-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathcompress.html
213 lines (194 loc) · 9.26 KB
/
compress.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
<!DOCTYPE html>
<html lang="en" data-content_root="./">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>7. Compressing indexes for transmission — ProPhyle 0.3.3.2 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
<link rel="stylesheet" type="text/css" href="_static/sphinx13.css?v=ec60a4c3" />
<script src="_static/documentation_options.js?v=e7e3125d"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<link rel="search" type="application/opensearchdescription+xml"
title="Search within ProPhyle 0.3.3.2 documentation"
href="_static/opensearch.xml"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="8. File formats" href="formats.html" />
<link rel="prev" title="6. Classifying reads" href="classify.html" />
<link href='https://fonts.googleapis.com/css?family=Open+Sans:300,400,700'
rel='stylesheet' type='text/css' />
<style type="text/css">
table.right { float: right; margin-left: 20px; }
table.right td { border: 1px solid #ccc; }
</style>
<script type="text/javascript">
// intelligent scrolling of the sidebar content
$(window).scroll(function() {
var sb = $('.sphinxsidebarwrapper');
var win = $(window);
var sbh = sb.height();
var offset = $('.sphinxsidebar').position()['top'];
var wintop = win.scrollTop();
var winbot = wintop + win.innerHeight();
var curtop = sb.position()['top'];
var curbot = curtop + sbh;
// does sidebar fit in window?
if (sbh < win.innerHeight()) {
// yes: easy case -- always keep at the top
sb.css('top', $u.min([$u.max([0, wintop - offset - 10]),
$(document).height() - sbh - 200]));
} else {
// no: only scroll if top/bottom edge of sidebar is at
// top/bottom edge of window
if (curtop > wintop && curbot > winbot) {
sb.css('top', $u.max([wintop - offset - 10, 0]));
} else if (curtop < wintop && curbot < winbot) {
sb.css('top', $u.min([winbot - sbh - offset - 20,
$(document).height() - sbh - 200]));
}
}
});
</script>
</head><body>
<div class="pageheader">
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="install.html">Get it</a></li>
<li><a href="contents.html">Docs</a></li>
<li><a href="http://github.com/prophyle/prophyle">Extend/Develop</a></li>
</ul>
<div>
<a href="index.html">
<!--
<img src="_static/sphinxheader.png" alt="SPHINX" />
-->
<div style="color:white;font-size:240%">ProPhyle</div>
<div style="color:white;font-size:140%">DNA sequence classification</div>
</a>
</div>
</div>
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="formats.html" title="8. File formats"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="classify.html" title="6. Classifying reads"
accesskey="P">previous</a> |</li>
<li><a href="index.html">ProPhyle home</a> |</li>
<li><a href="contents.html">Documentation</a> »</li>
<li class="nav-item nav-item-this"><a href=""><span class="section-number">7. </span>Compressing indexes for transmission</a></li>
</ul>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="contents.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">7. Compressing indexes for transmission</a><ul>
<li><a class="reference internal" href="#compression">7.1. Compression</a></li>
<li><a class="reference internal" href="#decompression">7.2. Decompression</a></li>
</ul>
</li>
</ul>
</div>
<div>
<h4>Previous topic</h4>
<p class="topless"><a href="classify.html"
title="previous chapter"><span class="section-number">6. </span>Classifying reads</a></p>
</div>
<div>
<h4>Next topic</h4>
<p class="topless"><a href="formats.html"
title="next chapter"><span class="section-number">8. </span>File formats</a></p>
</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/compress.rst.txt"
rel="nofollow">Show Source</a></li>
</ul>
</div>
<search id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
<input type="submit" value="Go" />
</form>
</div>
</search>
<script>document.getElementById('searchbox').style.display = "block"</script>
</div>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<section id="compressing-indexes-for-transmission">
<span id="index-0"></span><span id="compress"></span><h1><span class="section-number">7. </span>Compressing indexes for transmission<a class="headerlink" href="#compressing-indexes-for-transmission" title="Link to this heading">¶</a></h1>
<p>To simplify archiving indexes and their transmission over the Internet, ProPhyle
provides a compression feature. This compression is based
on creating a <code class="docutils literal notranslate"><span class="pre">.tar.gz</span></code> archive containing all information necessary to
reconstruct the entire index.
For a specification of the format, see Section <a class="reference internal" href="formats.html"><span class="doc">File formats</span></a>.</p>
<section id="compression">
<h2><span class="section-number">7.1. </span>Compression<a class="headerlink" href="#compression" title="Link to this heading">¶</a></h2>
<p>An index can be compressed by</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>compress<span class="w"> </span><index.dir><span class="w"> </span><span class="o">[</span><archive.tar.gz><span class="o">]</span>
</pre></div>
</div>
<p>If <code class="docutils literal notranslate"><span class="pre"><archive.tar.gz></span></code> is not provided, ProPhyle will derive the filename from the name of the index.</p>
</section>
<section id="decompression">
<h2><span class="section-number">7.2. </span>Decompression<a class="headerlink" href="#decompression" title="Link to this heading">¶</a></h2>
<p>A compressed index can then be decompressed by</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>prophyle<span class="w"> </span>decompress<span class="w"> </span><span class="o">[</span>-K<span class="o">]</span><span class="w"> </span><archive.tar.gz><span class="w"> </span><span class="o">[</span><output.dir><span class="o">]</span>
</pre></div>
</div>
<p>Decompression includes reconstructing the sampled suffix array and the k-LCP bit array.
If the option <code class="docutils literal notranslate"><span class="pre">-K</span></code> is provided, k-LCP will not be reconstructed.</p>
</section>
</section>
<div class="clearer"></div>
</div>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="formats.html" title="8. File formats"
>next</a> |</li>
<li class="right" >
<a href="classify.html" title="6. Classifying reads"
>previous</a> |</li>
<li><a href="index.html">ProPhyle home</a> |</li>
<li><a href="contents.html">Documentation</a> »</li>
<li class="nav-item nav-item-this"><a href=""><span class="section-number">7. </span>Compressing indexes for transmission</a></li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2015-2024, Karel Břinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
</div>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-112241191-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-112241191-1');
</script>
</body>
</html>