bio-samtools 0.4.1 → 0.4.2

Sign up to get free protection for your applications and to get access to all the features.
Files changed (74) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +60 -6
  3. data/doc/Bio.html +171 -0
  4. data/doc/Bio/DB.html +163 -0
  5. data/doc/Bio/DB/Alignment.html +780 -0
  6. data/doc/Bio/DB/SAM.html +1241 -0
  7. data/doc/Bio/DB/SAM/Library.html +217 -0
  8. data/doc/Bio/DB/SAM/Tools.html +331 -0
  9. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
  10. data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
  11. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
  12. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
  13. data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
  14. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
  15. data/doc/Bio/DB/SAMException.html +205 -0
  16. data/doc/Bio/DB/Tag.html +254 -0
  17. data/doc/LICENSE_txt.html +881 -0
  18. data/doc/LibC.html +153 -0
  19. data/doc/Pileup.html +571 -0
  20. data/doc/Vcf.html +473 -0
  21. data/doc/created.rid +10 -1
  22. data/doc/images/add.png +0 -0
  23. data/doc/images/brick.png +0 -0
  24. data/doc/images/brick_link.png +0 -0
  25. data/doc/images/bug.png +0 -0
  26. data/doc/images/bullet_black.png +0 -0
  27. data/doc/images/bullet_toggle_minus.png +0 -0
  28. data/doc/images/bullet_toggle_plus.png +0 -0
  29. data/doc/images/date.png +0 -0
  30. data/doc/images/delete.png +0 -0
  31. data/doc/images/find.png +0 -0
  32. data/doc/images/loadingAnimation.gif +0 -0
  33. data/doc/images/macFFBgHack.png +0 -0
  34. data/doc/images/package.png +0 -0
  35. data/doc/images/page_green.png +0 -0
  36. data/doc/images/page_white_text.png +0 -0
  37. data/doc/images/page_white_width.png +0 -0
  38. data/doc/images/plugin.png +0 -0
  39. data/doc/images/ruby.png +0 -0
  40. data/doc/images/tag_blue.png +0 -0
  41. data/doc/images/tag_green.png +0 -0
  42. data/doc/images/transparent.png +0 -0
  43. data/doc/images/wrench.png +0 -0
  44. data/doc/images/wrench_orange.png +0 -0
  45. data/doc/images/zoom.png +0 -0
  46. data/doc/index.html +109 -21
  47. data/doc/js/darkfish.js +153 -0
  48. data/doc/js/jquery.js +18 -0
  49. data/doc/js/navigation.js +142 -0
  50. data/doc/js/search.js +94 -0
  51. data/doc/js/search_index.js +1 -0
  52. data/doc/js/searcher.js +228 -0
  53. data/doc/lib/bio-samtools_rb.html +115 -0
  54. data/doc/lib/bio/db/sam/bam_rb.html +121 -0
  55. data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
  56. data/doc/lib/bio/db/sam/library_rb.html +115 -0
  57. data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
  58. data/doc/lib/bio/db/sam/sam_rb.html +121 -0
  59. data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
  60. data/doc/lib/bio/db/sam_rb.html +115 -0
  61. data/doc/rdoc.css +543 -0
  62. data/doc/table_of_contents.html +186 -0
  63. data/ext/Makefile-bioruby.patch +1 -1
  64. data/ext/Rakefile +8 -1
  65. data/ext/mkrf_conf.rb +8 -1
  66. data/lib/bio/db/sam.rb +140 -27
  67. data/lib/bio/db/sam/vcf.rb +0 -1
  68. data/test/basictest.rb +4 -4
  69. data/test/test_basic.rb +50 -34
  70. metadata +79 -25
  71. data/test/coverage.rb +0 -26
  72. data/test/coverage_plot.rb +0 -28
  73. data/test/feature.rb +0 -0
  74. data/test/test_pileup.rb +0 -68
data/doc/Bio/DB/SAMException.html ADDED
@@ -0,0 +1,205 @@
1
+ <!DOCTYPE html>
2
+
3
+ <html>
4
+ <head>
5
+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
+
7
+ <title>Class: Bio::DB::SAMException</title>
8
+
9
+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
10
+
11
+ <script type="text/javascript">
12
+ var rdoc_rel_prefix = "../../";
13
+ </script>
14
+
15
+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
16
+ <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
17
+ <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
18
+ <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
19
+ <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
20
+ <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
21
+
22
+
23
+ <body id="top" class="class">
24
+ <nav id="metadata">
25
+ <nav id="home-section" class="section">
26
+ <h3 class="section-header">
27
+ <a href="../../index.html">Home</a>
28
+ <a href="../../table_of_contents.html#classes">Classes</a>
29
+ <a href="../../table_of_contents.html#methods">Methods</a>
30
+ </h3>
31
+ </nav>
32
+
33
+
34
+ <nav id="search-section" class="section project-section" class="initially-hidden">
35
+ <form action="#" method="get" accept-charset="utf-8">
36
+ <h3 class="section-header">
37
+ <input type="text" name="search" placeholder="Search" id="search-field"
38
+ title="Type to search, Up and Down to navigate, Enter to load">
39
+ </h3>
40
+ </form>
41
+
42
+ <ul id="search-results" class="initially-hidden"></ul>
43
+ </nav>
44
+
45
+
46
+ <div id="file-metadata">
47
+ <nav id="file-list-section" class="section">
48
+ <h3 class="section-header">Defined In</h3>
49
+ <ul>
50
+ <li>lib/bio/db/sam.rb
51
+ </ul>
52
+ </nav>
53
+
54
+
55
+ </div>
56
+
57
+ <div id="class-metadata">
58
+
59
+ <nav id="parent-class-section" class="section">
60
+ <h3 class="section-header">Parent</h3>
61
+
62
+ <p class="link">RuntimeError
63
+
64
+ </nav>
65
+
66
+
67
+ <!-- Method Quickref -->
68
+ <nav id="method-list-section" class="section">
69
+ <h3 class="section-header">Methods</h3>
70
+
71
+ <ul class="link-list">
72
+
73
+ <li><a href="#method-c-new">::new</a>
74
+
75
+ </ul>
76
+ </nav>
77
+
78
+ </div>
79
+
80
+ <div id="project-metadata">
81
+ <nav id="fileindex-section" class="section project-section">
82
+ <h3 class="section-header">Pages</h3>
83
+
84
+ <ul>
85
+
86
+ <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
87
+
88
+ </ul>
89
+ </nav>
90
+
91
+ <nav id="classindex-section" class="section project-section">
92
+ <h3 class="section-header">Class and Module Index</h3>
93
+
94
+ <ul class="link-list">
95
+
96
+ <li><a href="../../Bio.html">Bio</a>
97
+
98
+ <li><a href="../../Bio/DB.html">Bio::DB</a>
99
+
100
+ <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
101
+
102
+ <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
103
+
104
+ <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
105
+
106
+ <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
107
+
108
+ <li><a href="../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
109
+
110
+ <li><a href="../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
111
+
112
+ <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
113
+
114
+ <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
115
+
116
+ <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
117
+
118
+ <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
119
+
120
+ <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
121
+
122
+ <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
123
+
124
+ <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
125
+
126
+ <li><a href="../../LibC.html">LibC</a>
127
+
128
+ <li><a href="../../Pileup.html">Pileup</a>
129
+
130
+ <li><a href="../../Vcf.html">Vcf</a>
131
+
132
+ </ul>
133
+ </nav>
134
+
135
+ </div>
136
+ </nav>
137
+
138
+ <div id="documentation">
139
+ <h1 class="class">class Bio::DB::SAMException</h1>
140
+
141
+ <div id="description" class="description">
142
+
143
+ </div><!-- description -->
144
+
145
+
146
+
147
+
148
+ <section id="5Buntitled-5D" class="documentation-section">
149
+
150
+
151
+
152
+
153
+
154
+
155
+
156
+
157
+ <!-- Methods -->
158
+
159
+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
160
+ <h3 class="section-header">Public Class Methods</h3>
161
+
162
+
163
+ <div id="method-c-new" class="method-detail ">
164
+
165
+ <div class="method-heading">
166
+ <span class="method-name">new</span><span
167
+ class="method-args">()</span>
168
+ <span class="method-click-advice">click to toggle source</span>
169
+ </div>
170
+
171
+
172
+ <div class="method-description">
173
+
174
+ <p>we can add further variables to give information of the excpetion</p>
175
+
176
+
177
+
178
+ <div class="method-source-code" id="new-source">
179
+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 638</span>
180
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>()
181
+
182
+ <span class="ruby-keyword">end</span></pre>
183
+ </div><!-- new-source -->
184
+
185
+ </div>
186
+
187
+
188
+
189
+
190
+ </div><!-- new-method -->
191
+
192
+
193
+ </section><!-- public-class-method-details -->
194
+
195
+ </section><!-- 5Buntitled-5D -->
196
+
197
+ </div><!-- documentation -->
198
+
199
+
200
+ <footer id="validator-badges">
201
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
202
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
203
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
204
+ </footer>
205
+
data/doc/Bio/DB/Tag.html ADDED
@@ -0,0 +1,254 @@
1
+ <!DOCTYPE html>
2
+
3
+ <html>
4
+ <head>
5
+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
+
7
+ <title>Class: Bio::DB::Tag</title>
8
+
9
+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
10
+
11
+ <script type="text/javascript">
12
+ var rdoc_rel_prefix = "../../";
13
+ </script>
14
+
15
+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
16
+ <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
17
+ <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
18
+ <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
19
+ <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
20
+ <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
21
+
22
+
23
+ <body id="top" class="class">
24
+ <nav id="metadata">
25
+ <nav id="home-section" class="section">
26
+ <h3 class="section-header">
27
+ <a href="../../index.html">Home</a>
28
+ <a href="../../table_of_contents.html#classes">Classes</a>
29
+ <a href="../../table_of_contents.html#methods">Methods</a>
30
+ </h3>
31
+ </nav>
32
+
33
+
34
+ <nav id="search-section" class="section project-section" class="initially-hidden">
35
+ <form action="#" method="get" accept-charset="utf-8">
36
+ <h3 class="section-header">
37
+ <input type="text" name="search" placeholder="Search" id="search-field"
38
+ title="Type to search, Up and Down to navigate, Enter to load">
39
+ </h3>
40
+ </form>
41
+
42
+ <ul id="search-results" class="initially-hidden"></ul>
43
+ </nav>
44
+
45
+
46
+ <div id="file-metadata">
47
+ <nav id="file-list-section" class="section">
48
+ <h3 class="section-header">Defined In</h3>
49
+ <ul>
50
+ <li>lib/bio/db/sam.rb
51
+ </ul>
52
+ </nav>
53
+
54
+
55
+ </div>
56
+
57
+ <div id="class-metadata">
58
+
59
+ <nav id="parent-class-section" class="section">
60
+ <h3 class="section-header">Parent</h3>
61
+
62
+ <p class="link">Object
63
+
64
+ </nav>
65
+
66
+
67
+ <!-- Method Quickref -->
68
+ <nav id="method-list-section" class="section">
69
+ <h3 class="section-header">Methods</h3>
70
+
71
+ <ul class="link-list">
72
+
73
+ <li><a href="#method-i-set">#set</a>
74
+
75
+ </ul>
76
+ </nav>
77
+
78
+ </div>
79
+
80
+ <div id="project-metadata">
81
+ <nav id="fileindex-section" class="section project-section">
82
+ <h3 class="section-header">Pages</h3>
83
+
84
+ <ul>
85
+
86
+ <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
87
+
88
+ </ul>
89
+ </nav>
90
+
91
+ <nav id="classindex-section" class="section project-section">
92
+ <h3 class="section-header">Class and Module Index</h3>
93
+
94
+ <ul class="link-list">
95
+
96
+ <li><a href="../../Bio.html">Bio</a>
97
+
98
+ <li><a href="../../Bio/DB.html">Bio::DB</a>
99
+
100
+ <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
101
+
102
+ <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
103
+
104
+ <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
105
+
106
+ <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
107
+
108
+ <li><a href="../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
109
+
110
+ <li><a href="../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
111
+
112
+ <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
113
+
114
+ <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
115
+
116
+ <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
117
+
118
+ <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
119
+
120
+ <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
121
+
122
+ <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
123
+
124
+ <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
125
+
126
+ <li><a href="../../LibC.html">LibC</a>
127
+
128
+ <li><a href="../../Pileup.html">Pileup</a>
129
+
130
+ <li><a href="../../Vcf.html">Vcf</a>
131
+
132
+ </ul>
133
+ </nav>
134
+
135
+ </div>
136
+ </nav>
137
+
138
+ <div id="documentation">
139
+ <h1 class="class">class Bio::DB::Tag</h1>
140
+
141
+ <div id="description" class="description">
142
+
143
+ </div><!-- description -->
144
+
145
+
146
+
147
+
148
+ <section id="5Buntitled-5D" class="documentation-section">
149
+
150
+
151
+
152
+
153
+
154
+
155
+
156
+ <!-- Attributes -->
157
+ <section id="attribute-method-details" class="method-section section">
158
+ <h3 class="section-header">Attributes</h3>
159
+
160
+
161
+ <div id="attribute-i-tag" class="method-detail">
162
+ <div class="method-heading attribute-method-heading">
163
+ <span class="method-name">tag</span><span
164
+ class="attribute-access-type">[RW]</span>
165
+ </div>
166
+
167
+ <div class="method-description">
168
+
169
+
170
+
171
+ </div>
172
+ </div>
173
+
174
+ <div id="attribute-i-type" class="method-detail">
175
+ <div class="method-heading attribute-method-heading">
176
+ <span class="method-name">type</span><span
177
+ class="attribute-access-type">[RW]</span>
178
+ </div>
179
+
180
+ <div class="method-description">
181
+
182
+
183
+
184
+ </div>
185
+ </div>
186
+
187
+ <div id="attribute-i-value" class="method-detail">
188
+ <div class="method-heading attribute-method-heading">
189
+ <span class="method-name">value</span><span
190
+ class="attribute-access-type">[RW]</span>
191
+ </div>
192
+
193
+ <div class="method-description">
194
+
195
+
196
+
197
+ </div>
198
+ </div>
199
+
200
+ </section><!-- attribute-method-details -->
201
+
202
+
203
+ <!-- Methods -->
204
+
205
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
206
+ <h3 class="section-header">Public Instance Methods</h3>
207
+
208
+
209
+ <div id="method-i-set" class="method-detail ">
210
+
211
+ <div class="method-heading">
212
+ <span class="method-name">set</span><span
213
+ class="method-args">(str)</span>
214
+ <span class="method-click-advice">click to toggle source</span>
215
+ </div>
216
+
217
+
218
+ <div class="method-description">
219
+
220
+
221
+
222
+
223
+
224
+ <div class="method-source-code" id="set-source">
225
+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 539</span>
226
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">str</span>)
227
+ <span class="ruby-identifier">v</span> = <span class="ruby-identifier">str</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
228
+ <span class="ruby-ivar">@tag</span> = <span class="ruby-identifier">v</span>[<span class="ruby-value">0</span>]
229
+ <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">v</span>[<span class="ruby-value">1</span>]
230
+ <span class="ruby-ivar">@value</span> = <span class="ruby-identifier">v</span>[<span class="ruby-value">2</span>]
231
+ <span class="ruby-keyword">end</span></pre>
232
+ </div><!-- set-source -->
233
+
234
+ </div>
235
+
236
+
237
+
238
+
239
+ </div><!-- set-method -->
240
+
241
+
242
+ </section><!-- public-instance-method-details -->
243
+
244
+ </section><!-- 5Buntitled-5D -->
245
+
246
+ </div><!-- documentation -->
247
+
248
+
249
+ <footer id="validator-badges">
250
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
251
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
252
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
253
+ </footer>
254
+