bio-samtools-wrapper 2.7.0

data/doc/created.rid

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+Tue, 18 Mar 2014 16:07:41 +0000
+./lib/bio/db/alignment.rb	Fri, 07 Mar 2014 11:50:30 +0000
+./lib/bio/db/pileup.rb	Fri, 07 Mar 2014 10:51:34 +0000
+./lib/bio/db/sam/faidx_old.rb	Thu, 28 Nov 2013 11:06:34 +0000
+./lib/bio/db/sam/library.rb	Thu, 28 Nov 2013 11:03:39 +0000
+./lib/bio/db/sam.rb	Tue, 18 Mar 2014 16:04:41 +0000
+./lib/bio/db/vcf.rb	Fri, 07 Mar 2014 12:38:34 +0000
+./lib/bio-samtools-wrapper.rb	Mon, 17 Mar 2014 15:46:18 +0000
+./LICENSE.txt	Thu, 28 Nov 2013 11:03:38 +0000

data/doc/fonts.css

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+/*
+ * Copyright 2010, 2012 Adobe Systems Incorporated (http://www.adobe.com/),
+ * with Reserved Font Name "Source". All Rights Reserved. Source is a
+ * trademark of Adobe Systems Incorporated in the United States and/or other
+ * countries.
+ *
+ * This Font Software is licensed under the SIL Open Font License, Version
+ * 1.1.
+ *
+ * This license is copied below, and is also available with a FAQ at:
+ * http://scripts.sil.org/OFL
+ */
+
+@font-face {
+  font-family: "Source Code Pro";
+  font-style: normal;
+  font-weight: 400;
+  src: local("Source Code Pro"),
+       local("SourceCodePro-Regular"),
+       url("fonts/SourceCodePro-Regular.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Source Code Pro";
+  font-style: normal;
+  font-weight: 700;
+  src: local("Source Code Pro Bold"),
+       local("SourceCodePro-Bold"),
+       url("fonts/SourceCodePro-Bold.ttf") format("truetype");
+}
+
+/*
+ * Copyright (c) 2010, Łukasz Dziedzic (dziedzic@typoland.com),
+ * with Reserved Font Name Lato.
+ *
+ * This Font Software is licensed under the SIL Open Font License, Version
+ * 1.1.
+ *
+ * This license is copied below, and is also available with a FAQ at:
+ * http://scripts.sil.org/OFL
+ */
+
+@font-face {
+  font-family: "Lato";
+  font-style: normal;
+  font-weight: 300;
+  src: local("Lato Light"),
+       local("Lato-Light"),
+       url("fonts/Lato-Light.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: italic;
+  font-weight: 300;
+  src: local("Lato Light Italic"),
+       local("Lato-LightItalic"),
+       url("fonts/Lato-LightItalic.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: normal;
+  font-weight: 700;
+  src: local("Lato Regular"),
+       local("Lato-Regular"),
+       url("fonts/Lato-Regular.ttf") format("truetype");
+}
+
+@font-face {
+  font-family: "Lato";
+  font-style: italic;
+  font-weight: 700;
+  src: local("Lato Italic"),
+       local("Lato-Italic"),
+       url("fonts/Lato-RegularItalic.ttf") format("truetype");
+}
+
+/*
+ * -----------------------------------------------------------
+ * SIL OPEN FONT LICENSE Version 1.1 - 26 February 2007
+ * -----------------------------------------------------------
+ *
+ * PREAMBLE
+ * The goals of the Open Font License (OFL) are to stimulate worldwide
+ * development of collaborative font projects, to support the font creation
+ * efforts of academic and linguistic communities, and to provide a free and
+ * open framework in which fonts may be shared and improved in partnership
+ * with others.
+ *
+ * The OFL allows the licensed fonts to be used, studied, modified and
+ * redistributed freely as long as they are not sold by themselves. The
+ * fonts, including any derivative works, can be bundled, embedded,
+ * redistributed and/or sold with any software provided that any reserved
+ * names are not used by derivative works. The fonts and derivatives,
+ * however, cannot be released under any other type of license. The
+ * requirement for fonts to remain under this license does not apply
+ * to any document created using the fonts or their derivatives.
+ *
+ * DEFINITIONS
+ * "Font Software" refers to the set of files released by the Copyright
+ * Holder(s) under this license and clearly marked as such. This may
+ * include source files, build scripts and documentation.
+ *
+ * "Reserved Font Name" refers to any names specified as such after the
+ * copyright statement(s).
+ *
+ * "Original Version" refers to the collection of Font Software components as
+ * distributed by the Copyright Holder(s).
+ *
+ * "Modified Version" refers to any derivative made by adding to, deleting,
+ * or substituting -- in part or in whole -- any of the components of the
+ * Original Version, by changing formats or by porting the Font Software to a
+ * new environment.
+ *
+ * "Author" refers to any designer, engineer, programmer, technical
+ * writer or other person who contributed to the Font Software.
+ *
+ * PERMISSION & CONDITIONS
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of the Font Software, to use, study, copy, merge, embed, modify,
+ * redistribute, and sell modified and unmodified copies of the Font
+ * Software, subject to the following conditions:
+ *
+ * 1) Neither the Font Software nor any of its individual components,
+ * in Original or Modified Versions, may be sold by itself.
+ *
+ * 2) Original or Modified Versions of the Font Software may be bundled,
+ * redistributed and/or sold with any software, provided that each copy
+ * contains the above copyright notice and this license. These can be
+ * included either as stand-alone text files, human-readable headers or
+ * in the appropriate machine-readable metadata fields within text or
+ * binary files as long as those fields can be easily viewed by the user.
+ *
+ * 3) No Modified Version of the Font Software may use the Reserved Font
+ * Name(s) unless explicit written permission is granted by the corresponding
+ * Copyright Holder. This restriction only applies to the primary font name as
+ * presented to the users.
+ *
+ * 4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+ * Software shall not be used to promote, endorse or advertise any
+ * Modified Version, except to acknowledge the contribution(s) of the
+ * Copyright Holder(s) and the Author(s) or with their explicit written
+ * permission.
+ *
+ * 5) The Font Software, modified or unmodified, in part or in whole,
+ * must be distributed entirely under this license, and must not be
+ * distributed under any other license. The requirement for fonts to
+ * remain under this license does not apply to any document created
+ * using the Font Software.
+ *
+ * TERMINATION
+ * This license becomes null and void if any of the above conditions are
+ * not met.
+ *
+ * DISCLAIMER
+ * THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+ * OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+ * COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+ * DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+ * OTHER DEALINGS IN THE FONT SOFTWARE.
+ */
+

data/doc/index.html

@@ -0,0 +1,106 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta charset="UTF-8">
+
+<title>Pileup</title>
+
+<link href="./fonts.css" rel="stylesheet">
+<link href="./rdoc.css" rel="stylesheet">
+
+<script type="text/javascript">
+  var rdoc_rel_prefix = "./";
+</script>
+
+<script src="./js/jquery.js"></script>
+<script src="./js/navigation.js"></script>
+<script src="./js/search_index.js"></script>
+<script src="./js/search.js"></script>
+<script src="./js/searcher.js"></script>
+<script src="./js/darkfish.js"></script>
+
+
+<body id="top" role="document" class="file">
+<nav role="navigation">
+  <div id="project-navigation">
+    <div id="home-section" role="region" title="Quick navigation" class="nav-section">
+  <h2>
+    <a href="./index.html" rel="home">Home</a>
+  </h2>
+
+  <div id="table-of-contents-navigation">
+    <a href="./table_of_contents.html#pages">Pages</a>
+    <a href="./table_of_contents.html#classes">Classes</a>
+    <a href="./table_of_contents.html#methods">Methods</a>
+  </div>
+</div>
+
+
+    <div id="search-section" role="search" class="project-section initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <div id="search-field-wrapper">
+      <input id="search-field" role="combobox" aria-label="Search"
+             aria-autocomplete="list" aria-controls="search-results"
+             type="text" name="search" placeholder="Search" spellcheck="false"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </div>
+
+    <ul id="search-results" aria-label="Search Results"
+        aria-busy="false" aria-expanded="false"
+        aria-atomic="false" class="initially-hidden"></ul>
+  </form>
+</div>
+
+  </div>
+
+  <div id="project-metadata">
+    <div id="fileindex-section" class="nav-section">
+  <h3>Pages</h3>
+
+  <ul class="link-list">
+  
+    <li><a href="./LICENSE_txt.html">LICENSE</a>
+  
+  </ul>
+</div>
+
+    <div id="classindex-section" class="nav-section">
+  <h3>Class and Module Index</h3>
+
+  <ul class="link-list">
+  
+    <li><a href="./Bio.html">Bio</a>
+  
+    <li><a href="./Bio/DB/Alignment.html">Bio::DB::Alignment</a>
+  
+    <li><a href="./Bio/DB/Pileup.html">Bio::DB::Pileup</a>
+  
+    <li><a href="./Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
+  
+    <li><a href="./Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
+  
+    <li><a href="./Bio/DB/Sam.html">Bio::DB::Sam</a>
+  
+    <li><a href="./Bio/DB/Tag.html">Bio::DB::Tag</a>
+  
+    <li><a href="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
+  
+  </ul>
+</div>
+
+  </div>
+</nav>
+
+<main role="main">
+<p>This is the API documentation for Pileup.
+</main>
+
+
+
+<footer id="validator-badges" role="contentinfo">
+  <p><a href="http://validator.w3.org/check/referer">Validate</a>
+  <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
+  <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
+</footer>
+

data/doc/js/darkfish.js

@@ -0,0 +1,140 @@
+/**
+ *
+ * Darkfish Page Functions
+ * $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
+ *
+ * Author: Michael Granger <mgranger@laika.com>
+ *
+ */
+
+/* Provide console simulation for firebug-less environments */
+if (!("console" in window) || !("firebug" in console)) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
+    "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
+
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+};
+
+
+/**
+ * Unwrap the first element that matches the given @expr@ from the targets and return them.
+ */
+$.fn.unwrap = function( expr ) {
+  return this.each( function() {
+    $(this).parents( expr ).eq( 0 ).after( this ).remove();
+  });
+};
+
+
+function showSource( e ) {
+  var target = e.target;
+  var codeSections = $(target).
+    parents('.method-detail').
+    find('.method-source-code');
+
+  $(target).
+    parents('.method-detail').
+    find('.method-source-code').
+    slideToggle();
+};
+
+function hookSourceViews() {
+  $('.method-heading').click( showSource );
+};
+
+function toggleDebuggingSection() {
+  $('.debugging-section').slideToggle();
+};
+
+function hookDebuggingToggle() {
+  $('#debugging-toggle img').click( toggleDebuggingSection );
+};
+
+function hookSearch() {
+  var input  = $('#search-field').eq(0);
+  var result = $('#search-results').eq(0);
+  $(result).show();
+
+  var search_section = $('#search-section').get(0);
+  $(search_section).show();
+
+  var search = new Search(search_data, input, result);
+
+  search.renderItem = function(result) {
+    var li = document.createElement('li');
+    var html = '';
+
+    // TODO add relative path to <script> per-page
+    html += '<p class="search-match"><a href="' + rdoc_rel_prefix + result.path + '">' + this.hlt(result.title);
+    if (result.params)
+      html += '<span class="params">' + result.params + '</span>';
+    html += '</a>';
+
+
+    if (result.namespace)
+      html += '<p class="search-namespace">' + this.hlt(result.namespace);
+
+    if (result.snippet)
+      html += '<div class="search-snippet">' + result.snippet + '</div>';
+
+    li.innerHTML = html;
+
+    return li;
+  }
+
+  search.select = function(result) {
+    var result_element = result.get(0);
+    window.location.href = result_element.firstChild.firstChild.href;
+  }
+
+  search.scrollIntoView = search.scrollInWindow;
+};
+
+function highlightTarget( anchor ) {
+  console.debug( "Highlighting target '%s'.", anchor );
+
+  $("a[name]").each( function() {
+    if ( $(this).attr("name") == anchor ) {
+      if ( !$(this).parent().parent().hasClass('target-section') ) {
+        console.debug( "Wrapping the target-section" );
+        $('div.method-detail').unwrap( 'div.target-section' );
+        $(this).parent().wrap( '<div class="target-section"></div>' );
+      } else {
+        console.debug( "Already wrapped." );
+      }
+    }
+  });
+};
+
+function highlightLocationTarget() {
+  console.debug( "Location hash: %s", window.location.hash );
+  if ( ! window.location.hash || window.location.hash.length == 0 ) return;
+
+  var anchor = window.location.hash.substring(1);
+  console.debug( "Found anchor: %s; matching %s", anchor, "a[name=" + anchor + "]" );
+
+  highlightTarget( anchor );
+};
+
+function highlightClickTarget( event ) {
+  console.debug( "Highlighting click target for event %o", event.target );
+  try {
+    var anchor = $(event.target).attr( 'href' ).substring(1);
+    console.debug( "Found target anchor: %s", anchor );
+    highlightTarget( anchor );
+  } catch ( err ) {
+    console.error( "Exception while highlighting: %o", err );
+  };
+};
+
+
+$(document).ready( function() {
+  hookSourceViews();
+  hookDebuggingToggle();
+  hookSearch();
+  highlightLocationTarget();
+
+  $('ul.link-list a').bind( "click", highlightClickTarget );
+});