bio-samtools-wrapper 2.7.0
Sign up to get free protection for your applications and to get access to all the features.
- 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
|
@@ -0,0 +1,552 @@
|
|
|
1
|
+
<!DOCTYPE html>
|
|
2
|
+
|
|
3
|
+
<html>
|
|
4
|
+
<head>
|
|
5
|
+
<meta charset="UTF-8">
|
|
6
|
+
|
|
7
|
+
<title>class Bio::DB::Alignment - 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-new">::new</a>
|
|
77
|
+
|
|
78
|
+
</ul>
|
|
79
|
+
</div>
|
|
80
|
+
|
|
81
|
+
</div>
|
|
82
|
+
</nav>
|
|
83
|
+
|
|
84
|
+
<main role="main" aria-labelledby="class-Bio::DB::Alignment">
|
|
85
|
+
<h1 id="class-Bio::DB::Alignment" class="class">
|
|
86
|
+
class Bio::DB::Alignment
|
|
87
|
+
</h1>
|
|
88
|
+
|
|
89
|
+
<section class="description">
|
|
90
|
+
|
|
91
|
+
<p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
|
|
92
|
+
documentation) <a
|
|
93
|
+
href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
|
|
94
|
+
href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
|
|
95
|
+
they are forward. It is the opposite to the definition in the BAM format
|
|
96
|
+
for clarity. primary is the negation of is_negative from the BAM format</p>
|
|
97
|
+
|
|
98
|
+
</section>
|
|
99
|
+
|
|
100
|
+
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
<section id="5Buntitled-5D" class="documentation-section">
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
|
|
110
|
+
|
|
111
|
+
<section class="attribute-method-details" class="method-section">
|
|
112
|
+
<header>
|
|
113
|
+
<h3>Attributes</h3>
|
|
114
|
+
</header>
|
|
115
|
+
|
|
116
|
+
|
|
117
|
+
<div id="attribute-i-al" class="method-detail">
|
|
118
|
+
<div class="method-heading attribute-method-heading">
|
|
119
|
+
<span class="method-name">al</span><span
|
|
120
|
+
class="attribute-access-type">[RW]</span>
|
|
121
|
+
</div>
|
|
122
|
+
|
|
123
|
+
<div class="method-description">
|
|
124
|
+
|
|
125
|
+
|
|
126
|
+
|
|
127
|
+
</div>
|
|
128
|
+
</div>
|
|
129
|
+
|
|
130
|
+
<div id="attribute-i-calend" class="method-detail">
|
|
131
|
+
<div class="method-heading attribute-method-heading">
|
|
132
|
+
<span class="method-name">calend</span><span
|
|
133
|
+
class="attribute-access-type">[RW]</span>
|
|
134
|
+
</div>
|
|
135
|
+
|
|
136
|
+
<div class="method-description">
|
|
137
|
+
|
|
138
|
+
|
|
139
|
+
|
|
140
|
+
</div>
|
|
141
|
+
</div>
|
|
142
|
+
|
|
143
|
+
<div id="attribute-i-cigar" class="method-detail">
|
|
144
|
+
<div class="method-heading attribute-method-heading">
|
|
145
|
+
<span class="method-name">cigar</span><span
|
|
146
|
+
class="attribute-access-type">[RW]</span>
|
|
147
|
+
</div>
|
|
148
|
+
|
|
149
|
+
<div class="method-description">
|
|
150
|
+
|
|
151
|
+
|
|
152
|
+
|
|
153
|
+
</div>
|
|
154
|
+
</div>
|
|
155
|
+
|
|
156
|
+
<div id="attribute-i-failed_quality" class="method-detail">
|
|
157
|
+
<div class="method-heading attribute-method-heading">
|
|
158
|
+
<span class="method-name">failed_quality</span><span
|
|
159
|
+
class="attribute-access-type">[RW]</span>
|
|
160
|
+
</div>
|
|
161
|
+
|
|
162
|
+
<div class="method-description">
|
|
163
|
+
|
|
164
|
+
|
|
165
|
+
|
|
166
|
+
</div>
|
|
167
|
+
</div>
|
|
168
|
+
|
|
169
|
+
<div id="attribute-i-first_in_pair" class="method-detail">
|
|
170
|
+
<div class="method-heading attribute-method-heading">
|
|
171
|
+
<span class="method-name">first_in_pair</span><span
|
|
172
|
+
class="attribute-access-type">[RW]</span>
|
|
173
|
+
</div>
|
|
174
|
+
|
|
175
|
+
<div class="method-description">
|
|
176
|
+
|
|
177
|
+
|
|
178
|
+
|
|
179
|
+
</div>
|
|
180
|
+
</div>
|
|
181
|
+
|
|
182
|
+
<div id="attribute-i-flag" class="method-detail">
|
|
183
|
+
<div class="method-heading attribute-method-heading">
|
|
184
|
+
<span class="method-name">flag</span><span
|
|
185
|
+
class="attribute-access-type">[RW]</span>
|
|
186
|
+
</div>
|
|
187
|
+
|
|
188
|
+
<div class="method-description">
|
|
189
|
+
|
|
190
|
+
|
|
191
|
+
|
|
192
|
+
</div>
|
|
193
|
+
</div>
|
|
194
|
+
|
|
195
|
+
<div id="attribute-i-is_duplicate" class="method-detail">
|
|
196
|
+
<div class="method-heading attribute-method-heading">
|
|
197
|
+
<span class="method-name">is_duplicate</span><span
|
|
198
|
+
class="attribute-access-type">[RW]</span>
|
|
199
|
+
</div>
|
|
200
|
+
|
|
201
|
+
<div class="method-description">
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
|
|
205
|
+
</div>
|
|
206
|
+
</div>
|
|
207
|
+
|
|
208
|
+
<div id="attribute-i-is_mapped" class="method-detail">
|
|
209
|
+
<div class="method-heading attribute-method-heading">
|
|
210
|
+
<span class="method-name">is_mapped</span><span
|
|
211
|
+
class="attribute-access-type">[RW]</span>
|
|
212
|
+
</div>
|
|
213
|
+
|
|
214
|
+
<div class="method-description">
|
|
215
|
+
|
|
216
|
+
|
|
217
|
+
|
|
218
|
+
</div>
|
|
219
|
+
</div>
|
|
220
|
+
|
|
221
|
+
<div id="attribute-i-is_paired" class="method-detail">
|
|
222
|
+
<div class="method-heading attribute-method-heading">
|
|
223
|
+
<span class="method-name">is_paired</span><span
|
|
224
|
+
class="attribute-access-type">[RW]</span>
|
|
225
|
+
</div>
|
|
226
|
+
|
|
227
|
+
<div class="method-description">
|
|
228
|
+
|
|
229
|
+
|
|
230
|
+
|
|
231
|
+
</div>
|
|
232
|
+
</div>
|
|
233
|
+
|
|
234
|
+
<div id="attribute-i-isize" class="method-detail">
|
|
235
|
+
<div class="method-heading attribute-method-heading">
|
|
236
|
+
<span class="method-name">isize</span><span
|
|
237
|
+
class="attribute-access-type">[RW]</span>
|
|
238
|
+
</div>
|
|
239
|
+
|
|
240
|
+
<div class="method-description">
|
|
241
|
+
|
|
242
|
+
|
|
243
|
+
|
|
244
|
+
</div>
|
|
245
|
+
</div>
|
|
246
|
+
|
|
247
|
+
<div id="attribute-i-mapq" class="method-detail">
|
|
248
|
+
<div class="method-heading attribute-method-heading">
|
|
249
|
+
<span class="method-name">mapq</span><span
|
|
250
|
+
class="attribute-access-type">[RW]</span>
|
|
251
|
+
</div>
|
|
252
|
+
|
|
253
|
+
<div class="method-description">
|
|
254
|
+
|
|
255
|
+
|
|
256
|
+
|
|
257
|
+
</div>
|
|
258
|
+
</div>
|
|
259
|
+
|
|
260
|
+
<div id="attribute-i-mate_strand" class="method-detail">
|
|
261
|
+
<div class="method-heading attribute-method-heading">
|
|
262
|
+
<span class="method-name">mate_strand</span><span
|
|
263
|
+
class="attribute-access-type">[RW]</span>
|
|
264
|
+
</div>
|
|
265
|
+
|
|
266
|
+
<div class="method-description">
|
|
267
|
+
|
|
268
|
+
|
|
269
|
+
|
|
270
|
+
</div>
|
|
271
|
+
</div>
|
|
272
|
+
|
|
273
|
+
<div id="attribute-i-mate_unmapped" class="method-detail">
|
|
274
|
+
<div class="method-heading attribute-method-heading">
|
|
275
|
+
<span class="method-name">mate_unmapped</span><span
|
|
276
|
+
class="attribute-access-type">[RW]</span>
|
|
277
|
+
</div>
|
|
278
|
+
|
|
279
|
+
<div class="method-description">
|
|
280
|
+
|
|
281
|
+
|
|
282
|
+
|
|
283
|
+
</div>
|
|
284
|
+
</div>
|
|
285
|
+
|
|
286
|
+
<div id="attribute-i-mpos" class="method-detail">
|
|
287
|
+
<div class="method-heading attribute-method-heading">
|
|
288
|
+
<span class="method-name">mpos</span><span
|
|
289
|
+
class="attribute-access-type">[RW]</span>
|
|
290
|
+
</div>
|
|
291
|
+
|
|
292
|
+
<div class="method-description">
|
|
293
|
+
|
|
294
|
+
|
|
295
|
+
|
|
296
|
+
</div>
|
|
297
|
+
</div>
|
|
298
|
+
|
|
299
|
+
<div id="attribute-i-mrnm" class="method-detail">
|
|
300
|
+
<div class="method-heading attribute-method-heading">
|
|
301
|
+
<span class="method-name">mrnm</span><span
|
|
302
|
+
class="attribute-access-type">[RW]</span>
|
|
303
|
+
</div>
|
|
304
|
+
|
|
305
|
+
<div class="method-description">
|
|
306
|
+
|
|
307
|
+
|
|
308
|
+
|
|
309
|
+
</div>
|
|
310
|
+
</div>
|
|
311
|
+
|
|
312
|
+
<div id="attribute-i-pos" class="method-detail">
|
|
313
|
+
<div class="method-heading attribute-method-heading">
|
|
314
|
+
<span class="method-name">pos</span><span
|
|
315
|
+
class="attribute-access-type">[RW]</span>
|
|
316
|
+
</div>
|
|
317
|
+
|
|
318
|
+
<div class="method-description">
|
|
319
|
+
|
|
320
|
+
|
|
321
|
+
|
|
322
|
+
</div>
|
|
323
|
+
</div>
|
|
324
|
+
|
|
325
|
+
<div id="attribute-i-primary" class="method-detail">
|
|
326
|
+
<div class="method-heading attribute-method-heading">
|
|
327
|
+
<span class="method-name">primary</span><span
|
|
328
|
+
class="attribute-access-type">[RW]</span>
|
|
329
|
+
</div>
|
|
330
|
+
|
|
331
|
+
<div class="method-description">
|
|
332
|
+
|
|
333
|
+
|
|
334
|
+
|
|
335
|
+
</div>
|
|
336
|
+
</div>
|
|
337
|
+
|
|
338
|
+
<div id="attribute-i-qlen" class="method-detail">
|
|
339
|
+
<div class="method-heading attribute-method-heading">
|
|
340
|
+
<span class="method-name">qlen</span><span
|
|
341
|
+
class="attribute-access-type">[RW]</span>
|
|
342
|
+
</div>
|
|
343
|
+
|
|
344
|
+
<div class="method-description">
|
|
345
|
+
|
|
346
|
+
|
|
347
|
+
|
|
348
|
+
</div>
|
|
349
|
+
</div>
|
|
350
|
+
|
|
351
|
+
<div id="attribute-i-qname" class="method-detail">
|
|
352
|
+
<div class="method-heading attribute-method-heading">
|
|
353
|
+
<span class="method-name">qname</span><span
|
|
354
|
+
class="attribute-access-type">[RW]</span>
|
|
355
|
+
</div>
|
|
356
|
+
|
|
357
|
+
<div class="method-description">
|
|
358
|
+
|
|
359
|
+
|
|
360
|
+
|
|
361
|
+
</div>
|
|
362
|
+
</div>
|
|
363
|
+
|
|
364
|
+
<div id="attribute-i-qual" class="method-detail">
|
|
365
|
+
<div class="method-heading attribute-method-heading">
|
|
366
|
+
<span class="method-name">qual</span><span
|
|
367
|
+
class="attribute-access-type">[RW]</span>
|
|
368
|
+
</div>
|
|
369
|
+
|
|
370
|
+
<div class="method-description">
|
|
371
|
+
|
|
372
|
+
|
|
373
|
+
|
|
374
|
+
</div>
|
|
375
|
+
</div>
|
|
376
|
+
|
|
377
|
+
<div id="attribute-i-query_strand" class="method-detail">
|
|
378
|
+
<div class="method-heading attribute-method-heading">
|
|
379
|
+
<span class="method-name">query_strand</span><span
|
|
380
|
+
class="attribute-access-type">[RW]</span>
|
|
381
|
+
</div>
|
|
382
|
+
|
|
383
|
+
<div class="method-description">
|
|
384
|
+
|
|
385
|
+
|
|
386
|
+
|
|
387
|
+
</div>
|
|
388
|
+
</div>
|
|
389
|
+
|
|
390
|
+
<div id="attribute-i-query_unmapped" class="method-detail">
|
|
391
|
+
<div class="method-heading attribute-method-heading">
|
|
392
|
+
<span class="method-name">query_unmapped</span><span
|
|
393
|
+
class="attribute-access-type">[RW]</span>
|
|
394
|
+
</div>
|
|
395
|
+
|
|
396
|
+
<div class="method-description">
|
|
397
|
+
|
|
398
|
+
|
|
399
|
+
|
|
400
|
+
</div>
|
|
401
|
+
</div>
|
|
402
|
+
|
|
403
|
+
<div id="attribute-i-rname" class="method-detail">
|
|
404
|
+
<div class="method-heading attribute-method-heading">
|
|
405
|
+
<span class="method-name">rname</span><span
|
|
406
|
+
class="attribute-access-type">[RW]</span>
|
|
407
|
+
</div>
|
|
408
|
+
|
|
409
|
+
<div class="method-description">
|
|
410
|
+
|
|
411
|
+
|
|
412
|
+
|
|
413
|
+
</div>
|
|
414
|
+
</div>
|
|
415
|
+
|
|
416
|
+
<div id="attribute-i-samstr" class="method-detail">
|
|
417
|
+
<div class="method-heading attribute-method-heading">
|
|
418
|
+
<span class="method-name">samstr</span><span
|
|
419
|
+
class="attribute-access-type">[RW]</span>
|
|
420
|
+
</div>
|
|
421
|
+
|
|
422
|
+
<div class="method-description">
|
|
423
|
+
|
|
424
|
+
|
|
425
|
+
|
|
426
|
+
</div>
|
|
427
|
+
</div>
|
|
428
|
+
|
|
429
|
+
<div id="attribute-i-second_in_pair" class="method-detail">
|
|
430
|
+
<div class="method-heading attribute-method-heading">
|
|
431
|
+
<span class="method-name">second_in_pair</span><span
|
|
432
|
+
class="attribute-access-type">[RW]</span>
|
|
433
|
+
</div>
|
|
434
|
+
|
|
435
|
+
<div class="method-description">
|
|
436
|
+
|
|
437
|
+
|
|
438
|
+
|
|
439
|
+
</div>
|
|
440
|
+
</div>
|
|
441
|
+
|
|
442
|
+
<div id="attribute-i-seq" class="method-detail">
|
|
443
|
+
<div class="method-heading attribute-method-heading">
|
|
444
|
+
<span class="method-name">seq</span><span
|
|
445
|
+
class="attribute-access-type">[RW]</span>
|
|
446
|
+
</div>
|
|
447
|
+
|
|
448
|
+
<div class="method-description">
|
|
449
|
+
|
|
450
|
+
|
|
451
|
+
|
|
452
|
+
</div>
|
|
453
|
+
</div>
|
|
454
|
+
|
|
455
|
+
<div id="attribute-i-tags" class="method-detail">
|
|
456
|
+
<div class="method-heading attribute-method-heading">
|
|
457
|
+
<span class="method-name">tags</span><span
|
|
458
|
+
class="attribute-access-type">[RW]</span>
|
|
459
|
+
</div>
|
|
460
|
+
|
|
461
|
+
<div class="method-description">
|
|
462
|
+
|
|
463
|
+
|
|
464
|
+
|
|
465
|
+
</div>
|
|
466
|
+
</div>
|
|
467
|
+
|
|
468
|
+
</section>
|
|
469
|
+
|
|
470
|
+
|
|
471
|
+
|
|
472
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section">
|
|
473
|
+
<header>
|
|
474
|
+
<h3>Public Class Methods</h3>
|
|
475
|
+
</header>
|
|
476
|
+
|
|
477
|
+
|
|
478
|
+
<div id="method-c-new" class="method-detail ">
|
|
479
|
+
|
|
480
|
+
<div class="method-heading">
|
|
481
|
+
<span class="method-name">new</span><span
|
|
482
|
+
class="method-args">(sam_string)</span>
|
|
483
|
+
|
|
484
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
485
|
+
|
|
486
|
+
</div>
|
|
487
|
+
|
|
488
|
+
|
|
489
|
+
<div class="method-description">
|
|
490
|
+
|
|
491
|
+
<p>parses the SAM string into its constituents and set its attributes</p>
|
|
492
|
+
|
|
493
|
+
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
<div class="method-source-code" id="new-source">
|
|
497
|
+
<pre><span class="ruby-comment"># File lib/bio/db/alignment.rb, line 24</span>
|
|
498
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">sam_string</span>)
|
|
499
|
+
<span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam_string</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">"\t"</span>)
|
|
500
|
+
<span class="ruby-ivar">@qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
|
|
501
|
+
<span class="ruby-ivar">@flag</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
|
|
502
|
+
<span class="ruby-ivar">@rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
|
|
503
|
+
<span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span>
|
|
504
|
+
<span class="ruby-ivar">@mapq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">4</span>].<span class="ruby-identifier">to_i</span>
|
|
505
|
+
<span class="ruby-ivar">@cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
|
|
506
|
+
<span class="ruby-ivar">@mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
|
|
507
|
+
<span class="ruby-ivar">@mpos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">to_i</span>
|
|
508
|
+
<span class="ruby-ivar">@isize</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">8</span>].<span class="ruby-identifier">to_i</span>
|
|
509
|
+
<span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
|
|
510
|
+
<span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
|
|
511
|
+
<span class="ruby-ivar">@tags</span> = {}
|
|
512
|
+
<span class="ruby-value">11</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">s</span>.<span class="ruby-identifier">size</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
|
|
513
|
+
<span class="ruby-identifier">t</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">Tag</span>.<span class="ruby-identifier">new</span>
|
|
514
|
+
<span class="ruby-identifier">t</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">s</span>[<span class="ruby-identifier">n</span>])
|
|
515
|
+
<span class="ruby-identifier">tags</span>[<span class="ruby-identifier">t</span>.<span class="ruby-identifier">tag</span>] = <span class="ruby-identifier">t</span>
|
|
516
|
+
}
|
|
517
|
+
|
|
518
|
+
<span class="ruby-ivar">@is_paired</span> = (<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0001</span>) <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
519
|
+
<span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0002</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
520
|
+
<span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0004</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
521
|
+
<span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0008</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
522
|
+
<span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0010</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>)
|
|
523
|
+
<span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0020</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>)
|
|
524
|
+
<span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0040</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
525
|
+
<span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0080</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
526
|
+
<span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0100</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>)
|
|
527
|
+
<span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0200</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
528
|
+
<span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&</span> <span class="ruby-value">0x0400</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
529
|
+
|
|
530
|
+
<span class="ruby-keyword">end</span></pre>
|
|
531
|
+
</div>
|
|
532
|
+
|
|
533
|
+
</div>
|
|
534
|
+
|
|
535
|
+
|
|
536
|
+
|
|
537
|
+
|
|
538
|
+
</div>
|
|
539
|
+
|
|
540
|
+
|
|
541
|
+
</section>
|
|
542
|
+
|
|
543
|
+
</section>
|
|
544
|
+
</main>
|
|
545
|
+
|
|
546
|
+
|
|
547
|
+
<footer id="validator-badges" role="contentinfo">
|
|
548
|
+
<p><a href="http://validator.w3.org/check/referer">Validate</a>
|
|
549
|
+
<p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
|
|
550
|
+
<p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
|
|
551
|
+
</footer>
|
|
552
|
+
|