Fixes #25: removed .lower() from `bamnostic.utils._handle_split_reg…

…ion()`

Addressing #25 brought up by @envanloo: keeping literal name of contig. Originally, the implementation was only thinking of contig names such as 'chr1' and '1'. Hindsight showed that this was a faulty assumption. By removing `.lower()` from `bamnostic.utils._handle_spit_region()`, `bamnostic` should preserve literal contig names.

bamnostic/utils.py

@@ -248,7 +248,7 @@ def _handle_split_region(split_roi, until_eof=False):
 
         # if the user gives an integer description of chromosome, convert to string
         if isinstance(split_roi[0], (str, int)):
-            split_roi[0] = str(split_roi[0]).lower()
+            split_roi[0] = str(split_roi[0])
 
         if None in split_roi[1:]:
             # make sure the user wants to continue if they have used an open-ended region

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": "v1.0.0,
-  "version": "v1.0.0",
+  "softwareVersion": "v1.0.1,
+  "version": "v1.0.1",
   "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",

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: 05da12486de356c99fdddd217c848d20
+config: 7fe887b2cbc5b91bf05ea54ef36c1a08
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; bamnostic 0.8.4b5 documentation</title>
+  <title>Overview: module code &mdash; bamnostic 1.0.1 documentation</title>
 
 
 
@@ -24,8 +24,7 @@
 
 
 
-
-    <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <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" /> 
@@ -57,7 +56,7 @@
 
 
               <div class="version">
-                0.8.4
+                1.0.1
               </div>
 
 
@@ -152,7 +151,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="bamnostic/bgzf.html">bamnostic.bgzf</a></li>
 <li><a href="bamnostic/core.html">bamnostic.core</a></li>
 <li><a href="bamnostic/utils.html">bamnostic.utils</a></li>
-<li><a href="tests/test_placeholder.html">tests.test_placeholder</a></li>
 </ul>
 
            </div>
@@ -165,7 +163,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2018, Marcus D. Sherman.
+        &copy; Copyright 2018, Marcus D. Sherman
 
     </p>
   </div>
@@ -184,28 +182,18 @@ <h1>All modules for which code is available</h1>
 
 
 
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../',
-            VERSION:'0.8.4b5',
-            LANGUAGE:'en',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true,
-            SOURCELINK_SUFFIX: '.txt'
-        };
-    </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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></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 async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+
 
 
 
-
-
-    <script type="text/javascript" src="../_static/js/theme.js"></script>
-
+  <script type="text/javascript" src="../_static/js/theme.js"></script>
 
   <script type="text/javascript">
       jQuery(function () {

docs/build/html/_sources/quickstart.rst.txt

@@ -26,7 +26,7 @@ within the package.
 
 .. code:: python
 
-    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
+    >>> bam = bs.AlignmentFile(bs.example_bam, 'rb')
 
 Get the header
 ~~~~~~~~~~~~~~

docs/build/html/_static/basic.css

@@ -81,6 +81,10 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
+div.sphinxsidebar #searchbox form.search {
+    overflow: hidden;
+}
+
 div.sphinxsidebar #searchbox input[type="text"] {
     float: left;
     width: 80%;
@@ -427,6 +431,13 @@ table.field-list td, table.field-list th {
     hyphens: manual;
 }
 
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {

docs/build/html/_static/doctools.js

@@ -150,7 +150,9 @@ var Documentation = {
     this.fixFirefoxAnchorBug();
     this.highlightSearchWords();
     this.initIndexTable();
-
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
   },
 
   /**
@@ -310,4 +312,4 @@ _ = Documentation.gettext;
 
 $(document).ready(function() {
   Documentation.init();
-});
+});