bio-samtools-wrapper 2.7.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +27 -0
- data/Gemfile +20 -0
- data/LICENSE.txt +702 -0
- data/README.md +501 -0
- data/Rakefile +73 -0
- data/VERSION +1 -0
- data/bin/bam_consensus.rb +85 -0
- data/bio-samtools-wrapper.gemspec +181 -0
- data/doc/Bio/DB/Alignment.html +552 -0
- data/doc/Bio/DB/Pileup.html +711 -0
- data/doc/Bio/DB/SAM/Library.html +167 -0
- data/doc/Bio/DB/SAM/Tools.html +109 -0
- data/doc/Bio/DB/SAM.html +1853 -0
- data/doc/Bio/DB/Tag.html +208 -0
- data/doc/Bio/DB/Vcf.html +431 -0
- data/doc/Bio/DB.html +105 -0
- data/doc/Bio.html +175 -0
- data/doc/LICENSE_txt.html +846 -0
- data/doc/created.rid +9 -0
- data/doc/fonts/Lato-Light.ttf +0 -0
- data/doc/fonts/Lato-LightItalic.ttf +0 -0
- data/doc/fonts/Lato-Regular.ttf +0 -0
- data/doc/fonts/Lato-RegularItalic.ttf +0 -0
- data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
- data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
- data/doc/fonts.css +167 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
- data/doc/images/bullet_black.png +0 -0
- data/doc/images/bullet_toggle_minus.png +0 -0
- data/doc/images/bullet_toggle_plus.png +0 -0
- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +106 -0
- data/doc/js/darkfish.js +140 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +109 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/rdoc.css +580 -0
- data/doc/table_of_contents.html +305 -0
- data/ext/Makefile-bioruby.patch +12 -0
- data/ext/Makefile-suse.patch +11 -0
- data/ext/mkrf_conf.rb +118 -0
- data/lib/bio/BIOExtensions.rb +89 -0
- data/lib/bio/db/alignment.rb +64 -0
- data/lib/bio/db/fastadb.rb +320 -0
- data/lib/bio/db/pileup.rb +273 -0
- data/lib/bio/db/sam/external/COPYING +21 -0
- data/lib/bio/db/sam/external/VERSION +1 -0
- data/lib/bio/db/sam/library.rb +32 -0
- data/lib/bio/db/sam.rb +778 -0
- data/lib/bio/db/vcf.rb +105 -0
- data/lib/bio-samtools-wrapper.rb +9 -0
- data/test/.gitignore +1 -0
- data/test/helper.rb +18 -0
- data/test/sample.vcf +24 -0
- data/test/samples/.gitignore +1 -0
- data/test/samples/LCI/NC_001988.ffn +2 -0
- data/test/samples/LCI/test.bam +0 -0
- data/test/samples/LCI/test.bam.bai +0 -0
- data/test/samples/small/dupes.bam +0 -0
- data/test/samples/small/dupes.sam +274 -0
- data/test/samples/small/ids2.txt +1 -0
- data/test/samples/small/map_for_reheader.sam +8 -0
- data/test/samples/small/map_to_merge1.bam +0 -0
- data/test/samples/small/map_to_merge1.bam.bai +0 -0
- data/test/samples/small/map_to_merge1.sam +8 -0
- data/test/samples/small/map_to_merge2.bam +0 -0
- data/test/samples/small/map_to_merge2.bam.bai +0 -0
- data/test/samples/small/map_to_merge2.sam +8 -0
- data/test/samples/small/no_md.sam +8 -0
- data/test/samples/small/sorted.bam +0 -0
- data/test/samples/small/sorted.bam.bai +0 -0
- data/test/samples/small/test.sai +0 -0
- data/test/samples/small/test.tam +10 -0
- data/test/samples/small/test_chr.fasta +1000 -0
- data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.amb +2 -0
- data/test/samples/small/test_chr.fasta.ann +3 -0
- data/test/samples/small/test_chr.fasta.bwt +0 -0
- data/test/samples/small/test_chr.fasta.pac +0 -0
- data/test/samples/small/test_chr.fasta.rbwt +0 -0
- data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rpac +0 -0
- data/test/samples/small/test_chr.fasta.rsa +0 -0
- data/test/samples/small/test_chr.fasta.sa +0 -0
- data/test/samples/small/test_cov.svg +273 -0
- data/test/samples/small/test_fastadb.fasta +34 -0
- data/test/samples/small/testu.bam +0 -0
- data/test/samples/small/testu.bed +2 -0
- data/test/test_bio-samtools-wrapper.rb +1 -0
- data/test/test_fastadb.rb +89 -0
- data/test/test_pileup.rb +90 -0
- data/test/test_sam.rb +421 -0
- data/test/test_vcf.rb +79 -0
- data/tutorial/tutorial.html +474 -0
- data/tutorial/tutorial.md +424 -0
- data/tutorial/tutorial.pdf +0 -0
- metadata +254 -0
data/doc/Bio/DB/SAM.html
ADDED
|
@@ -0,0 +1,1853 @@
|
|
|
1
|
+
<!DOCTYPE html>
|
|
2
|
+
|
|
3
|
+
<html>
|
|
4
|
+
<head>
|
|
5
|
+
<meta charset="UTF-8">
|
|
6
|
+
|
|
7
|
+
<title>class Bio::DB::Sam - Pileup</title>
|
|
8
|
+
|
|
9
|
+
<link href="../../fonts.css" rel="stylesheet">
|
|
10
|
+
<link href="../../rdoc.css" rel="stylesheet">
|
|
11
|
+
|
|
12
|
+
<script type="text/javascript">
|
|
13
|
+
var rdoc_rel_prefix = "../../";
|
|
14
|
+
</script>
|
|
15
|
+
|
|
16
|
+
<script src="../../js/jquery.js"></script>
|
|
17
|
+
<script src="../../js/navigation.js"></script>
|
|
18
|
+
<script src="../../js/search_index.js"></script>
|
|
19
|
+
<script src="../../js/search.js"></script>
|
|
20
|
+
<script src="../../js/searcher.js"></script>
|
|
21
|
+
<script src="../../js/darkfish.js"></script>
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
<body id="top" role="document" class="class">
|
|
25
|
+
<nav role="navigation">
|
|
26
|
+
<div id="project-navigation">
|
|
27
|
+
<div id="home-section" role="region" title="Quick navigation" class="nav-section">
|
|
28
|
+
<h2>
|
|
29
|
+
<a href="../../index.html" rel="home">Home</a>
|
|
30
|
+
</h2>
|
|
31
|
+
|
|
32
|
+
<div id="table-of-contents-navigation">
|
|
33
|
+
<a href="../../table_of_contents.html#pages">Pages</a>
|
|
34
|
+
<a href="../../table_of_contents.html#classes">Classes</a>
|
|
35
|
+
<a href="../../table_of_contents.html#methods">Methods</a>
|
|
36
|
+
</div>
|
|
37
|
+
</div>
|
|
38
|
+
|
|
39
|
+
<div id="search-section" role="search" class="project-section initially-hidden">
|
|
40
|
+
<form action="#" method="get" accept-charset="utf-8">
|
|
41
|
+
<div id="search-field-wrapper">
|
|
42
|
+
<input id="search-field" role="combobox" aria-label="Search"
|
|
43
|
+
aria-autocomplete="list" aria-controls="search-results"
|
|
44
|
+
type="text" name="search" placeholder="Search" spellcheck="false"
|
|
45
|
+
title="Type to search, Up and Down to navigate, Enter to load">
|
|
46
|
+
</div>
|
|
47
|
+
|
|
48
|
+
<ul id="search-results" aria-label="Search Results"
|
|
49
|
+
aria-busy="false" aria-expanded="false"
|
|
50
|
+
aria-atomic="false" class="initially-hidden"></ul>
|
|
51
|
+
</form>
|
|
52
|
+
</div>
|
|
53
|
+
|
|
54
|
+
</div>
|
|
55
|
+
|
|
56
|
+
|
|
57
|
+
|
|
58
|
+
<div id="class-metadata">
|
|
59
|
+
|
|
60
|
+
<div id="parent-class-section" class="nav-section">
|
|
61
|
+
<h3>Parent</h3>
|
|
62
|
+
|
|
63
|
+
|
|
64
|
+
<p class="link">Object
|
|
65
|
+
|
|
66
|
+
</div>
|
|
67
|
+
|
|
68
|
+
|
|
69
|
+
|
|
70
|
+
<!-- Method Quickref -->
|
|
71
|
+
<div id="method-list-section" class="nav-section">
|
|
72
|
+
<h3>Methods</h3>
|
|
73
|
+
|
|
74
|
+
<ul class="link-list" role="directory">
|
|
75
|
+
|
|
76
|
+
<li ><a href="#method-c-docs">::docs</a>
|
|
77
|
+
|
|
78
|
+
<li ><a href="#method-c-new">::new</a>
|
|
79
|
+
|
|
80
|
+
<li ><a href="#method-i-average_coverage">#average_coverage</a>
|
|
81
|
+
|
|
82
|
+
<li ><a href="#method-i-calmd">#calmd</a>
|
|
83
|
+
|
|
84
|
+
<li ><a href="#method-i-cat">#cat</a>
|
|
85
|
+
|
|
86
|
+
<li ><a href="#method-i-chromosome_coverage">#chromosome_coverage</a>
|
|
87
|
+
|
|
88
|
+
<li ><a href="#method-i-depth">#depth</a>
|
|
89
|
+
|
|
90
|
+
<li ><a href="#method-i-faidx">#faidx</a>
|
|
91
|
+
|
|
92
|
+
<li ><a href="#method-i-fetch">#fetch</a>
|
|
93
|
+
|
|
94
|
+
<li ><a href="#method-i-fetch_reference">#fetch_reference</a>
|
|
95
|
+
|
|
96
|
+
<li ><a href="#method-i-fetch_with_function">#fetch_with_function</a>
|
|
97
|
+
|
|
98
|
+
<li ><a href="#method-i-fix_mates">#fix_mates</a>
|
|
99
|
+
|
|
100
|
+
<li ><a href="#method-i-fixmate">#fixmate</a>
|
|
101
|
+
|
|
102
|
+
<li ><a href="#method-i-flag_stats">#flag_stats</a>
|
|
103
|
+
|
|
104
|
+
<li ><a href="#method-i-flagstat">#flagstat</a>
|
|
105
|
+
|
|
106
|
+
<li ><a href="#method-i-idxstats">#idxstats</a>
|
|
107
|
+
|
|
108
|
+
<li ><a href="#method-i-index">#index</a>
|
|
109
|
+
|
|
110
|
+
<li ><a href="#method-i-index_stats">#index_stats</a>
|
|
111
|
+
|
|
112
|
+
<li ><a href="#method-i-merge">#merge</a>
|
|
113
|
+
|
|
114
|
+
<li ><a href="#method-i-mpileup">#mpileup</a>
|
|
115
|
+
|
|
116
|
+
<li ><a href="#method-i-open">#open</a>
|
|
117
|
+
|
|
118
|
+
<li ><a href="#method-i-phase">#phase</a>
|
|
119
|
+
|
|
120
|
+
<li ><a href="#method-i-plot_chromosome_coverage">#plot_chromosome_coverage</a>
|
|
121
|
+
|
|
122
|
+
<li ><a href="#method-i-reheader">#reheader</a>
|
|
123
|
+
|
|
124
|
+
<li ><a href="#method-i-remove_duplicates">#remove_duplicates</a>
|
|
125
|
+
|
|
126
|
+
<li ><a href="#method-i-rmdup">#rmdup</a>
|
|
127
|
+
|
|
128
|
+
<li ><a href="#method-i-sort">#sort</a>
|
|
129
|
+
|
|
130
|
+
<li ><a href="#method-i-targetcut">#targetcut</a>
|
|
131
|
+
|
|
132
|
+
<li ><a href="#method-i-tview">#tview</a>
|
|
133
|
+
|
|
134
|
+
<li ><a href="#method-i-view">#view</a>
|
|
135
|
+
|
|
136
|
+
</ul>
|
|
137
|
+
</div>
|
|
138
|
+
|
|
139
|
+
</div>
|
|
140
|
+
</nav>
|
|
141
|
+
|
|
142
|
+
<main role="main" aria-labelledby="class-Bio::DB::Sam">
|
|
143
|
+
<h1 id="class-Bio::DB::Sam" class="class">
|
|
144
|
+
class Bio::DB::Sam
|
|
145
|
+
</h1>
|
|
146
|
+
|
|
147
|
+
<section class="description">
|
|
148
|
+
|
|
149
|
+
</section>
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
|
|
154
|
+
<section id="5Buntitled-5D" class="documentation-section">
|
|
155
|
+
|
|
156
|
+
|
|
157
|
+
|
|
158
|
+
|
|
159
|
+
|
|
160
|
+
|
|
161
|
+
|
|
162
|
+
<section class="attribute-method-details" class="method-section">
|
|
163
|
+
<header>
|
|
164
|
+
<h3>Attributes</h3>
|
|
165
|
+
</header>
|
|
166
|
+
|
|
167
|
+
|
|
168
|
+
<div id="attribute-i-bam" class="method-detail">
|
|
169
|
+
<div class="method-heading attribute-method-heading">
|
|
170
|
+
<span class="method-name">bam</span><span
|
|
171
|
+
class="attribute-access-type">[RW]</span>
|
|
172
|
+
</div>
|
|
173
|
+
|
|
174
|
+
<div class="method-description">
|
|
175
|
+
|
|
176
|
+
|
|
177
|
+
|
|
178
|
+
</div>
|
|
179
|
+
</div>
|
|
180
|
+
|
|
181
|
+
<div id="attribute-i-bcftools" class="method-detail">
|
|
182
|
+
<div class="method-heading attribute-method-heading">
|
|
183
|
+
<span class="method-name">bcftools</span><span
|
|
184
|
+
class="attribute-access-type">[RW]</span>
|
|
185
|
+
</div>
|
|
186
|
+
|
|
187
|
+
<div class="method-description">
|
|
188
|
+
|
|
189
|
+
|
|
190
|
+
|
|
191
|
+
</div>
|
|
192
|
+
</div>
|
|
193
|
+
|
|
194
|
+
<div id="attribute-i-fasta" class="method-detail">
|
|
195
|
+
<div class="method-heading attribute-method-heading">
|
|
196
|
+
<span class="method-name">fasta</span><span
|
|
197
|
+
class="attribute-access-type">[RW]</span>
|
|
198
|
+
</div>
|
|
199
|
+
|
|
200
|
+
<div class="method-description">
|
|
201
|
+
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
</div>
|
|
205
|
+
</div>
|
|
206
|
+
|
|
207
|
+
<div id="attribute-i-last_command" class="method-detail">
|
|
208
|
+
<div class="method-heading attribute-method-heading">
|
|
209
|
+
<span class="method-name">last_command</span><span
|
|
210
|
+
class="attribute-access-type">[RW]</span>
|
|
211
|
+
</div>
|
|
212
|
+
|
|
213
|
+
<div class="method-description">
|
|
214
|
+
|
|
215
|
+
|
|
216
|
+
|
|
217
|
+
</div>
|
|
218
|
+
</div>
|
|
219
|
+
|
|
220
|
+
<div id="attribute-i-samtools" class="method-detail">
|
|
221
|
+
<div class="method-heading attribute-method-heading">
|
|
222
|
+
<span class="method-name">samtools</span><span
|
|
223
|
+
class="attribute-access-type">[RW]</span>
|
|
224
|
+
</div>
|
|
225
|
+
|
|
226
|
+
<div class="method-description">
|
|
227
|
+
|
|
228
|
+
|
|
229
|
+
|
|
230
|
+
</div>
|
|
231
|
+
</div>
|
|
232
|
+
|
|
233
|
+
</section>
|
|
234
|
+
|
|
235
|
+
|
|
236
|
+
|
|
237
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section">
|
|
238
|
+
<header>
|
|
239
|
+
<h3>Public Class Methods</h3>
|
|
240
|
+
</header>
|
|
241
|
+
|
|
242
|
+
|
|
243
|
+
<div id="method-c-docs" class="method-detail ">
|
|
244
|
+
|
|
245
|
+
<div class="method-heading">
|
|
246
|
+
<span class="method-name">docs</span><span
|
|
247
|
+
class="method-args">(program, command)</span>
|
|
248
|
+
|
|
249
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
250
|
+
|
|
251
|
+
</div>
|
|
252
|
+
|
|
253
|
+
|
|
254
|
+
<div class="method-description">
|
|
255
|
+
|
|
256
|
+
<ul><li>
|
|
257
|
+
<p>program - one of 'samtools' 'bcftools'</p>
|
|
258
|
+
</li><li>
|
|
259
|
+
<p>command - one of the commands relevant to the program</p>
|
|
260
|
+
</li></ul>
|
|
261
|
+
|
|
262
|
+
|
|
263
|
+
|
|
264
|
+
|
|
265
|
+
<div class="method-source-code" id="docs-source">
|
|
266
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 401</span>
|
|
267
|
+
<span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">docs</span>(<span class="ruby-identifier">program</span>, <span class="ruby-identifier">command</span>)
|
|
268
|
+
<span class="ruby-keyword">return</span> <span class="ruby-string">"program must be 'samtools' or 'bcftools'"</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> [<span class="ruby-string">'samtools'</span>, <span class="ruby-string">'bcftools'</span>].<span class="ruby-identifier">include?</span> <span class="ruby-identifier">program</span>
|
|
269
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{program} #{command}"</span>
|
|
270
|
+
<span class="ruby-node">%x#{command}`</span>
|
|
271
|
+
<span class="ruby-keyword">end</span></pre>
|
|
272
|
+
</div>
|
|
273
|
+
|
|
274
|
+
</div>
|
|
275
|
+
|
|
276
|
+
|
|
277
|
+
|
|
278
|
+
|
|
279
|
+
</div>
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
<div id="method-c-new" class="method-detail ">
|
|
283
|
+
|
|
284
|
+
<div class="method-heading">
|
|
285
|
+
<span class="method-name">new</span><span
|
|
286
|
+
class="method-args">(args)</span>
|
|
287
|
+
|
|
288
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
289
|
+
|
|
290
|
+
</div>
|
|
291
|
+
|
|
292
|
+
|
|
293
|
+
<div class="method-description">
|
|
294
|
+
|
|
295
|
+
<p>Creates a new <a href="Sam.html">Bio::DB::Sam</a> object</p>
|
|
296
|
+
<ul><li>
|
|
297
|
+
<p>fasta [String] - the path to the Fasta reference sequence</p>
|
|
298
|
+
</li><li>
|
|
299
|
+
<p>bam [String] - path to bam files</p>
|
|
300
|
+
</li><li>
|
|
301
|
+
<p>samtools [String] - path to alternative installation of samtools</p>
|
|
302
|
+
</li><li>
|
|
303
|
+
<p>bcftools [String] - path to alternative installation of bcftools</p>
|
|
304
|
+
</li><li>
|
|
305
|
+
<p>returns [Bio::DB::Sam] a new `Bio::DB::Sam` object</p>
|
|
306
|
+
</li></ul>
|
|
307
|
+
|
|
308
|
+
|
|
309
|
+
|
|
310
|
+
|
|
311
|
+
<div class="method-source-code" id="new-source">
|
|
312
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 13</span>
|
|
313
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
|
|
314
|
+
<span class="ruby-ivar">@fasta</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:fasta</span>]
|
|
315
|
+
<span class="ruby-ivar">@bam</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:bam</span>]
|
|
316
|
+
<span class="ruby-ivar">@samtools</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:samtools</span>] <span class="ruby-operator">||</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">join</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">expand_path</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword">__FILE__</span>)),<span class="ruby-string">'sam'</span>,<span class="ruby-string">'external'</span>,<span class="ruby-string">'samtools'</span>)
|
|
317
|
+
<span class="ruby-ivar">@bcftools</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:bcftools</span>] <span class="ruby-operator">||</span> <span class="ruby-constant">File</span>.<span class="ruby-identifier">join</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">expand_path</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword">__FILE__</span>)),<span class="ruby-string">'sam'</span>,<span class="ruby-string">'external'</span>,<span class="ruby-string">'bcftools'</span>)
|
|
318
|
+
|
|
319
|
+
<span class="ruby-ivar">@files</span> = [<span class="ruby-ivar">@files</span>] <span class="ruby-keyword">if</span> <span class="ruby-ivar">@files</span>.<span class="ruby-identifier">instance_of?</span>(<span class="ruby-constant">String</span>)
|
|
320
|
+
|
|
321
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-keyword">nil</span>
|
|
322
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-string">"Need Fasta and at least one BAM or SAM"</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-ivar">@fasta</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">not</span> <span class="ruby-ivar">@bam</span>
|
|
323
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">IOError</span>, <span class="ruby-string">"File not found"</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> <span class="ruby-identifier">files_ok?</span>
|
|
324
|
+
<span class="ruby-ivar">@bams</span> = [<span class="ruby-ivar">@bams</span>] <span class="ruby-keyword">if</span> <span class="ruby-ivar">@bams</span>.<span class="ruby-identifier">instance_of?</span> <span class="ruby-constant">String</span>
|
|
325
|
+
|
|
326
|
+
<span class="ruby-keyword">end</span></pre>
|
|
327
|
+
</div>
|
|
328
|
+
|
|
329
|
+
</div>
|
|
330
|
+
|
|
331
|
+
|
|
332
|
+
|
|
333
|
+
|
|
334
|
+
</div>
|
|
335
|
+
|
|
336
|
+
|
|
337
|
+
</section>
|
|
338
|
+
|
|
339
|
+
<section id="public-instance-5Buntitled-5D-method-details" class="method-section">
|
|
340
|
+
<header>
|
|
341
|
+
<h3>Public Instance Methods</h3>
|
|
342
|
+
</header>
|
|
343
|
+
|
|
344
|
+
|
|
345
|
+
<div id="method-i-average_coverage" class="method-detail ">
|
|
346
|
+
|
|
347
|
+
<div class="method-heading">
|
|
348
|
+
<span class="method-name">average_coverage</span><span
|
|
349
|
+
class="method-args">(chr,start,length)</span>
|
|
350
|
+
|
|
351
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
352
|
+
|
|
353
|
+
</div>
|
|
354
|
+
|
|
355
|
+
|
|
356
|
+
<div class="method-description">
|
|
357
|
+
|
|
358
|
+
<p>returns the average coverage over the region queried</p>
|
|
359
|
+
<ul><li>
|
|
360
|
+
<p>chr - the reference name</p>
|
|
361
|
+
</li><li>
|
|
362
|
+
<p>start - the start position</p>
|
|
363
|
+
</li><li>
|
|
364
|
+
<p>length - the length of the region queried</p>
|
|
365
|
+
</li></ul>
|
|
366
|
+
|
|
367
|
+
|
|
368
|
+
|
|
369
|
+
|
|
370
|
+
<div class="method-source-code" id="average_coverage-source">
|
|
371
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 167</span>
|
|
372
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">average_coverage</span>(<span class="ruby-identifier">chr</span>,<span class="ruby-identifier">start</span>,<span class="ruby-identifier">length</span>)
|
|
373
|
+
<span class="ruby-identifier">arr</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chr</span>,<span class="ruby-identifier">start</span>,<span class="ruby-identifier">length</span>)
|
|
374
|
+
<span class="ruby-identifier">arr</span>.<span class="ruby-identifier">inject</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>, <span class="ruby-identifier">el</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">el</span> }.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">arr</span>.<span class="ruby-identifier">size</span>
|
|
375
|
+
<span class="ruby-keyword">end</span></pre>
|
|
376
|
+
</div>
|
|
377
|
+
|
|
378
|
+
</div>
|
|
379
|
+
|
|
380
|
+
|
|
381
|
+
|
|
382
|
+
|
|
383
|
+
</div>
|
|
384
|
+
|
|
385
|
+
|
|
386
|
+
<div id="method-i-calmd" class="method-detail ">
|
|
387
|
+
|
|
388
|
+
<div class="method-heading">
|
|
389
|
+
<span class="method-name">calmd</span><span
|
|
390
|
+
class="method-args">(opts={}, &block)</span>
|
|
391
|
+
|
|
392
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
393
|
+
|
|
394
|
+
</div>
|
|
395
|
+
|
|
396
|
+
|
|
397
|
+
<div class="method-description">
|
|
398
|
+
|
|
399
|
+
<p>Generate the MD tag. If the MD tag is already present, this command will
|
|
400
|
+
give a warning if the MD tag generated is different from the existing tag.
|
|
401
|
+
Output SAM by default.</p>
|
|
402
|
+
<ul><li>
|
|
403
|
+
<p>A - When used jointly with -r this option overwrites the original base
|
|
404
|
+
quality.</p>
|
|
405
|
+
</li><li>
|
|
406
|
+
<p>e - Convert a the read base to = if it is identical to the aligned
|
|
407
|
+
reference base. Indel caller does not support the = bases at the moment.</p>
|
|
408
|
+
</li><li>
|
|
409
|
+
<p>u - Output uncompressed BAM</p>
|
|
410
|
+
</li><li>
|
|
411
|
+
<p>b - Output compressed BAM</p>
|
|
412
|
+
</li><li>
|
|
413
|
+
<p>S - The input is SAM with header lines</p>
|
|
414
|
+
</li><li>
|
|
415
|
+
<p>C - [INT] Coefficient to cap mapping quality of poorly mapped reads. See
|
|
416
|
+
the pileup command for details. [0]</p>
|
|
417
|
+
</li><li>
|
|
418
|
+
<p>r - Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).</p>
|
|
419
|
+
</li><li>
|
|
420
|
+
<p>E - Extended BAQ calculation. This option trades specificity for
|
|
421
|
+
sensitivity, though the effect is minor.</p>
|
|
422
|
+
</li></ul>
|
|
423
|
+
|
|
424
|
+
|
|
425
|
+
|
|
426
|
+
|
|
427
|
+
<div class="method-source-code" id="calmd-source">
|
|
428
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 492</span>
|
|
429
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">calmd</span>(<span class="ruby-identifier">opts</span>={}, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
430
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">"calmd"</span>, <span class="ruby-identifier">opts</span>, [<span class="ruby-value">:E</span>, <span class="ruby-value">:e</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:b</span>, <span class="ruby-value">:S</span>, <span class="ruby-value">:r</span>] )<span class="ruby-operator">+</span> <span class="ruby-string">" "</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta</span>
|
|
431
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
432
|
+
<span class="ruby-identifier">type</span> = <span class="ruby-value">:text</span>
|
|
433
|
+
<span class="ruby-identifier">klass</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Alignment</span>
|
|
434
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-identifier">klass</span>, <span class="ruby-identifier">type</span>, <span class="ruby-keyword">true</span>, <span class="ruby-string">"@"</span>,<span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
435
|
+
<span class="ruby-keyword">end</span></pre>
|
|
436
|
+
</div>
|
|
437
|
+
|
|
438
|
+
</div>
|
|
439
|
+
|
|
440
|
+
|
|
441
|
+
|
|
442
|
+
|
|
443
|
+
</div>
|
|
444
|
+
|
|
445
|
+
|
|
446
|
+
<div id="method-i-cat" class="method-detail ">
|
|
447
|
+
|
|
448
|
+
<div class="method-heading">
|
|
449
|
+
<span class="method-name">cat</span><span
|
|
450
|
+
class="method-args">(opts={})</span>
|
|
451
|
+
|
|
452
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
453
|
+
|
|
454
|
+
</div>
|
|
455
|
+
|
|
456
|
+
|
|
457
|
+
<div class="method-description">
|
|
458
|
+
|
|
459
|
+
<p>Concatenate BAMs. The sequence dictionary of each input BAM must be
|
|
460
|
+
identical.</p>
|
|
461
|
+
<ul><li>
|
|
462
|
+
<p>h - header.sam</p>
|
|
463
|
+
</li><li>
|
|
464
|
+
<p>out -[FILE] out file name</p>
|
|
465
|
+
</li><li>
|
|
466
|
+
<p>bams -[FILES] or <a href="Sam.html">Bio::DB::Sam</a> list of input bams, or
|
|
467
|
+
<a href="Sam.html">Bio::DB::Sam</a> objects</p>
|
|
468
|
+
</li></ul>
|
|
469
|
+
|
|
470
|
+
|
|
471
|
+
|
|
472
|
+
|
|
473
|
+
<div class="method-source-code" id="cat-source">
|
|
474
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 383</span>
|
|
475
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">cat</span>(<span class="ruby-identifier">opts</span>={})
|
|
476
|
+
<span class="ruby-identifier">out</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:out</span>]
|
|
477
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:out</span>)
|
|
478
|
+
|
|
479
|
+
<span class="ruby-identifier">bam_list</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:bams</span>].<span class="ruby-identifier">collect</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">b</span><span class="ruby-operator">|</span>
|
|
480
|
+
<span class="ruby-identifier">b</span>.<span class="ruby-identifier">bam</span> <span class="ruby-keyword">rescue</span> <span class="ruby-identifier">b</span>
|
|
481
|
+
<span class="ruby-keyword">end</span>.<span class="ruby-identifier">join</span>(<span class="ruby-string">' '</span>)
|
|
482
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:bams</span>)
|
|
483
|
+
<span class="ruby-identifier">options</span> = <span class="ruby-identifier">commandify</span>(<span class="ruby-identifier">opts</span>, [<span class="ruby-value">:h</span>] )
|
|
484
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} cat #{options} -o #{out} #{bam_list}"</span>
|
|
485
|
+
<span class="ruby-identifier">puts</span> <span class="ruby-identifier">command</span>
|
|
486
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
487
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
488
|
+
|
|
489
|
+
<span class="ruby-keyword">end</span></pre>
|
|
490
|
+
</div>
|
|
491
|
+
|
|
492
|
+
</div>
|
|
493
|
+
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
|
|
497
|
+
</div>
|
|
498
|
+
|
|
499
|
+
|
|
500
|
+
<div id="method-i-chromosome_coverage" class="method-detail ">
|
|
501
|
+
|
|
502
|
+
<div class="method-heading">
|
|
503
|
+
<span class="method-name">chromosome_coverage</span><span
|
|
504
|
+
class="method-args">(chr,start,length)</span>
|
|
505
|
+
|
|
506
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
507
|
+
|
|
508
|
+
</div>
|
|
509
|
+
|
|
510
|
+
|
|
511
|
+
<div class="method-description">
|
|
512
|
+
|
|
513
|
+
<p>returns an array of coverage for each location for which there are mapped
|
|
514
|
+
reads</p>
|
|
515
|
+
<ul><li>
|
|
516
|
+
<p>chr - the reference name</p>
|
|
517
|
+
</li><li>
|
|
518
|
+
<p>start - the start position</p>
|
|
519
|
+
</li><li>
|
|
520
|
+
<p>length - the length of the region queried</p>
|
|
521
|
+
</li></ul>
|
|
522
|
+
|
|
523
|
+
|
|
524
|
+
|
|
525
|
+
|
|
526
|
+
<div class="method-source-code" id="chromosome_coverage-source">
|
|
527
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 102</span>
|
|
528
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chr</span>,<span class="ruby-identifier">start</span>,<span class="ruby-identifier">length</span>)
|
|
529
|
+
<span class="ruby-identifier">result</span> = []
|
|
530
|
+
<span class="ruby-identifier">region</span> = <span class="ruby-node">"#{chr}:#{start}-#{start + length}"</span>
|
|
531
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">mpileup</span>(<span class="ruby-value">:r</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">region</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span>
|
|
532
|
+
<span class="ruby-identifier">result</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">p</span>.<span class="ruby-identifier">coverage</span>
|
|
533
|
+
<span class="ruby-keyword">end</span>
|
|
534
|
+
<span class="ruby-identifier">result</span>
|
|
535
|
+
<span class="ruby-keyword">end</span></pre>
|
|
536
|
+
</div>
|
|
537
|
+
|
|
538
|
+
</div>
|
|
539
|
+
|
|
540
|
+
|
|
541
|
+
|
|
542
|
+
|
|
543
|
+
</div>
|
|
544
|
+
|
|
545
|
+
|
|
546
|
+
<div id="method-i-depth" class="method-detail ">
|
|
547
|
+
|
|
548
|
+
<div class="method-heading">
|
|
549
|
+
<span class="method-name">depth</span><span
|
|
550
|
+
class="method-args">(opts={}) { |split(/\t/)| ... }</span>
|
|
551
|
+
|
|
552
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
553
|
+
|
|
554
|
+
</div>
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
<div class="method-description">
|
|
558
|
+
|
|
559
|
+
<p>returns an array for each position with [sequence_name, position, depth]</p>
|
|
560
|
+
<ul><li>
|
|
561
|
+
<p>b - list of positions or regions in BED format</p>
|
|
562
|
+
</li><li>
|
|
563
|
+
<p>l - [INT] minQLen</p>
|
|
564
|
+
</li><li>
|
|
565
|
+
<p>q - [INT] base quality threshold</p>
|
|
566
|
+
</li><li>
|
|
567
|
+
<p>Q - [INT] mapping quality threshold</p>
|
|
568
|
+
</li><li>
|
|
569
|
+
<p>r - [chr:from-to] region</p>
|
|
570
|
+
</li></ul>
|
|
571
|
+
|
|
572
|
+
|
|
573
|
+
|
|
574
|
+
|
|
575
|
+
<div class="method-source-code" id="depth-source">
|
|
576
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 538</span>
|
|
577
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">depth</span>(<span class="ruby-identifier">opts</span>={})
|
|
578
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">"depth"</span>, <span class="ruby-identifier">opts</span>)
|
|
579
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
580
|
+
<span class="ruby-comment">#puts command</span>
|
|
581
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-constant">String</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
582
|
+
<span class="ruby-keyword">yield</span> <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
|
|
583
|
+
<span class="ruby-keyword">end</span>
|
|
584
|
+
|
|
585
|
+
<span class="ruby-keyword">end</span></pre>
|
|
586
|
+
</div>
|
|
587
|
+
|
|
588
|
+
</div>
|
|
589
|
+
|
|
590
|
+
|
|
591
|
+
|
|
592
|
+
|
|
593
|
+
</div>
|
|
594
|
+
|
|
595
|
+
|
|
596
|
+
<div id="method-i-faidx" class="method-detail ">
|
|
597
|
+
|
|
598
|
+
<div class="method-heading">
|
|
599
|
+
<span class="method-name">faidx</span><span
|
|
600
|
+
class="method-args">(opts={})</span>
|
|
601
|
+
|
|
602
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
603
|
+
|
|
604
|
+
</div>
|
|
605
|
+
|
|
606
|
+
|
|
607
|
+
<div class="method-description">
|
|
608
|
+
|
|
609
|
+
<p>Index reference sequence in the FASTA format or extract subsequence from
|
|
610
|
+
indexed reference sequence. If no region is specified, faidx will index the
|
|
611
|
+
file and create <ref.fasta>.fai on the disk. If regions are
|
|
612
|
+
speficified, the subsequences will be retrieved and printed to stdout in
|
|
613
|
+
the FASTA format. Options - if a subsequence is required</p>
|
|
614
|
+
<ul><li>
|
|
615
|
+
<p>chr - [STRING] the reference name of the subsequence</p>
|
|
616
|
+
</li><li>
|
|
617
|
+
<p>start - [INT] the start position for the subsequence</p>
|
|
618
|
+
</li><li>
|
|
619
|
+
<p>stop - [INT] the stop position for the subsequence</p>
|
|
620
|
+
</li></ul>
|
|
621
|
+
|
|
622
|
+
|
|
623
|
+
|
|
624
|
+
|
|
625
|
+
<div class="method-source-code" id="faidx-source">
|
|
626
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 275</span>
|
|
627
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">faidx</span>(<span class="ruby-identifier">opts</span>={})
|
|
628
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">has_key?</span>(<span class="ruby-value">:chr</span>) <span class="ruby-keyword">and</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">has_key?</span>(<span class="ruby-value">:start</span>) <span class="ruby-keyword">and</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">has_key?</span>(<span class="ruby-value">:stop</span>)
|
|
629
|
+
<span class="ruby-identifier">opts</span>={<span class="ruby-value">:as_bio</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">false</span>}
|
|
630
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">fetch_reference</span>(<span class="ruby-value">:chr</span>,<span class="ruby-value">:start</span>,<span class="ruby-value">:stop</span>,<span class="ruby-identifier">opts</span>)
|
|
631
|
+
<span class="ruby-keyword">else</span>
|
|
632
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} faidx #{@fasta}"</span>
|
|
633
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
634
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
635
|
+
<span class="ruby-keyword">end</span>
|
|
636
|
+
<span class="ruby-keyword">end</span></pre>
|
|
637
|
+
</div>
|
|
638
|
+
|
|
639
|
+
</div>
|
|
640
|
+
|
|
641
|
+
|
|
642
|
+
|
|
643
|
+
|
|
644
|
+
</div>
|
|
645
|
+
|
|
646
|
+
|
|
647
|
+
<div id="method-i-fetch" class="method-detail ">
|
|
648
|
+
|
|
649
|
+
<div class="method-heading">
|
|
650
|
+
<span class="method-name">fetch</span><span
|
|
651
|
+
class="method-args">(chr, start,stop, &block)</span>
|
|
652
|
+
|
|
653
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
654
|
+
|
|
655
|
+
</div>
|
|
656
|
+
|
|
657
|
+
|
|
658
|
+
<div class="method-description">
|
|
659
|
+
|
|
660
|
+
<p>fetches a subsequence and calls code block</p>
|
|
661
|
+
<ul><li>
|
|
662
|
+
<p>chr - the reference name for the subsequence</p>
|
|
663
|
+
</li><li>
|
|
664
|
+
<p>start - the start position for the subsequence</p>
|
|
665
|
+
</li><li>
|
|
666
|
+
<p>stop - the stop position for the subsequence</p>
|
|
667
|
+
</li><li>
|
|
668
|
+
<p>&block - the the block of code to execute</p>
|
|
669
|
+
</li></ul>
|
|
670
|
+
|
|
671
|
+
|
|
672
|
+
|
|
673
|
+
|
|
674
|
+
<div class="method-source-code" id="fetch-source">
|
|
675
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 87</span>
|
|
676
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch</span>(<span class="ruby-identifier">chr</span>, <span class="ruby-identifier">start</span>,<span class="ruby-identifier">stop</span>, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
677
|
+
<span class="ruby-identifier">view</span>(
|
|
678
|
+
<span class="ruby-value">:chr</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">chr</span>,
|
|
679
|
+
<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span>,
|
|
680
|
+
<span class="ruby-value">:stop</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">stop</span>,
|
|
681
|
+
<span class="ruby-operator">&</span><span class="ruby-identifier">block</span>
|
|
682
|
+
)
|
|
683
|
+
<span class="ruby-keyword">end</span></pre>
|
|
684
|
+
</div>
|
|
685
|
+
|
|
686
|
+
</div>
|
|
687
|
+
|
|
688
|
+
|
|
689
|
+
<div class="aliases">
|
|
690
|
+
Also aliased as: <a href="Sam.html#method-i-fetch_with_function">fetch_with_function</a>
|
|
691
|
+
</div>
|
|
692
|
+
|
|
693
|
+
|
|
694
|
+
|
|
695
|
+
</div>
|
|
696
|
+
|
|
697
|
+
|
|
698
|
+
<div id="method-i-fetch_reference" class="method-detail ">
|
|
699
|
+
|
|
700
|
+
<div class="method-heading">
|
|
701
|
+
<span class="method-name">fetch_reference</span><span
|
|
702
|
+
class="method-args">(chr,start,stop, opts={:as_bio => false})</span>
|
|
703
|
+
|
|
704
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
705
|
+
|
|
706
|
+
</div>
|
|
707
|
+
|
|
708
|
+
|
|
709
|
+
<div class="method-description">
|
|
710
|
+
|
|
711
|
+
<p>fetches a subsequence from a reference genome and option returns it as a
|
|
712
|
+
Bio::Sequence::NA object</p>
|
|
713
|
+
<ul><li>
|
|
714
|
+
<p>chr - [STRING] the reference name for the subsequence</p>
|
|
715
|
+
</li><li>
|
|
716
|
+
<p>start - [INT] the start position for the subsequence</p>
|
|
717
|
+
</li><li>
|
|
718
|
+
<p>stop - [INT] the stop position for the subsequence</p>
|
|
719
|
+
</li><li>
|
|
720
|
+
<p>as_bio - boolean stating if the returned object should be a
|
|
721
|
+
Bio::Sequence::NA object</p>
|
|
722
|
+
</li></ul>
|
|
723
|
+
|
|
724
|
+
|
|
725
|
+
|
|
726
|
+
|
|
727
|
+
<div class="method-source-code" id="fetch_reference-source">
|
|
728
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 258</span>
|
|
729
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch_reference</span>(<span class="ruby-identifier">chr</span>,<span class="ruby-identifier">start</span>,<span class="ruby-identifier">stop</span>, <span class="ruby-identifier">opts</span>={<span class="ruby-value">:as_bio</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">false</span>})
|
|
730
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} faidx #{@fasta} #{chr}:#{start}-#{stop}"</span>
|
|
731
|
+
<span class="ruby-comment">#puts command</span>
|
|
732
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
733
|
+
<span class="ruby-identifier">seq</span> = <span class="ruby-string">""</span>
|
|
734
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-constant">String</span>, <span class="ruby-value">:text</span> ) {<span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span> <span class="ruby-identifier">seq</span> = <span class="ruby-identifier">seq</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">line</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">=~</span> <span class="ruby-regexp">/^>/</span>}
|
|
735
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:as_bio</span>]
|
|
736
|
+
<span class="ruby-identifier">seq</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Sequence</span><span class="ruby-operator">::</span><span class="ruby-constant">NA</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">seq</span>).<span class="ruby-identifier">to_fasta</span>(<span class="ruby-node">"#{chr}:#{start}-#{stop}"</span>)
|
|
737
|
+
<span class="ruby-keyword">end</span>
|
|
738
|
+
<span class="ruby-identifier">seq</span>
|
|
739
|
+
<span class="ruby-keyword">end</span></pre>
|
|
740
|
+
</div>
|
|
741
|
+
|
|
742
|
+
</div>
|
|
743
|
+
|
|
744
|
+
|
|
745
|
+
|
|
746
|
+
|
|
747
|
+
</div>
|
|
748
|
+
|
|
749
|
+
|
|
750
|
+
<div id="method-i-fetch_with_function" class="method-detail method-alias">
|
|
751
|
+
|
|
752
|
+
<div class="method-heading">
|
|
753
|
+
<span class="method-name">fetch_with_function</span><span
|
|
754
|
+
class="method-args">(chr, start,stop, &block)</span>
|
|
755
|
+
|
|
756
|
+
</div>
|
|
757
|
+
|
|
758
|
+
|
|
759
|
+
<div class="method-description">
|
|
760
|
+
|
|
761
|
+
|
|
762
|
+
|
|
763
|
+
|
|
764
|
+
|
|
765
|
+
|
|
766
|
+
</div>
|
|
767
|
+
|
|
768
|
+
|
|
769
|
+
|
|
770
|
+
|
|
771
|
+
<div class="aliases">
|
|
772
|
+
Alias for: <a href="Sam.html#method-i-fetch">fetch</a>
|
|
773
|
+
</div>
|
|
774
|
+
|
|
775
|
+
</div>
|
|
776
|
+
|
|
777
|
+
|
|
778
|
+
<div id="method-i-fix_mates" class="method-detail ">
|
|
779
|
+
|
|
780
|
+
<div class="method-heading">
|
|
781
|
+
<span class="method-name">fix_mates</span><span
|
|
782
|
+
class="method-args">(opts={})</span>
|
|
783
|
+
|
|
784
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
785
|
+
|
|
786
|
+
</div>
|
|
787
|
+
|
|
788
|
+
|
|
789
|
+
<div class="method-description">
|
|
790
|
+
|
|
791
|
+
<p>Fill in mate coordinates, ISIZE and mate related flags from a name-sorted
|
|
792
|
+
alignment</p>
|
|
793
|
+
<ul><li>
|
|
794
|
+
<p>out_bam name of outfile</p>
|
|
795
|
+
</li><li>
|
|
796
|
+
<p>r - remove unmapped reads and secondary alignments</p>
|
|
797
|
+
</li></ul>
|
|
798
|
+
|
|
799
|
+
|
|
800
|
+
|
|
801
|
+
|
|
802
|
+
<div class="method-source-code" id="fix_mates-source">
|
|
803
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 298</span>
|
|
804
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">fix_mates</span>(<span class="ruby-identifier">opts</span>={})
|
|
805
|
+
<span class="ruby-comment">#opts.merge!({:out_index=>nil})</span>
|
|
806
|
+
<span class="ruby-identifier">remove_reads</span> = <span class="ruby-string">""</span>
|
|
807
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:r</span>]
|
|
808
|
+
<span class="ruby-identifier">remove_reads</span> = <span class="ruby-string">"-r"</span>
|
|
809
|
+
<span class="ruby-keyword">end</span>
|
|
810
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} fixmate #{remove_reads} #{@bam} #{opts[:out_bam]}"</span>
|
|
811
|
+
<span class="ruby-comment">#puts command</span>
|
|
812
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
813
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
814
|
+
<span class="ruby-keyword">end</span></pre>
|
|
815
|
+
</div>
|
|
816
|
+
|
|
817
|
+
</div>
|
|
818
|
+
|
|
819
|
+
|
|
820
|
+
<div class="aliases">
|
|
821
|
+
Also aliased as: <a href="Sam.html#method-i-fixmate">fixmate</a>
|
|
822
|
+
</div>
|
|
823
|
+
|
|
824
|
+
|
|
825
|
+
|
|
826
|
+
</div>
|
|
827
|
+
|
|
828
|
+
|
|
829
|
+
<div id="method-i-fixmate" class="method-detail method-alias">
|
|
830
|
+
|
|
831
|
+
<div class="method-heading">
|
|
832
|
+
<span class="method-name">fixmate</span><span
|
|
833
|
+
class="method-args">(opts={})</span>
|
|
834
|
+
|
|
835
|
+
</div>
|
|
836
|
+
|
|
837
|
+
|
|
838
|
+
<div class="method-description">
|
|
839
|
+
|
|
840
|
+
|
|
841
|
+
|
|
842
|
+
|
|
843
|
+
|
|
844
|
+
|
|
845
|
+
</div>
|
|
846
|
+
|
|
847
|
+
|
|
848
|
+
|
|
849
|
+
|
|
850
|
+
<div class="aliases">
|
|
851
|
+
Alias for: <a href="Sam.html#method-i-fix_mates">fix_mates</a>
|
|
852
|
+
</div>
|
|
853
|
+
|
|
854
|
+
</div>
|
|
855
|
+
|
|
856
|
+
|
|
857
|
+
<div id="method-i-flag_stats" class="method-detail ">
|
|
858
|
+
|
|
859
|
+
<div class="method-heading">
|
|
860
|
+
<span class="method-name">flag_stats</span><span
|
|
861
|
+
class="method-args">(opts={})</span>
|
|
862
|
+
|
|
863
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
864
|
+
|
|
865
|
+
</div>
|
|
866
|
+
|
|
867
|
+
|
|
868
|
+
<div class="method-description">
|
|
869
|
+
|
|
870
|
+
<p>generate simple stats with regard to the number and pairing of reads mapped
|
|
871
|
+
to a reference</p>
|
|
872
|
+
|
|
873
|
+
|
|
874
|
+
|
|
875
|
+
|
|
876
|
+
<div class="method-source-code" id="flag_stats-source">
|
|
877
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 313</span>
|
|
878
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">flag_stats</span>(<span class="ruby-identifier">opts</span>={})
|
|
879
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">"flagstat"</span>, <span class="ruby-identifier">opts</span>, [])
|
|
880
|
+
<span class="ruby-comment">#puts command</span>
|
|
881
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
882
|
+
<span class="ruby-identifier">strings</span> = []
|
|
883
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>,<span class="ruby-constant">String</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span> <span class="ruby-identifier">strings</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>}
|
|
884
|
+
<span class="ruby-identifier">strings</span>
|
|
885
|
+
<span class="ruby-keyword">end</span></pre>
|
|
886
|
+
</div>
|
|
887
|
+
|
|
888
|
+
</div>
|
|
889
|
+
|
|
890
|
+
|
|
891
|
+
<div class="aliases">
|
|
892
|
+
Also aliased as: <a href="Sam.html#method-i-flagstat">flagstat</a>
|
|
893
|
+
</div>
|
|
894
|
+
|
|
895
|
+
|
|
896
|
+
|
|
897
|
+
</div>
|
|
898
|
+
|
|
899
|
+
|
|
900
|
+
<div id="method-i-flagstat" class="method-detail method-alias">
|
|
901
|
+
|
|
902
|
+
<div class="method-heading">
|
|
903
|
+
<span class="method-name">flagstat</span><span
|
|
904
|
+
class="method-args">(opts={})</span>
|
|
905
|
+
|
|
906
|
+
</div>
|
|
907
|
+
|
|
908
|
+
|
|
909
|
+
<div class="method-description">
|
|
910
|
+
|
|
911
|
+
|
|
912
|
+
|
|
913
|
+
|
|
914
|
+
|
|
915
|
+
|
|
916
|
+
</div>
|
|
917
|
+
|
|
918
|
+
|
|
919
|
+
|
|
920
|
+
|
|
921
|
+
<div class="aliases">
|
|
922
|
+
Alias for: <a href="Sam.html#method-i-flag_stats">flag_stats</a>
|
|
923
|
+
</div>
|
|
924
|
+
|
|
925
|
+
</div>
|
|
926
|
+
|
|
927
|
+
|
|
928
|
+
<div id="method-i-idxstats" class="method-detail method-alias">
|
|
929
|
+
|
|
930
|
+
<div class="method-heading">
|
|
931
|
+
<span class="method-name">idxstats</span><span
|
|
932
|
+
class="method-args">()</span>
|
|
933
|
+
|
|
934
|
+
</div>
|
|
935
|
+
|
|
936
|
+
|
|
937
|
+
<div class="method-description">
|
|
938
|
+
|
|
939
|
+
|
|
940
|
+
|
|
941
|
+
|
|
942
|
+
|
|
943
|
+
|
|
944
|
+
</div>
|
|
945
|
+
|
|
946
|
+
|
|
947
|
+
|
|
948
|
+
|
|
949
|
+
<div class="aliases">
|
|
950
|
+
Alias for: <a href="Sam.html#method-i-index_stats">index_stats</a>
|
|
951
|
+
</div>
|
|
952
|
+
|
|
953
|
+
</div>
|
|
954
|
+
|
|
955
|
+
|
|
956
|
+
<div id="method-i-index" class="method-detail ">
|
|
957
|
+
|
|
958
|
+
<div class="method-heading">
|
|
959
|
+
<span class="method-name">index</span><span
|
|
960
|
+
class="method-args">(opts={})</span>
|
|
961
|
+
|
|
962
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
963
|
+
|
|
964
|
+
</div>
|
|
965
|
+
|
|
966
|
+
|
|
967
|
+
<div class="method-description">
|
|
968
|
+
|
|
969
|
+
<p>Index sorted alignment for fast random access. Index file
|
|
970
|
+
<aln.bam>.bai will be created of no out_index is provided.</p>
|
|
971
|
+
<ul><li>
|
|
972
|
+
<p>out_index - [STRING] name of index</p>
|
|
973
|
+
</li></ul>
|
|
974
|
+
|
|
975
|
+
|
|
976
|
+
|
|
977
|
+
|
|
978
|
+
<div class="method-source-code" id="index-source">
|
|
979
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 288</span>
|
|
980
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">index</span>(<span class="ruby-identifier">opts</span>={})
|
|
981
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} index #{@bam} #{opts[:out_index]}"</span>
|
|
982
|
+
<span class="ruby-comment">#puts command</span>
|
|
983
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
984
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
985
|
+
<span class="ruby-keyword">end</span></pre>
|
|
986
|
+
</div>
|
|
987
|
+
|
|
988
|
+
</div>
|
|
989
|
+
|
|
990
|
+
|
|
991
|
+
|
|
992
|
+
|
|
993
|
+
</div>
|
|
994
|
+
|
|
995
|
+
|
|
996
|
+
<div id="method-i-index_stats" class="method-detail ">
|
|
997
|
+
|
|
998
|
+
<div class="method-heading">
|
|
999
|
+
<span class="method-name">index_stats</span><span
|
|
1000
|
+
class="method-args">()</span>
|
|
1001
|
+
|
|
1002
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1003
|
+
|
|
1004
|
+
</div>
|
|
1005
|
+
|
|
1006
|
+
|
|
1007
|
+
<div class="method-description">
|
|
1008
|
+
|
|
1009
|
+
<p>Retrieve and print stats in the index file. The output is TAB delimited
|
|
1010
|
+
with each line consisting of reference sequence name, sequence length,
|
|
1011
|
+
number of mapped reads and number unmapped reads.</p>
|
|
1012
|
+
|
|
1013
|
+
|
|
1014
|
+
|
|
1015
|
+
|
|
1016
|
+
<div class="method-source-code" id="index_stats-source">
|
|
1017
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 325</span>
|
|
1018
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">index_stats</span>
|
|
1019
|
+
<span class="ruby-identifier">stats</span> = {}
|
|
1020
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-node">"idxstats #{@bam}"</span>, {}, [])
|
|
1021
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1022
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-constant">String</span>, <span class="ruby-value">:text</span>, <span class="ruby-keyword">true</span>, <span class="ruby-node">"#"</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">line</span><span class="ruby-operator">|</span>
|
|
1023
|
+
<span class="ruby-identifier">info</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
|
|
1024
|
+
<span class="ruby-identifier">stats</span>[ <span class="ruby-identifier">info</span>[<span class="ruby-value">0</span>] ] = {<span class="ruby-value">:length</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:mapped_reads</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">2</span>].<span class="ruby-identifier">to_i</span>, <span class="ruby-value">:unmapped_reads</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">info</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span> }
|
|
1025
|
+
<span class="ruby-keyword">end</span>
|
|
1026
|
+
<span class="ruby-identifier">stats</span>
|
|
1027
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1028
|
+
</div>
|
|
1029
|
+
|
|
1030
|
+
</div>
|
|
1031
|
+
|
|
1032
|
+
|
|
1033
|
+
<div class="aliases">
|
|
1034
|
+
Also aliased as: <a href="Sam.html#method-i-idxstats">idxstats</a>
|
|
1035
|
+
</div>
|
|
1036
|
+
|
|
1037
|
+
|
|
1038
|
+
|
|
1039
|
+
</div>
|
|
1040
|
+
|
|
1041
|
+
|
|
1042
|
+
<div id="method-i-merge" class="method-detail ">
|
|
1043
|
+
|
|
1044
|
+
<div class="method-heading">
|
|
1045
|
+
<span class="method-name">merge</span><span
|
|
1046
|
+
class="method-args">(opts={})</span>
|
|
1047
|
+
|
|
1048
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1049
|
+
|
|
1050
|
+
</div>
|
|
1051
|
+
|
|
1052
|
+
|
|
1053
|
+
<div class="method-description">
|
|
1054
|
+
|
|
1055
|
+
<p>Merge multiple sorted alignments</p>
|
|
1056
|
+
<ul><li>
|
|
1057
|
+
<p>n - sort by read names</p>
|
|
1058
|
+
</li><li>
|
|
1059
|
+
<p>r - attach RG tag (inferred from file names)</p>
|
|
1060
|
+
</li><li>
|
|
1061
|
+
<p>u - uncompressed BAM output</p>
|
|
1062
|
+
</li><li>
|
|
1063
|
+
<p>f - overwrite the output BAM if exist</p>
|
|
1064
|
+
</li><li>
|
|
1065
|
+
<p>one - compress level 1</p>
|
|
1066
|
+
</li><li>
|
|
1067
|
+
<p>l - [INT] compression level, from 0 to 9 [-1]</p>
|
|
1068
|
+
</li><li>
|
|
1069
|
+
<p>at - [INT] number of BAM compression threads [0]</p>
|
|
1070
|
+
</li><li>
|
|
1071
|
+
<p>R - [STRING] merge file in the specified region STR [all]</p>
|
|
1072
|
+
</li><li>
|
|
1073
|
+
<p>h - [FILE] copy the header in FILE to <out.bam> [in1.bam]</p>
|
|
1074
|
+
</li><li>
|
|
1075
|
+
<p>out - [FILE] out file name</p>
|
|
1076
|
+
</li><li>
|
|
1077
|
+
<p>bams - [FILES] or <a href="Sam.html">Bio::DB::Sam</a> list of input bams,
|
|
1078
|
+
or <a href="Sam.html">Bio::DB::Sam</a> objects</p>
|
|
1079
|
+
</li></ul>
|
|
1080
|
+
|
|
1081
|
+
|
|
1082
|
+
|
|
1083
|
+
|
|
1084
|
+
<div class="method-source-code" id="merge-source">
|
|
1085
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 350</span>
|
|
1086
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">merge</span>(<span class="ruby-identifier">opts</span>={})
|
|
1087
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:one</span>]
|
|
1088
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'1'</span>] = <span class="ruby-keyword">nil</span>
|
|
1089
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:one</span>)
|
|
1090
|
+
<span class="ruby-keyword">end</span>
|
|
1091
|
+
|
|
1092
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:at</span>]
|
|
1093
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'@'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:at</span>]
|
|
1094
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:at</span>)
|
|
1095
|
+
<span class="ruby-keyword">end</span>
|
|
1096
|
+
|
|
1097
|
+
<span class="ruby-identifier">out</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:out</span>]
|
|
1098
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:out</span>)
|
|
1099
|
+
|
|
1100
|
+
<span class="ruby-identifier">bam_list</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:bams</span>].<span class="ruby-identifier">collect</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">b</span><span class="ruby-operator">|</span>
|
|
1101
|
+
<span class="ruby-identifier">b</span>.<span class="ruby-identifier">bam</span> <span class="ruby-keyword">rescue</span> <span class="ruby-identifier">b</span>
|
|
1102
|
+
<span class="ruby-keyword">end</span>.<span class="ruby-identifier">join</span>(<span class="ruby-string">' '</span>)
|
|
1103
|
+
|
|
1104
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:bams</span>)
|
|
1105
|
+
<span class="ruby-identifier">options</span> = <span class="ruby-identifier">commandify</span>(<span class="ruby-identifier">opts</span>, [<span class="ruby-value">:n</span>, <span class="ruby-value">:r</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:f</span>, <span class="ruby-string">'1'</span>] )
|
|
1106
|
+
<span class="ruby-comment">#command = "#{form_opt_string(@samtools, "merge", opts, [:n, :r, :u, :f, '1'] )} #{out} #{bam_list}"</span>
|
|
1107
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} merge #{options} #{out} #{bam_list}"</span>
|
|
1108
|
+
|
|
1109
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1110
|
+
<span class="ruby-identifier">puts</span> <span class="ruby-identifier">command</span>
|
|
1111
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1112
|
+
|
|
1113
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1114
|
+
</div>
|
|
1115
|
+
|
|
1116
|
+
</div>
|
|
1117
|
+
|
|
1118
|
+
|
|
1119
|
+
|
|
1120
|
+
|
|
1121
|
+
</div>
|
|
1122
|
+
|
|
1123
|
+
|
|
1124
|
+
<div id="method-i-mpileup" class="method-detail ">
|
|
1125
|
+
|
|
1126
|
+
<div class="method-heading">
|
|
1127
|
+
<span class="method-name">mpileup</span><span
|
|
1128
|
+
class="method-args">(opts={}, &block)</span>
|
|
1129
|
+
|
|
1130
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1131
|
+
|
|
1132
|
+
</div>
|
|
1133
|
+
|
|
1134
|
+
|
|
1135
|
+
<div class="method-description">
|
|
1136
|
+
|
|
1137
|
+
<p>returns a <a href="Pileup.html">Bio::DB::Pileup</a> or Bio::DB::VCF object</p>
|
|
1138
|
+
<ul><li>
|
|
1139
|
+
<p>region - Only generate pileup in region [chrom:start-stop]</p>
|
|
1140
|
+
</li><li>
|
|
1141
|
+
<p>illumina_quals - Assume the quality is in the Illumina 1.3+ encoding</p>
|
|
1142
|
+
</li><li>
|
|
1143
|
+
<p>count_anomalous - Do not skip anomalous read pairs in variant calling</p>
|
|
1144
|
+
</li><li>
|
|
1145
|
+
<p>no_baq - Disable probabilistic realignment for the computation of base
|
|
1146
|
+
alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base
|
|
1147
|
+
being misaligned. Applying this option greatly helps to reduce false SNPs
|
|
1148
|
+
caused by misalignments.</p>
|
|
1149
|
+
</li><li>
|
|
1150
|
+
<p>adjust_mapq - [INT] Coefficient for downgrading mapping quality for reads
|
|
1151
|
+
containing excessive mismatches. Given a read with a phred-scaled
|
|
1152
|
+
probability q of being generated from the mapped position, the new mapping
|
|
1153
|
+
quality is about sqrt((INT-q)/INT)*INT. A zero value disables this
|
|
1154
|
+
functionality; if enabled, the recommended value for BWA is 50. [0]</p>
|
|
1155
|
+
</li><li>
|
|
1156
|
+
<p>max_per_bam_depth - [INT] At a position, read maximally INT reads per input
|
|
1157
|
+
BAM. [250]</p>
|
|
1158
|
+
</li><li>
|
|
1159
|
+
<p>extended_baq - Extended BAQ computation. This option helps sensitivity
|
|
1160
|
+
especially for MNPs, but may hurt specificity a little bit.</p>
|
|
1161
|
+
</li><li>
|
|
1162
|
+
<p>exclude_reads_file - [FILE] exclude read groups listed in FILE [null]</p>
|
|
1163
|
+
</li><li>
|
|
1164
|
+
<p>list_of_positions - [FILE] BED or position list file containing a list of
|
|
1165
|
+
regions or sites where pileup or BCF should be generated [null]</p>
|
|
1166
|
+
</li><li>
|
|
1167
|
+
<p>mapping_quality_cap - [INT] cap mapping quality at INT [60]</p>
|
|
1168
|
+
</li><li>
|
|
1169
|
+
<p>ignore_rg - ignore read group tags</p>
|
|
1170
|
+
</li><li>
|
|
1171
|
+
<p>min_mapping_quality - [INT] skip alignments with mapQ smaller than INT [0]</p>
|
|
1172
|
+
</li><li>
|
|
1173
|
+
<p>min_base_quality - [INT] skip bases with baseQ/BAQ smaller than INT [13]</p>
|
|
1174
|
+
</li><li>
|
|
1175
|
+
<p>##following options are for the -g -u option</p>
|
|
1176
|
+
</li><li>
|
|
1177
|
+
<p>genotype_calling - generate BCF output (genotype likelihoods)</p>
|
|
1178
|
+
</li><li>
|
|
1179
|
+
<p>uncompressed_bcf - generate uncompress BCF output</p>
|
|
1180
|
+
</li><li>
|
|
1181
|
+
<p>extension_sequencing_probability - [INT] Phred-scaled gap extension seq
|
|
1182
|
+
error probability [20]</p>
|
|
1183
|
+
</li><li>
|
|
1184
|
+
<p>homopolymer_error_coefficient - [INT] coefficient for homopolymer errors
|
|
1185
|
+
[100]</p>
|
|
1186
|
+
</li><li>
|
|
1187
|
+
<p>no_indels - do not perform indel calling</p>
|
|
1188
|
+
</li><li>
|
|
1189
|
+
<p>skip_indel_over_average_depth - [INT] max per-sample depth for INDEL
|
|
1190
|
+
calling [250]</p>
|
|
1191
|
+
</li><li>
|
|
1192
|
+
<p>gap_open_sequencing_error_probability - [INT] Phred-scaled gap open
|
|
1193
|
+
sequencing error probability [40]</p>
|
|
1194
|
+
</li><li>
|
|
1195
|
+
<p>platforms - [STRING] comma separated list of platforms for indels [all]</p>
|
|
1196
|
+
</li></ul>
|
|
1197
|
+
|
|
1198
|
+
|
|
1199
|
+
|
|
1200
|
+
|
|
1201
|
+
<div class="method-source-code" id="mpileup-source">
|
|
1202
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 195</span>
|
|
1203
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup</span>(<span class="ruby-identifier">opts</span>={}, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
1204
|
+
<span class="ruby-comment">#long option form to short samtools form..</span>
|
|
1205
|
+
<span class="ruby-identifier">long_opts</span> = {
|
|
1206
|
+
<span class="ruby-value">:region</span> =<span class="ruby-operator">></span> <span class="ruby-value">:r</span>,
|
|
1207
|
+
<span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">></span> <span class="ruby-value">:six</span>,
|
|
1208
|
+
<span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">></span> <span class="ruby-value">:A</span>,
|
|
1209
|
+
<span class="ruby-value">:no_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:B</span>,
|
|
1210
|
+
<span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:C</span>,
|
|
1211
|
+
<span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">></span> <span class="ruby-value">:d</span>,
|
|
1212
|
+
<span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">></span> <span class="ruby-value">:E</span>,
|
|
1213
|
+
<span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">></span> <span class="ruby-value">:G</span>,
|
|
1214
|
+
<span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">></span> <span class="ruby-value">:l</span>,
|
|
1215
|
+
<span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">></span> <span class="ruby-value">:M</span>,
|
|
1216
|
+
<span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">></span> <span class="ruby-value">:R</span>,
|
|
1217
|
+
<span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:q</span>,
|
|
1218
|
+
<span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">></span> <span class="ruby-value">:Q</span>,
|
|
1219
|
+
<span class="ruby-comment">###following options are for the -g -u option</span>
|
|
1220
|
+
<span class="ruby-value">:genotype_calling</span> =<span class="ruby-operator">></span> <span class="ruby-value">:g</span>,
|
|
1221
|
+
<span class="ruby-value">:uncompressed_bcf</span> =<span class="ruby-operator">></span> <span class="ruby-value">:u</span>,
|
|
1222
|
+
<span class="ruby-value">:extension_sequencing_probability</span> =<span class="ruby-operator">></span> <span class="ruby-value">:e</span>,
|
|
1223
|
+
<span class="ruby-value">:homopolymer_error_coefficient</span> =<span class="ruby-operator">></span> <span class="ruby-value">:h</span>,
|
|
1224
|
+
<span class="ruby-value">:no_indels</span> =<span class="ruby-operator">></span> <span class="ruby-value">:I</span>,
|
|
1225
|
+
<span class="ruby-value">:skip_indel_over_average_depth</span> =<span class="ruby-operator">></span> <span class="ruby-value">:L</span>,
|
|
1226
|
+
<span class="ruby-value">:gap_open_sequencing_error_probability</span> =<span class="ruby-operator">></span> <span class="ruby-value">:o</span>,
|
|
1227
|
+
<span class="ruby-value">:platforms</span> =<span class="ruby-operator">></span> <span class="ruby-value">:P</span>
|
|
1228
|
+
}
|
|
1229
|
+
|
|
1230
|
+
<span class="ruby-comment">##convert any long_opts to short opts </span>
|
|
1231
|
+
<span class="ruby-identifier">temp_opts</span> = <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">dup</span>
|
|
1232
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each_pair</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
|
|
1233
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
|
|
1234
|
+
<span class="ruby-identifier">temp_opts</span>[<span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]] = <span class="ruby-identifier">v</span>
|
|
1235
|
+
<span class="ruby-identifier">temp_opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
|
|
1236
|
+
<span class="ruby-keyword">end</span>
|
|
1237
|
+
<span class="ruby-keyword">end</span>
|
|
1238
|
+
<span class="ruby-identifier">opts</span> = <span class="ruby-identifier">temp_opts</span>
|
|
1239
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>] = <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:g</span>] <span class="ruby-comment">#so that we always get uncompressed output</span>
|
|
1240
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:g</span>)
|
|
1241
|
+
|
|
1242
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-value">:f</span>] = <span class="ruby-ivar">@fasta</span>
|
|
1243
|
+
|
|
1244
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:six</span>]
|
|
1245
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">"6"</span>] = <span class="ruby-keyword">nil</span>
|
|
1246
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:six</span>)
|
|
1247
|
+
<span class="ruby-keyword">end</span>
|
|
1248
|
+
|
|
1249
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">"mpileup"</span>, <span class="ruby-identifier">opts</span>, [<span class="ruby-value">:R</span>, <span class="ruby-value">:B</span>, <span class="ruby-value">:E</span>, <span class="ruby-string">"6"</span>, <span class="ruby-value">:A</span>, <span class="ruby-value">:g</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:I</span>] )
|
|
1250
|
+
|
|
1251
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
|
|
1252
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">command</span> <span class="ruby-operator">+</span> <span class="ruby-node">" | #{@bcftools} view -cg -"</span>
|
|
1253
|
+
<span class="ruby-keyword">end</span>
|
|
1254
|
+
|
|
1255
|
+
<span class="ruby-identifier">klass</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>] <span class="ruby-operator">?</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Vcf</span> <span class="ruby-operator">:</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Pileup</span>
|
|
1256
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1257
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-identifier">klass</span>, <span class="ruby-value">:text</span>, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
1258
|
+
|
|
1259
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1260
|
+
</div>
|
|
1261
|
+
|
|
1262
|
+
</div>
|
|
1263
|
+
|
|
1264
|
+
|
|
1265
|
+
|
|
1266
|
+
|
|
1267
|
+
</div>
|
|
1268
|
+
|
|
1269
|
+
|
|
1270
|
+
<div id="method-i-open" class="method-detail ">
|
|
1271
|
+
|
|
1272
|
+
<div class="method-heading">
|
|
1273
|
+
<span class="method-name">open</span><span
|
|
1274
|
+
class="method-args">()</span>
|
|
1275
|
+
|
|
1276
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1277
|
+
|
|
1278
|
+
</div>
|
|
1279
|
+
|
|
1280
|
+
|
|
1281
|
+
<div class="method-description">
|
|
1282
|
+
|
|
1283
|
+
<p>backward compatibility method, returns true if file exists otherwise,
|
|
1284
|
+
complains and quits.</p>
|
|
1285
|
+
|
|
1286
|
+
|
|
1287
|
+
|
|
1288
|
+
|
|
1289
|
+
<div class="method-source-code" id="open-source">
|
|
1290
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 29</span>
|
|
1291
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">open</span>
|
|
1292
|
+
<span class="ruby-identifier">files_ok?</span>
|
|
1293
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1294
|
+
</div>
|
|
1295
|
+
|
|
1296
|
+
</div>
|
|
1297
|
+
|
|
1298
|
+
|
|
1299
|
+
|
|
1300
|
+
|
|
1301
|
+
</div>
|
|
1302
|
+
|
|
1303
|
+
|
|
1304
|
+
<div id="method-i-phase" class="method-detail ">
|
|
1305
|
+
|
|
1306
|
+
<div class="method-heading">
|
|
1307
|
+
<span class="method-name">phase</span><span
|
|
1308
|
+
class="method-args">(opts={})</span>
|
|
1309
|
+
|
|
1310
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1311
|
+
|
|
1312
|
+
</div>
|
|
1313
|
+
|
|
1314
|
+
|
|
1315
|
+
<div class="method-description">
|
|
1316
|
+
|
|
1317
|
+
<p>Call and phase heterozygous SNPs</p>
|
|
1318
|
+
<ul><li>
|
|
1319
|
+
<p>A - Drop reads with ambiguous phase.</p>
|
|
1320
|
+
</li><li>
|
|
1321
|
+
<p>b - [STR] Prefix of BAM output. When this option is in use, phase-0 reads
|
|
1322
|
+
will be saved in file STR.0.bam and phase-1 reads in STR.1.bam. Phase
|
|
1323
|
+
unknown reads will be randomly allocated to one of the two files. Chimeric
|
|
1324
|
+
reads with switch errors will be saved in STR.chimeric.bam. [null]</p>
|
|
1325
|
+
</li><li>
|
|
1326
|
+
<p>F - Do not attempt to fix chimeric reads.</p>
|
|
1327
|
+
</li><li>
|
|
1328
|
+
<p>k - [INT] Maximum length for local phasing. [13]</p>
|
|
1329
|
+
</li><li>
|
|
1330
|
+
<p>q - [INT] Minimum Phred-scaled LOD to call a heterozygote. [40]</p>
|
|
1331
|
+
</li><li>
|
|
1332
|
+
<p>Q - [INT] Minimum base quality to be used in het calling. [13]</p>
|
|
1333
|
+
</li></ul>
|
|
1334
|
+
|
|
1335
|
+
|
|
1336
|
+
|
|
1337
|
+
|
|
1338
|
+
<div class="method-source-code" id="phase-source">
|
|
1339
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 525</span>
|
|
1340
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">phase</span>(<span class="ruby-identifier">opts</span>={})
|
|
1341
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{form_opt_string(@samtools, "phase", opts, [:A, :F] )}"</span>
|
|
1342
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1343
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1344
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1345
|
+
</div>
|
|
1346
|
+
|
|
1347
|
+
</div>
|
|
1348
|
+
|
|
1349
|
+
|
|
1350
|
+
|
|
1351
|
+
|
|
1352
|
+
</div>
|
|
1353
|
+
|
|
1354
|
+
|
|
1355
|
+
<div id="method-i-plot_chromosome_coverage" class="method-detail ">
|
|
1356
|
+
|
|
1357
|
+
<div class="method-heading">
|
|
1358
|
+
<span class="method-name">plot_chromosome_coverage</span><span
|
|
1359
|
+
class="method-args">(chr,start,length, opts={})</span>
|
|
1360
|
+
|
|
1361
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1362
|
+
|
|
1363
|
+
</div>
|
|
1364
|
+
|
|
1365
|
+
|
|
1366
|
+
<div class="method-description">
|
|
1367
|
+
|
|
1368
|
+
<p>returns an array of coverage for each location for which there are mapped
|
|
1369
|
+
reads</p>
|
|
1370
|
+
<ul><li>
|
|
1371
|
+
<p>chr - the reference name</p>
|
|
1372
|
+
</li><li>
|
|
1373
|
+
<p>start - the start position</p>
|
|
1374
|
+
</li><li>
|
|
1375
|
+
<p>length - the length of the region queried</p>
|
|
1376
|
+
</li></ul>
|
|
1377
|
+
|
|
1378
|
+
<p>OPTIONS</p>
|
|
1379
|
+
<ul><li>
|
|
1380
|
+
<p>bin - the amount of bins to split the histogram into. A mean score for each
|
|
1381
|
+
bin will be plotted. [default 30 bins]</p>
|
|
1382
|
+
</li><li>
|
|
1383
|
+
<p>svg - a file to write the svg image to [default a String object containing
|
|
1384
|
+
the SVG]</p>
|
|
1385
|
+
</li></ul>
|
|
1386
|
+
|
|
1387
|
+
|
|
1388
|
+
|
|
1389
|
+
|
|
1390
|
+
<div class="method-source-code" id="plot_chromosome_coverage-source">
|
|
1391
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 119</span>
|
|
1392
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">plot_chromosome_coverage</span>(<span class="ruby-identifier">chr</span>,<span class="ruby-identifier">start</span>,<span class="ruby-identifier">length</span>, <span class="ruby-identifier">opts</span>={})
|
|
1393
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:bin</span>]
|
|
1394
|
+
<span class="ruby-identifier">bin</span> = <span class="ruby-identifier">length</span><span class="ruby-operator">/</span><span class="ruby-identifier">opts</span>[<span class="ruby-value">:bin</span>]
|
|
1395
|
+
<span class="ruby-keyword">else</span>
|
|
1396
|
+
<span class="ruby-identifier">bin</span> = <span class="ruby-identifier">length</span><span class="ruby-operator">/</span><span class="ruby-value">30</span>
|
|
1397
|
+
<span class="ruby-keyword">end</span>
|
|
1398
|
+
<span class="ruby-identifier">result</span> = []
|
|
1399
|
+
<span class="ruby-identifier">region</span> = <span class="ruby-node">"#{chr}:#{start}-#{start + length}"</span>
|
|
1400
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">mpileup</span>(<span class="ruby-value">:r</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">region</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span>
|
|
1401
|
+
<span class="ruby-identifier">result</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">p</span>.<span class="ruby-identifier">coverage</span>
|
|
1402
|
+
<span class="ruby-keyword">end</span>
|
|
1403
|
+
<span class="ruby-identifier">p</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">Page</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:width</span> =<span class="ruby-operator">></span> <span class="ruby-value">1000</span>,
|
|
1404
|
+
<span class="ruby-value">:height</span> =<span class="ruby-operator">></span> <span class="ruby-value">200</span>,
|
|
1405
|
+
<span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">></span> <span class="ruby-value">10</span>,
|
|
1406
|
+
<span class="ruby-value">:font_size</span> =<span class="ruby-operator">></span> <span class="ruby-value">14</span>
|
|
1407
|
+
)
|
|
1408
|
+
<span class="ruby-identifier">data_track</span> = <span class="ruby-identifier">p</span>.<span class="ruby-identifier">add_track</span>(<span class="ruby-value">:glyph</span> =<span class="ruby-operator">></span> <span class="ruby-value">:histogram</span>,
|
|
1409
|
+
<span class="ruby-value">:stroke_color</span> =<span class="ruby-operator">></span> <span class="ruby-string">'black'</span>,
|
|
1410
|
+
<span class="ruby-value">:fill_color</span> =<span class="ruby-operator">></span> <span class="ruby-string">'gold'</span>,
|
|
1411
|
+
<span class="ruby-value">:track_height</span> =<span class="ruby-operator">></span> <span class="ruby-value">150</span>,
|
|
1412
|
+
<span class="ruby-value">:name</span> =<span class="ruby-operator">></span> <span class="ruby-string">'read coverage'</span>,
|
|
1413
|
+
<span class="ruby-value">:label</span> =<span class="ruby-operator">></span> <span class="ruby-keyword">true</span>,
|
|
1414
|
+
<span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">></span> <span class="ruby-string">'1'</span>,
|
|
1415
|
+
<span class="ruby-value">:x_round</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span>,
|
|
1416
|
+
<span class="ruby-value">:y_round</span> =<span class="ruby-operator">></span> <span class="ruby-value">1</span> )
|
|
1417
|
+
<span class="ruby-identifier">index</span> = <span class="ruby-value">0</span>;
|
|
1418
|
+
<span class="ruby-identifier">result</span>.<span class="ruby-identifier">each_slice</span>(<span class="ruby-identifier">bin</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">slice</span><span class="ruby-operator">|</span>
|
|
1419
|
+
<span class="ruby-comment">#result.each_with_index {|val, index|</span>
|
|
1420
|
+
<span class="ruby-identifier">data_feature</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">Graphics</span><span class="ruby-operator">::</span><span class="ruby-constant">MiniFeature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:start</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">index</span>,
|
|
1421
|
+
<span class="ruby-value">:end</span> =<span class="ruby-operator">></span> (<span class="ruby-identifier">start</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">index</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">bin</span>),
|
|
1422
|
+
<span class="ruby-value">:segment_height</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">slice</span>.<span class="ruby-identifier">inject</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>,<span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">x</span> }.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">slice</span>.<span class="ruby-identifier">size</span>)
|
|
1423
|
+
<span class="ruby-identifier">data_track</span>.<span class="ruby-identifier">add</span>(<span class="ruby-identifier">data_feature</span>)
|
|
1424
|
+
<span class="ruby-identifier">index</span><span class="ruby-operator">+=</span><span class="ruby-identifier">bin</span>
|
|
1425
|
+
}
|
|
1426
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:svg</span>]
|
|
1427
|
+
<span class="ruby-identifier">svg</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:svg</span>].<span class="ruby-identifier">to_s</span>
|
|
1428
|
+
<span class="ruby-identifier">p</span>.<span class="ruby-identifier">write</span>(<span class="ruby-identifier">svg</span>)
|
|
1429
|
+
<span class="ruby-keyword">else</span>
|
|
1430
|
+
<span class="ruby-keyword">return</span> <span class="ruby-identifier">p</span>.<span class="ruby-identifier">get_markup</span>
|
|
1431
|
+
<span class="ruby-keyword">end</span>
|
|
1432
|
+
|
|
1433
|
+
|
|
1434
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1435
|
+
</div>
|
|
1436
|
+
|
|
1437
|
+
</div>
|
|
1438
|
+
|
|
1439
|
+
|
|
1440
|
+
|
|
1441
|
+
|
|
1442
|
+
</div>
|
|
1443
|
+
|
|
1444
|
+
|
|
1445
|
+
<div id="method-i-reheader" class="method-detail ">
|
|
1446
|
+
|
|
1447
|
+
<div class="method-heading">
|
|
1448
|
+
<span class="method-name">reheader</span><span
|
|
1449
|
+
class="method-args">(header_sam, opts={})</span>
|
|
1450
|
+
|
|
1451
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1452
|
+
|
|
1453
|
+
</div>
|
|
1454
|
+
|
|
1455
|
+
|
|
1456
|
+
<div class="method-description">
|
|
1457
|
+
|
|
1458
|
+
<p>Replace the header of the current bam file with the header in header_sam</p>
|
|
1459
|
+
<ul><li>
|
|
1460
|
+
<p>header_sam - the sam file from which the new header will be taken</p>
|
|
1461
|
+
</li><li>
|
|
1462
|
+
<p>out - [FILE] output bam file</p>
|
|
1463
|
+
</li></ul>
|
|
1464
|
+
|
|
1465
|
+
|
|
1466
|
+
|
|
1467
|
+
|
|
1468
|
+
<div class="method-source-code" id="reheader-source">
|
|
1469
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 471</span>
|
|
1470
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">reheader</span>(<span class="ruby-identifier">header_sam</span>, <span class="ruby-identifier">opts</span>={})
|
|
1471
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">has_key?</span>(<span class="ruby-value">:out</span>)
|
|
1472
|
+
<span class="ruby-identifier">out</span>=<span class="ruby-identifier">opts</span>[<span class="ruby-value">:out</span>]
|
|
1473
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} reheader #{header_sam} #{@bam} > #{out}"</span>
|
|
1474
|
+
<span class="ruby-keyword">else</span>
|
|
1475
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{@samtools} reheader #{header_sam} #{@bam}"</span>
|
|
1476
|
+
<span class="ruby-keyword">end</span>
|
|
1477
|
+
<span class="ruby-identifier">puts</span> <span class="ruby-identifier">command</span>
|
|
1478
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1479
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1480
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1481
|
+
</div>
|
|
1482
|
+
|
|
1483
|
+
</div>
|
|
1484
|
+
|
|
1485
|
+
|
|
1486
|
+
|
|
1487
|
+
|
|
1488
|
+
</div>
|
|
1489
|
+
|
|
1490
|
+
|
|
1491
|
+
<div id="method-i-remove_duplicates" class="method-detail ">
|
|
1492
|
+
|
|
1493
|
+
<div class="method-heading">
|
|
1494
|
+
<span class="method-name">remove_duplicates</span><span
|
|
1495
|
+
class="method-args">(opts={})</span>
|
|
1496
|
+
|
|
1497
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1498
|
+
|
|
1499
|
+
</div>
|
|
1500
|
+
|
|
1501
|
+
|
|
1502
|
+
<div class="method-description">
|
|
1503
|
+
|
|
1504
|
+
<p>Remove potential PCR duplicates: if multiple read pairs have identical
|
|
1505
|
+
external coordinates, only retain the pair with highest mapping quality.</p>
|
|
1506
|
+
<ul><li>
|
|
1507
|
+
<p>s - rmdup for SE reads</p>
|
|
1508
|
+
</li><li>
|
|
1509
|
+
<p>S - treat PE reads as SE in rmdup (force -s)</p>
|
|
1510
|
+
</li><li>
|
|
1511
|
+
<p>out - [FILE] output bam</p>
|
|
1512
|
+
</li></ul>
|
|
1513
|
+
|
|
1514
|
+
|
|
1515
|
+
|
|
1516
|
+
|
|
1517
|
+
<div class="method-source-code" id="remove_duplicates-source">
|
|
1518
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 411</span>
|
|
1519
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">remove_duplicates</span>(<span class="ruby-identifier">opts</span>={})
|
|
1520
|
+
<span class="ruby-identifier">out</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:out</span>]
|
|
1521
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:out</span>)
|
|
1522
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{form_opt_string(@samtools, "rmdup", opts, [:s, :S])} #{out} #{@bam}"</span>
|
|
1523
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1524
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1525
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1526
|
+
</div>
|
|
1527
|
+
|
|
1528
|
+
</div>
|
|
1529
|
+
|
|
1530
|
+
|
|
1531
|
+
<div class="aliases">
|
|
1532
|
+
Also aliased as: <a href="Sam.html#method-i-rmdup">rmdup</a>
|
|
1533
|
+
</div>
|
|
1534
|
+
|
|
1535
|
+
|
|
1536
|
+
|
|
1537
|
+
</div>
|
|
1538
|
+
|
|
1539
|
+
|
|
1540
|
+
<div id="method-i-rmdup" class="method-detail method-alias">
|
|
1541
|
+
|
|
1542
|
+
<div class="method-heading">
|
|
1543
|
+
<span class="method-name">rmdup</span><span
|
|
1544
|
+
class="method-args">(opts={})</span>
|
|
1545
|
+
|
|
1546
|
+
</div>
|
|
1547
|
+
|
|
1548
|
+
|
|
1549
|
+
<div class="method-description">
|
|
1550
|
+
|
|
1551
|
+
|
|
1552
|
+
|
|
1553
|
+
|
|
1554
|
+
|
|
1555
|
+
|
|
1556
|
+
</div>
|
|
1557
|
+
|
|
1558
|
+
|
|
1559
|
+
|
|
1560
|
+
|
|
1561
|
+
<div class="aliases">
|
|
1562
|
+
Alias for: <a href="Sam.html#method-i-remove_duplicates">remove_duplicates</a>
|
|
1563
|
+
</div>
|
|
1564
|
+
|
|
1565
|
+
</div>
|
|
1566
|
+
|
|
1567
|
+
|
|
1568
|
+
<div id="method-i-sort" class="method-detail ">
|
|
1569
|
+
|
|
1570
|
+
<div class="method-heading">
|
|
1571
|
+
<span class="method-name">sort</span><span
|
|
1572
|
+
class="method-args">(opts={})</span>
|
|
1573
|
+
|
|
1574
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1575
|
+
|
|
1576
|
+
</div>
|
|
1577
|
+
|
|
1578
|
+
|
|
1579
|
+
<div class="method-description">
|
|
1580
|
+
|
|
1581
|
+
<p>Sort alignments by leftmost coordinates</p>
|
|
1582
|
+
<ul><li>
|
|
1583
|
+
<p>n - sort by read name</p>
|
|
1584
|
+
</li><li>
|
|
1585
|
+
<p>f - use <out.prefix> as full file name instead of prefix</p>
|
|
1586
|
+
</li><li>
|
|
1587
|
+
<p>o - final output to stdout returns bio::db::alignment</p>
|
|
1588
|
+
</li><li>
|
|
1589
|
+
<p>l - [INT] compression level, from 0 to 9 [-1]</p>
|
|
1590
|
+
</li><li>
|
|
1591
|
+
<p>at - [INT] number of sorting and compression threads [1]</p>
|
|
1592
|
+
</li><li>
|
|
1593
|
+
<p>m - [INT] max memory per thread; suffix K/M/G recognized [768M]</p>
|
|
1594
|
+
</li><li>
|
|
1595
|
+
<p>prefix - [STRING] prefix for output bamfile</p>
|
|
1596
|
+
</li></ul>
|
|
1597
|
+
|
|
1598
|
+
|
|
1599
|
+
|
|
1600
|
+
|
|
1601
|
+
<div class="method-source-code" id="sort-source">
|
|
1602
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 429</span>
|
|
1603
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">sort</span>(<span class="ruby-identifier">opts</span>={})
|
|
1604
|
+
<span class="ruby-keyword">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">opts</span>.<span class="ruby-identifier">has_key?</span>(<span class="ruby-value">:prefix</span>)
|
|
1605
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">merge!</span>({<span class="ruby-value">:prefix</span> =<span class="ruby-operator">></span> <span class="ruby-string">"sorted"</span>})
|
|
1606
|
+
<span class="ruby-keyword">end</span>
|
|
1607
|
+
<span class="ruby-identifier">prefix</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:prefix</span>]
|
|
1608
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:prefix</span>)
|
|
1609
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">"sort"</span>, <span class="ruby-identifier">opts</span>, [<span class="ruby-value">:n</span>, <span class="ruby-value">:f</span>, <span class="ruby-value">:o</span>])
|
|
1610
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">command</span> <span class="ruby-operator">+</span> <span class="ruby-string">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">prefix</span>
|
|
1611
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1612
|
+
<span class="ruby-comment">#puts command</span>
|
|
1613
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:o</span>]
|
|
1614
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Alignment</span>)
|
|
1615
|
+
<span class="ruby-keyword">else</span>
|
|
1616
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1617
|
+
<span class="ruby-keyword">end</span>
|
|
1618
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1619
|
+
</div>
|
|
1620
|
+
|
|
1621
|
+
</div>
|
|
1622
|
+
|
|
1623
|
+
|
|
1624
|
+
|
|
1625
|
+
|
|
1626
|
+
</div>
|
|
1627
|
+
|
|
1628
|
+
|
|
1629
|
+
<div id="method-i-targetcut" class="method-detail ">
|
|
1630
|
+
|
|
1631
|
+
<div class="method-heading">
|
|
1632
|
+
<span class="method-name">targetcut</span><span
|
|
1633
|
+
class="method-args">(opts={})</span>
|
|
1634
|
+
|
|
1635
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1636
|
+
|
|
1637
|
+
</div>
|
|
1638
|
+
|
|
1639
|
+
|
|
1640
|
+
<div class="method-description">
|
|
1641
|
+
|
|
1642
|
+
<p>Identifies target regions by examining the continuity of read depth,
|
|
1643
|
+
computes haploid consensus sequences of targets and outputs a SAM with each
|
|
1644
|
+
sequence corresponding to a target. When option -f is in use, BAQ will be
|
|
1645
|
+
applied.</p>
|
|
1646
|
+
<ul><li>
|
|
1647
|
+
<p>Q - [INT] Minimum base quality for a base to be considered [13]</p>
|
|
1648
|
+
</li><li>
|
|
1649
|
+
<p>i - in penalty</p>
|
|
1650
|
+
</li><li>
|
|
1651
|
+
<p>0 - em0</p>
|
|
1652
|
+
</li><li>
|
|
1653
|
+
<p>1 - em1</p>
|
|
1654
|
+
</li><li>
|
|
1655
|
+
<p>2 - em2</p>
|
|
1656
|
+
</li><li>
|
|
1657
|
+
<p>f - reference</p>
|
|
1658
|
+
</li></ul>
|
|
1659
|
+
|
|
1660
|
+
|
|
1661
|
+
|
|
1662
|
+
|
|
1663
|
+
<div class="method-source-code" id="targetcut-source">
|
|
1664
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 507</span>
|
|
1665
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">targetcut</span>(<span class="ruby-identifier">opts</span>={})
|
|
1666
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:f</span>]
|
|
1667
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'f'</span>] = <span class="ruby-ivar">@fasta</span>
|
|
1668
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:s</span>)
|
|
1669
|
+
<span class="ruby-keyword">end</span>
|
|
1670
|
+
|
|
1671
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{form_opt_string(@samtools, "targetcut", opts, [] )}"</span>
|
|
1672
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1673
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1674
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1675
|
+
</div>
|
|
1676
|
+
|
|
1677
|
+
</div>
|
|
1678
|
+
|
|
1679
|
+
|
|
1680
|
+
|
|
1681
|
+
|
|
1682
|
+
</div>
|
|
1683
|
+
|
|
1684
|
+
|
|
1685
|
+
<div id="method-i-tview" class="method-detail ">
|
|
1686
|
+
|
|
1687
|
+
<div class="method-heading">
|
|
1688
|
+
<span class="method-name">tview</span><span
|
|
1689
|
+
class="method-args">(opts={})</span>
|
|
1690
|
+
|
|
1691
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1692
|
+
|
|
1693
|
+
</div>
|
|
1694
|
+
|
|
1695
|
+
|
|
1696
|
+
<div class="method-description">
|
|
1697
|
+
|
|
1698
|
+
<p>used to generate a text alignment viewer</p>
|
|
1699
|
+
<ul><li>
|
|
1700
|
+
<p>d - display, output as (H)tml or (C)urses or (T)ext</p>
|
|
1701
|
+
</li><li>
|
|
1702
|
+
<p>p - [chr:pos] go directly to this position</p>
|
|
1703
|
+
</li><li>
|
|
1704
|
+
<p>s - [STR] display only reads from this sample or group</p>
|
|
1705
|
+
</li></ul>
|
|
1706
|
+
|
|
1707
|
+
|
|
1708
|
+
|
|
1709
|
+
|
|
1710
|
+
<div class="method-source-code" id="tview-source">
|
|
1711
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 450</span>
|
|
1712
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">tview</span>(<span class="ruby-identifier">opts</span>={})
|
|
1713
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:d</span>]
|
|
1714
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'d'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:d</span>]
|
|
1715
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:d</span>)
|
|
1716
|
+
<span class="ruby-keyword">end</span>
|
|
1717
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:p</span>]
|
|
1718
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'p'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:p</span>]
|
|
1719
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:p</span>)
|
|
1720
|
+
<span class="ruby-keyword">end</span>
|
|
1721
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:s</span>]
|
|
1722
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'s'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:s</span>]
|
|
1723
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:s</span>)
|
|
1724
|
+
<span class="ruby-keyword">end</span>
|
|
1725
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-node">"#{form_opt_string(@samtools, "tview", opts)}"</span>
|
|
1726
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1727
|
+
<span class="ruby-identifier">system</span>(<span class="ruby-identifier">command</span>)
|
|
1728
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1729
|
+
</div>
|
|
1730
|
+
|
|
1731
|
+
</div>
|
|
1732
|
+
|
|
1733
|
+
|
|
1734
|
+
|
|
1735
|
+
|
|
1736
|
+
</div>
|
|
1737
|
+
|
|
1738
|
+
|
|
1739
|
+
<div id="method-i-view" class="method-detail ">
|
|
1740
|
+
|
|
1741
|
+
<div class="method-heading">
|
|
1742
|
+
<span class="method-name">view</span><span
|
|
1743
|
+
class="method-args">(opts={},&block)</span>
|
|
1744
|
+
|
|
1745
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
1746
|
+
|
|
1747
|
+
</div>
|
|
1748
|
+
|
|
1749
|
+
|
|
1750
|
+
<div class="method-description">
|
|
1751
|
+
|
|
1752
|
+
<p>runs the samtools view command</p>
|
|
1753
|
+
<ul><li>
|
|
1754
|
+
<p>b - output BAM</p>
|
|
1755
|
+
</li><li>
|
|
1756
|
+
<p>h - print header for the SAM output</p>
|
|
1757
|
+
</li><li>
|
|
1758
|
+
<p>H - print header only (no alignments)</p>
|
|
1759
|
+
</li><li>
|
|
1760
|
+
<p>S - input is SAM</p>
|
|
1761
|
+
</li><li>
|
|
1762
|
+
<p>u - uncompressed BAM output (force -b)</p>
|
|
1763
|
+
</li><li>
|
|
1764
|
+
<p>one - fast compression (force -b)</p>
|
|
1765
|
+
</li><li>
|
|
1766
|
+
<p>x - output FLAG in HEX (samtools-C specific)</p>
|
|
1767
|
+
</li><li>
|
|
1768
|
+
<p>X - output FLAG in string (samtools-C specific)</p>
|
|
1769
|
+
</li><li>
|
|
1770
|
+
<p>c - print only the count of matching records</p>
|
|
1771
|
+
</li><li>
|
|
1772
|
+
<p>B - collapse the backward CIGAR operation</p>
|
|
1773
|
+
</li><li>
|
|
1774
|
+
<p>at - INT number of BAM compression threads [0]</p>
|
|
1775
|
+
</li><li>
|
|
1776
|
+
<p>L - FILE output alignments overlapping the input BED FILE [null]</p>
|
|
1777
|
+
</li><li>
|
|
1778
|
+
<p>t - FILE list of reference names and lengths (force -S) [null]</p>
|
|
1779
|
+
</li><li>
|
|
1780
|
+
<p>T - FILE reference sequence file (force -S) [null]</p>
|
|
1781
|
+
</li><li>
|
|
1782
|
+
<p>o - FILE output file name [stdout]</p>
|
|
1783
|
+
</li><li>
|
|
1784
|
+
<p>R - FILE list of read groups to be outputted [null]</p>
|
|
1785
|
+
</li><li>
|
|
1786
|
+
<p>f - INT required flag 0 for unset [0]</p>
|
|
1787
|
+
</li><li>
|
|
1788
|
+
<p>F - INT filtering flag 0 for unset [0]</p>
|
|
1789
|
+
</li><li>
|
|
1790
|
+
<p>q - INT minimum mapping quality [0]</p>
|
|
1791
|
+
</li><li>
|
|
1792
|
+
<p>l - STR only output reads in library STR [null]</p>
|
|
1793
|
+
</li><li>
|
|
1794
|
+
<p>r - STR only output reads in read group STR [null]</p>
|
|
1795
|
+
</li><li>
|
|
1796
|
+
<p>s - FLOAT fraction of templates to subsample; integer part as seed [-1]</p>
|
|
1797
|
+
</li><li>
|
|
1798
|
+
<p>chr - name of reference sequence to get alignments from</p>
|
|
1799
|
+
</li><li>
|
|
1800
|
+
<p>start - start position on reference sequence</p>
|
|
1801
|
+
</li><li>
|
|
1802
|
+
<p>stop - end postion on reference sequence</p>
|
|
1803
|
+
</li></ul>
|
|
1804
|
+
|
|
1805
|
+
|
|
1806
|
+
|
|
1807
|
+
|
|
1808
|
+
<div class="method-source-code" id="view-source">
|
|
1809
|
+
<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 59</span>
|
|
1810
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">view</span>(<span class="ruby-identifier">opts</span>={},<span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
1811
|
+
<span class="ruby-identifier">region</span> = <span class="ruby-constant">String</span>.<span class="ruby-identifier">new</span>
|
|
1812
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:chr</span>] <span class="ruby-keyword">and</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:start</span>] <span class="ruby-keyword">and</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:stop</span>]
|
|
1813
|
+
<span class="ruby-identifier">region</span> = <span class="ruby-node">"#{opts[:chr]}:#{opts[:start]}-#{opts[:stop]}"</span>
|
|
1814
|
+
[<span class="ruby-value">:chr</span>, <span class="ruby-value">:start</span>, <span class="ruby-value">:stop</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">o</span><span class="ruby-operator">|</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">o</span>)}
|
|
1815
|
+
<span class="ruby-keyword">end</span>
|
|
1816
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:at</span>]
|
|
1817
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'@'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:at</span>]
|
|
1818
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:at</span>)
|
|
1819
|
+
<span class="ruby-keyword">end</span>
|
|
1820
|
+
|
|
1821
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:one</span>]
|
|
1822
|
+
<span class="ruby-identifier">opts</span>[<span class="ruby-string">'1'</span>] = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:one</span>]
|
|
1823
|
+
<span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:one</span>)
|
|
1824
|
+
<span class="ruby-keyword">end</span>
|
|
1825
|
+
|
|
1826
|
+
<span class="ruby-identifier">command</span> = <span class="ruby-identifier">form_opt_string</span>(<span class="ruby-ivar">@samtools</span>, <span class="ruby-string">'view'</span>, <span class="ruby-identifier">opts</span>, [<span class="ruby-value">:b</span>, <span class="ruby-value">:h</span>, <span class="ruby-value">:H</span>, <span class="ruby-value">:S</span>, <span class="ruby-value">:u</span>, <span class="ruby-string">'1'</span>, <span class="ruby-value">:x</span>, <span class="ruby-value">:X</span>, <span class="ruby-value">:c</span>, <span class="ruby-value">:B</span>]) <span class="ruby-operator">+</span> <span class="ruby-string">" "</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">region</span>
|
|
1827
|
+
<span class="ruby-ivar">@last_command</span> = <span class="ruby-identifier">command</span>
|
|
1828
|
+
<span class="ruby-identifier">type</span> = (<span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>] <span class="ruby-keyword">or</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:b</span>]) <span class="ruby-operator">?</span> <span class="ruby-value">:binary</span> <span class="ruby-operator">:</span> <span class="ruby-value">:text</span>
|
|
1829
|
+
<span class="ruby-identifier">klass</span> = (<span class="ruby-identifier">type</span> <span class="ruby-operator">==</span> <span class="ruby-value">:binary</span>) <span class="ruby-operator">?</span> <span class="ruby-constant">String</span> <span class="ruby-operator">:</span> <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">Alignment</span>
|
|
1830
|
+
<span class="ruby-identifier">yield_from_pipe</span>(<span class="ruby-identifier">command</span>, <span class="ruby-identifier">klass</span>, <span class="ruby-identifier">type</span>, <span class="ruby-operator">&</span><span class="ruby-identifier">block</span>)
|
|
1831
|
+
<span class="ruby-keyword">end</span></pre>
|
|
1832
|
+
</div>
|
|
1833
|
+
|
|
1834
|
+
</div>
|
|
1835
|
+
|
|
1836
|
+
|
|
1837
|
+
|
|
1838
|
+
|
|
1839
|
+
</div>
|
|
1840
|
+
|
|
1841
|
+
|
|
1842
|
+
</section>
|
|
1843
|
+
|
|
1844
|
+
</section>
|
|
1845
|
+
</main>
|
|
1846
|
+
|
|
1847
|
+
|
|
1848
|
+
<footer id="validator-badges" role="contentinfo">
|
|
1849
|
+
<p><a href="http://validator.w3.org/check/referer">Validate</a>
|
|
1850
|
+
<p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
|
|
1851
|
+
<p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
|
|
1852
|
+
</footer>
|
|
1853
|
+
|