bio-samtools 0.4.1 → 0.4.2

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.
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/SAM/Tools/Bam1CoreT.html ADDED
@@ -0,0 +1,159 @@
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::SAM::Tools::Bam1CoreT</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/bam.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">FFI::Struct
63
+
64
+ </nav>
65
+
66
+
67
+
68
+ </div>
69
+
70
+ <div id="project-metadata">
71
+ <nav id="fileindex-section" class="section project-section">
72
+ <h3 class="section-header">Pages</h3>
73
+
74
+ <ul>
75
+
76
+ <li class="file"><a href="../../../../LICENSE_txt.html">LICENSE</a>
77
+
78
+ </ul>
79
+ </nav>
80
+
81
+ <nav id="classindex-section" class="section project-section">
82
+ <h3 class="section-header">Class and Module Index</h3>
83
+
84
+ <ul class="link-list">
85
+
86
+ <li><a href="../../../../Bio.html">Bio</a>
87
+
88
+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
89
+
90
+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
91
+
92
+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
93
+
94
+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
95
+
96
+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
97
+
98
+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
99
+
100
+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
101
+
102
+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
103
+
104
+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
105
+
106
+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
107
+
108
+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
109
+
110
+ <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
111
+
112
+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
113
+
114
+ <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
115
+
116
+ <li><a href="../../../../LibC.html">LibC</a>
117
+
118
+ <li><a href="../../../../Pileup.html">Pileup</a>
119
+
120
+ <li><a href="../../../../Vcf.html">Vcf</a>
121
+
122
+ </ul>
123
+ </nav>
124
+
125
+ </div>
126
+ </nav>
127
+
128
+ <div id="documentation">
129
+ <h1 class="class">class Bio::DB::SAM::Tools::Bam1CoreT</h1>
130
+
131
+ <div id="description" class="description">
132
+
133
+ </div><!-- description -->
134
+
135
+
136
+
137
+
138
+ <section id="5Buntitled-5D" class="documentation-section">
139
+
140
+
141
+
142
+
143
+
144
+
145
+
146
+
147
+ <!-- Methods -->
148
+
149
+ </section><!-- 5Buntitled-5D -->
150
+
151
+ </div><!-- documentation -->
152
+
153
+
154
+ <footer id="validator-badges">
155
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
156
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
157
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
158
+ </footer>
159
+
data/doc/Bio/DB/SAM/Tools/Bam1T.html ADDED
@@ -0,0 +1,220 @@
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::SAM::Tools::Bam1T</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/bam.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">FFI::Struct
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-qname">#qname</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::SAM::Tools::Bam1T</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
+ <!-- Constants -->
155
+ <section id="constants-list" class="section">
156
+ <h3 class="section-header">Constants</h3>
157
+ <dl>
158
+
159
+ <dt id="Bam_NT16_Rev_Table">Bam_NT16_Rev_Table
160
+
161
+ <dd class="description">
162
+
163
+
164
+ </dl>
165
+ </section>
166
+
167
+
168
+
169
+
170
+ <!-- Methods -->
171
+
172
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
173
+ <h3 class="section-header">Public Instance Methods</h3>
174
+
175
+
176
+ <div id="method-i-qname" class="method-detail ">
177
+
178
+ <div class="method-heading">
179
+ <span class="method-name">qname</span><span
180
+ class="method-args">()</span>
181
+ <span class="method-click-advice">click to toggle source</span>
182
+ </div>
183
+
184
+
185
+ <div class="method-description">
186
+
187
+
188
+
189
+
190
+
191
+ <div class="method-source-code" id="qname-source">
192
+ <pre><span class="ruby-comment"># File lib/bio/db/sam/bam.rb, line 63</span>
193
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">qname</span>
194
+ <span class="ruby-comment">#bam1_qname(b) ((char*)((b)-&gt;data))</span>
195
+ <span class="ruby-identifier">data</span> = <span class="ruby-keyword">self</span>[<span class="ruby-value">:data</span>]
196
+ <span class="ruby-identifier">data</span>.<span class="ruby-identifier">read_string</span>()
197
+ <span class="ruby-keyword">end</span></pre>
198
+ </div><!-- qname-source -->
199
+
200
+ </div>
201
+
202
+
203
+
204
+
205
+ </div><!-- qname-method -->
206
+
207
+
208
+ </section><!-- public-instance-method-details -->
209
+
210
+ </section><!-- 5Buntitled-5D -->
211
+
212
+ </div><!-- documentation -->
213
+
214
+
215
+ <footer id="validator-badges">
216
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
217
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
218
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
219
+ </footer>
220
+
data/doc/Bio/DB/SAM/Tools/BamHeaderT.html ADDED
@@ -0,0 +1,249 @@
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::SAM::Tools::BamHeaderT</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/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">FFI::Struct
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-text">#text</a>
74
+
75
+ <li><a href="#method-i-text-3D">#text=</a>
76
+
77
+ </ul>
78
+ </nav>
79
+
80
+ </div>
81
+
82
+ <div id="project-metadata">
83
+ <nav id="fileindex-section" class="section project-section">
84
+ <h3 class="section-header">Pages</h3>
85
+
86
+ <ul>
87
+
88
+ <li class="file"><a href="../../../../LICENSE_txt.html">LICENSE</a>
89
+
90
+ </ul>
91
+ </nav>
92
+
93
+ <nav id="classindex-section" class="section project-section">
94
+ <h3 class="section-header">Class and Module Index</h3>
95
+
96
+ <ul class="link-list">
97
+
98
+ <li><a href="../../../../Bio.html">Bio</a>
99
+
100
+ <li><a href="../../../../Bio/DB.html">Bio::DB</a>
101
+
102
+ <li><a href="../../../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
103
+
104
+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
105
+
106
+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
107
+
108
+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
109
+
110
+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
111
+
112
+ <li><a href="../../../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
113
+
114
+ <li><a href="../../../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
115
+
116
+ <li><a href="../../../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
117
+
118
+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
119
+
120
+ <li><a href="../../../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
121
+
122
+ <li><a href="../../../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
123
+
124
+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
125
+
126
+ <li><a href="../../../../Bio/DB/Tag.html">Bio::DB::Tag</a>
127
+
128
+ <li><a href="../../../../LibC.html">LibC</a>
129
+
130
+ <li><a href="../../../../Pileup.html">Pileup</a>
131
+
132
+ <li><a href="../../../../Vcf.html">Vcf</a>
133
+
134
+ </ul>
135
+ </nav>
136
+
137
+ </div>
138
+ </nav>
139
+
140
+ <div id="documentation">
141
+ <h1 class="class">class Bio::DB::SAM::Tools::BamHeaderT</h1>
142
+
143
+ <div id="description" class="description">
144
+
145
+ <p>typedef struct {</p>
146
+
147
+ <pre>int32_t n_targets;
148
+ char **target_name;
149
+ uint32_t *target_len;
150
+ void *dict, *hash, *rg2lib;
151
+ int l_text;
152
+ char *text;</pre>
153
+
154
+ <p>} bam_header_t;</p>
155
+
156
+ </div><!-- description -->
157
+
158
+
159
+
160
+
161
+ <section id="5Buntitled-5D" class="documentation-section">
162
+
163
+
164
+
165
+
166
+
167
+
168
+
169
+
170
+ <!-- Methods -->
171
+
172
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
173
+ <h3 class="section-header">Public Instance Methods</h3>
174
+
175
+
176
+ <div id="method-i-text" class="method-detail ">
177
+
178
+ <div class="method-heading">
179
+ <span class="method-name">text</span><span
180
+ class="method-args">()</span>
181
+ <span class="method-click-advice">click to toggle source</span>
182
+ </div>
183
+
184
+
185
+ <div class="method-description">
186
+
187
+
188
+
189
+
190
+
191
+ <div class="method-source-code" id="text-source">
192
+ <pre><span class="ruby-comment"># File lib/bio/db/sam/sam.rb, line 42</span>
193
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">text</span>
194
+ <span class="ruby-ivar">@text</span>.<span class="ruby-identifier">get_string</span>(<span class="ruby-value">0</span>)
195
+ <span class="ruby-keyword">end</span></pre>
196
+ </div><!-- text-source -->
197
+
198
+ </div>
199
+
200
+
201
+
202
+
203
+ </div><!-- text-method -->
204
+
205
+
206
+ <div id="method-i-text-3D" class="method-detail ">
207
+
208
+ <div class="method-heading">
209
+ <span class="method-name">text=</span><span
210
+ class="method-args">(str)</span>
211
+ <span class="method-click-advice">click to toggle source</span>
212
+ </div>
213
+
214
+
215
+ <div class="method-description">
216
+
217
+
218
+
219
+
220
+
221
+ <div class="method-source-code" id="text-3D-source">
222
+ <pre><span class="ruby-comment"># File lib/bio/db/sam/sam.rb, line 38</span>
223
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">text=</span>(<span class="ruby-identifier">str</span>)
224
+ <span class="ruby-ivar">@text</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">str</span>)
225
+ <span class="ruby-keyword">self</span>[<span class="ruby-value">:text</span>] = <span class="ruby-ivar">@text</span>
226
+ <span class="ruby-keyword">end</span></pre>
227
+ </div><!-- text-3D-source -->
228
+
229
+ </div>
230
+
231
+
232
+
233
+
234
+ </div><!-- text-3D-method -->
235
+
236
+
237
+ </section><!-- public-instance-method-details -->
238
+
239
+ </section><!-- 5Buntitled-5D -->
240
+
241
+ </div><!-- documentation -->
242
+
243
+
244
+ <footer id="validator-badges">
245
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
246
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
247
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
248
+ </footer>
249
+