --git a/codemeta.json b/codemeta.json
@@ -37,8 +37,8 @@
   "description": "BAMnostic is a Pure Python OS, version, and runtime agnostic BAM file parser",
   "keywords": "BAM, pysam, genomics, genetics, htslib, samtools",
   "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE",
-  "softwareVersion": "v1.0.7,
-  "version": "v1.0.7",
+  "softwareVersion": "v1.0.8,
+  "version": "v1.0.8",
   "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "issueTracker": "https://github.com/betteridiot/bamnostic/issues",

diff --git a/docs/build/doctrees/bamnostic.doctree b/docs/build/doctrees/bamnostic.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6d491e59de0287a809983c89c4c65de7
+config: 76b369e4848f1079a3c98dd019f878b8
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/bamnostic/bai.html b/docs/build/html/_modules/bamnostic/bai.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.bai &mdash; bamnostic 1.0.7 documentation</title>
+  <title>bamnostic.bai &mdash; bamnostic 1.0.8 documentation</title>
 
 
 
@@ -17,32 +17,35 @@
 
 
 
-
-
+  <script type="text/javascript" src="../../_static/js/modernizr.min.js"></script>
 
 
+      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../../_static/jquery.js"></script>
+        <script type="text/javascript" src="../../_static/underscore.js"></script>
+        <script type="text/javascript" src="../../_static/doctools.js"></script>
+        <script type="text/javascript" src="../../_static/language_data.js"></script>
+        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <script type="text/javascript" src="../../_static/js/theme.js"></script>
 
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+    
 
+
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     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
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 </head>
 
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+        <div class="wy-side-nav-search" >
 
 
 
@@ -56,7 +59,7 @@
 
 
               <div class="version">
-                1.0.7
+                1.0.8
               </div>
 
 
@@ -636,26 +639,16 @@ <h1>Source code for bamnostic.bai</h1><div class="highlight"><pre>
 
 
 
-
-
-
-
-      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
-        <script type="text/javascript" src="../../_static/jquery.js"></script>
-        <script type="text/javascript" src="../../_static/underscore.js"></script>
-        <script type="text/javascript" src="../../_static/doctools.js"></script>
-        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-
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-  <script type="text/javascript" src="../../_static/js/theme.js"></script>
-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
+
+
+
+
+
 
 </body>
 </html>
diff --git a/docs/build/html/_modules/bamnostic/bgzf.html b/docs/build/html/_modules/bamnostic/bgzf.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.bgzf &mdash; bamnostic 1.0.7 documentation</title>
+  <title>bamnostic.bgzf &mdash; bamnostic 1.0.8 documentation</title>
 
 
 
@@ -17,32 +17,35 @@
 
 
 
-
-
+  <script type="text/javascript" src="../../_static/js/modernizr.min.js"></script>
 
 
+      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../../_static/jquery.js"></script>
+        <script type="text/javascript" src="../../_static/underscore.js"></script>
+        <script type="text/javascript" src="../../_static/doctools.js"></script>
+        <script type="text/javascript" src="../../_static/language_data.js"></script>
+        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <script type="text/javascript" src="../../_static/js/theme.js"></script>
 
-
+    
 
+
   <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
-
-
-  <script src="../../_static/js/modernizr.min.js"></script>
-
 </head>
 
 <body class="wy-body-for-nav">
 
 
   <div class="wy-grid-for-nav">
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     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
-        <div class="wy-side-nav-search">
+        <div class="wy-side-nav-search" >
 
 
 
@@ -56,7 +59,7 @@
 
 
               <div class="version">
-                1.0.7
+                1.0.8
               </div>
 
 
@@ -805,26 +808,16 @@ <h1>Source code for bamnostic.bgzf</h1><div class="highlight"><pre>
 
 
 
-
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-      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
-        <script type="text/javascript" src="../../_static/jquery.js"></script>
-        <script type="text/javascript" src="../../_static/underscore.js"></script>
-        <script type="text/javascript" src="../../_static/doctools.js"></script>
-        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-
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-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
+
+
+
+
+
 
 </body>
 </html>
diff --git a/docs/build/html/_modules/bamnostic/core.html b/docs/build/html/_modules/bamnostic/core.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>bamnostic.core &mdash; bamnostic 1.0.7 documentation</title>
+  <title>bamnostic.core &mdash; bamnostic 1.0.8 documentation</title>
 
 
 
@@ -17,32 +17,35 @@
 
 
 
-
-
+  <script type="text/javascript" src="../../_static/js/modernizr.min.js"></script>
 
 
+      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+        <script type="text/javascript" src="../../_static/jquery.js"></script>
+        <script type="text/javascript" src="../../_static/underscore.js"></script>
+        <script type="text/javascript" src="../../_static/doctools.js"></script>
+        <script type="text/javascript" src="../../_static/language_data.js"></script>
+        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
+    <script type="text/javascript" src="../../_static/js/theme.js"></script>
 
-
+    
 
+
   <link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
-
-
-  <script src="../../_static/js/modernizr.min.js"></script>
-
 </head>
 
 <body class="wy-body-for-nav">
 
 
   <div class="wy-grid-for-nav">
-
 
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
-        <div class="wy-side-nav-search">
+        <div class="wy-side-nav-search" >
 
 
 
@@ -56,7 +59,7 @@
 
 
               <div class="version">
-                1.0.7
+                1.0.8
               </div>
 
 
@@ -424,7 +427,11 @@ <h1>Source code for bamnostic.core</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">read_name</span> <span class="o">=</span> <span class="n">unpack</span><span class="p">(</span><span class="s1">&#39;&lt;</span><span class="si">{}</span><span class="s1">s&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_l_read_name</span><span class="p">),</span> <span class="bp">self</span><span class="o">.</span><span class="n">_range_popper</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_l_read_name</span><span class="p">))</span><span class="o">.</span><span class="n">decode</span><span class="p">()[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">tid</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">reference_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">refID</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">reference_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_io</span><span class="o">.</span><span class="n">_header</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">refID</span><span class="p">][</span><span class="mi">0</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">reference_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_io</span><span class="o">.</span><span class="n">_header</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">refID</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">refID</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_io</span><span class="o">.</span><span class="n">_header</span><span class="o">.</span><span class="n">refs</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">reference_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_io</span><span class="o">.</span><span class="n">_header</span><span class="o">.</span><span class="n">refs</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
 
     <span class="k">def</span> <span class="nf">_cigar_builder</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Just unpacks the cigar data to be processed later. Ensures the cursor</span>
@@ -1010,26 +1017,16 @@ <h1>Source code for bamnostic.core</h1><div class="highlight"><pre>
 
 
 
-
-
-
-
-      <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
-        <script type="text/javascript" src="../../_static/jquery.js"></script>
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-
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-
   <script type="text/javascript">
       jQuery(function () {
           SphinxRtdTheme.Navigation.enable(true);
       });
-  </script> 
+  </script>
+
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+
 
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