bio-samtools 0.6.2 → 2.0.3

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 (160) hide show
  1. checksums.yaml +4 -4
  2. data/Gemfile +3 -2
  3. data/README.md +4 -7
  4. data/VERSION +1 -1
  5. data/bio-samtools.gemspec +47 -105
  6. data/doc/Bio.html +68 -131
  7. data/doc/Bio/DB.html +51 -111
  8. data/doc/Bio/DB/Alignment.html +135 -363
  9. data/doc/Bio/DB/Pileup.html +183 -170
  10. data/doc/Bio/DB/SAM.html +1396 -820
  11. data/doc/Bio/DB/SAM/Library.html +73 -123
  12. data/doc/Bio/DB/SAM/Tools.html +51 -273
  13. data/doc/Bio/DB/Tag.html +78 -124
  14. data/doc/Bio/DB/Vcf.html +111 -147
  15. data/doc/LICENSE_txt.html +113 -148
  16. data/doc/created.rid +9 -10
  17. data/doc/fonts.css +167 -0
  18. data/doc/fonts/Lato-Light.ttf +0 -0
  19. data/doc/fonts/Lato-LightItalic.ttf +0 -0
  20. data/doc/fonts/Lato-Regular.ttf +0 -0
  21. data/doc/fonts/Lato-RegularItalic.ttf +0 -0
  22. data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
  23. data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
  24. data/doc/images/add.png +0 -0
  25. data/doc/images/arrow_up.png +0 -0
  26. data/doc/images/delete.png +0 -0
  27. data/doc/images/tag_blue.png +0 -0
  28. data/doc/index.html +48 -54
  29. data/doc/js/darkfish.js +9 -22
  30. data/doc/js/search.js +20 -5
  31. data/doc/js/search_index.js +1 -1
  32. data/doc/rdoc.css +255 -218
  33. data/doc/table_of_contents.html +256 -137
  34. data/ext/Rakefile +57 -0
  35. data/lib/bio-samtools.rb +7 -2
  36. data/lib/bio/BIOExtensions.rb +89 -0
  37. data/lib/bio/db/alignment.rb +59 -0
  38. data/lib/bio/db/fastadb.rb +255 -0
  39. data/lib/bio/db/pileup.rb +221 -172
  40. data/lib/bio/db/sam.rb +639 -589
  41. data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
  42. data/lib/bio/db/vcf.rb +69 -68
  43. data/test/.gitignore +1 -0
  44. data/test/{test_basic.rb → old_test_basic.rb} +33 -1
  45. data/test/samples/small/dupes.bam +0 -0
  46. data/test/samples/small/dupes.sam +274 -0
  47. data/test/samples/small/map_for_reheader.sam +8 -0
  48. data/test/samples/small/map_to_merge1.bam +0 -0
  49. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  50. data/test/samples/small/map_to_merge1.sam +8 -0
  51. data/test/samples/small/map_to_merge2.bam +0 -0
  52. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  53. data/test/samples/small/map_to_merge2.sam +8 -0
  54. data/test/samples/small/no_md.sam +8 -0
  55. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  56. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  57. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  58. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  59. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  60. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  61. data/test/samples/small/test_cov.svg +273 -0
  62. data/test/samples/small/testu.bam.bai +0 -0
  63. data/test/svg +133 -0
  64. data/test/test_pileup.rb +84 -0
  65. data/test/test_sam.rb +331 -0
  66. data/test/test_vcf.rb +11 -0
  67. data/{doc → tutorial}/tutorial.html +0 -0
  68. data/{doc → tutorial}/tutorial.pdf +0 -0
  69. metadata +56 -114
  70. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
  71. data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
  72. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
  73. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
  74. data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
  75. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
  76. data/doc/Bio/DB/SAMException.html +0 -205
  77. data/doc/LibC.html +0 -155
  78. data/doc/Pileup.html +0 -571
  79. data/doc/Vcf.html +0 -473
  80. data/doc/basic_styles.css +0 -31
  81. data/doc/classes/Bio.html +0 -139
  82. data/doc/classes/Bio/DB.html +0 -137
  83. data/doc/classes/Bio/DB/Alignment.html +0 -441
  84. data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
  85. data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
  86. data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
  87. data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
  88. data/doc/classes/Bio/DB/SAM.html +0 -510
  89. data/doc/classes/Bio/DB/SAM/Library.html +0 -135
  90. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
  91. data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
  92. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
  93. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
  94. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
  95. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
  96. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
  97. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
  98. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
  99. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
  100. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
  101. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
  102. data/doc/classes/Bio/DB/SAMException.html +0 -140
  103. data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
  104. data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
  105. data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
  106. data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
  107. data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
  108. data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
  109. data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
  110. data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
  111. data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
  112. data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
  113. data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
  114. data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
  115. data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
  116. data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
  117. data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
  118. data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
  119. data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
  120. data/doc/classes/Bio/DB/Tag.html +0 -160
  121. data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
  122. data/doc/classes/LibC.html +0 -105
  123. data/doc/classes/Pileup.html +0 -374
  124. data/doc/classes/Pileup.src/M000001.html +0 -34
  125. data/doc/classes/Pileup.src/M000002.html +0 -21
  126. data/doc/classes/Pileup.src/M000003.html +0 -21
  127. data/doc/classes/Pileup.src/M000004.html +0 -21
  128. data/doc/classes/Pileup.src/M000005.html +0 -31
  129. data/doc/files/lib/bio-samtools_rb.html +0 -109
  130. data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
  131. data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
  132. data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
  133. data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
  134. data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
  135. data/doc/files/lib/bio/db/sam_rb.html +0 -111
  136. data/doc/fr_class_index.html +0 -43
  137. data/doc/fr_file_index.html +0 -33
  138. data/doc/fr_method_index.html +0 -58
  139. data/doc/lib/bio-samtools_rb.html +0 -115
  140. data/doc/lib/bio/db/pileup_rb.html +0 -171
  141. data/doc/lib/bio/db/sam/bam_rb.html +0 -121
  142. data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
  143. data/doc/lib/bio/db/sam/library_rb.html +0 -115
  144. data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
  145. data/doc/lib/bio/db/sam/sam_rb.html +0 -121
  146. data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
  147. data/doc/lib/bio/db/sam_rb.html +0 -115
  148. data/doc/lib/bio/db/vcf_rb.html +0 -124
  149. data/doc/rdoc-style.css +0 -208
  150. data/lib/bio/db/sam/bam.rb +0 -210
  151. data/lib/bio/db/sam/sam.rb +0 -86
  152. data/test/samples/pipe_char/test.bam +0 -0
  153. data/test/samples/pipe_char/test.bam.bai +0 -0
  154. data/test/samples/pipe_char/test.tam +0 -10
  155. data/test/samples/pipe_char/test_chr.fasta +0 -1000
  156. data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
  157. data/test/samples/small/test +0 -0
  158. data/test/samples/small/test.bam +0 -0
  159. data/test/samples/small/test.fa +0 -20
  160. data/test/samples/small/test.fai +0 -0
data/doc/Bio/DB/SAM.html CHANGED
@@ -2,181 +2,151 @@
2
2
 
3
3
  <html>
4
4
  <head>
5
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
5
+ <meta charset="UTF-8">
6
6
 
7
7
  <title>class Bio::DB::Sam - Pileup</title>
8
8
 
9
- <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
9
+ <link href="../../fonts.css" rel="stylesheet">
10
+ <link href="../../rdoc.css" rel="stylesheet">
10
11
 
11
12
  <script type="text/javascript">
12
13
  var rdoc_rel_prefix = "../../";
13
14
  </script>
14
15
 
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>
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>
21
22
 
22
23
 
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>
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>
28
34
  <a href="../../table_of_contents.html#classes">Classes</a>
29
35
  <a href="../../table_of_contents.html#methods">Methods</a>
30
- </h3>
31
- </nav>
32
-
36
+ </div>
37
+ </div>
33
38
 
34
- <nav id="search-section" class="section project-section" class="initially-hidden">
39
+ <div id="search-section" role="search" class="project-section initially-hidden">
35
40
  <form action="#" method="get" accept-charset="utf-8">
36
- <h3 class="section-header">
37
- <input type="text" name="search" placeholder="Search" id="search-field"
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"
38
45
  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
-
46
+ </div>
45
47
 
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>
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
53
 
54
-
55
54
  </div>
56
55
 
56
+
57
+
57
58
  <div id="class-metadata">
58
59
 
59
- <nav id="parent-class-section" class="section">
60
- <h3 class="section-header">Parent</h3>
60
+ <div id="parent-class-section" class="nav-section">
61
+ <h3>Parent</h3>
62
+
61
63
 
62
64
  <p class="link">Object
63
65
 
64
- </nav>
66
+ </div>
65
67
 
66
68
 
69
+
67
70
  <!-- Method Quickref -->
68
- <nav id="method-list-section" class="section">
69
- <h3 class="section-header">Methods</h3>
71
+ <div id="method-list-section" class="nav-section">
72
+ <h3>Methods</h3>
70
73
 
71
- <ul class="link-list">
74
+ <ul class="link-list" role="directory">
72
75
 
73
- <li><a href="#method-c-finalize">::finalize</a>
76
+ <li ><a href="#method-c-docs">::docs</a>
74
77
 
75
- <li><a href="#method-c-merge">::merge</a>
78
+ <li ><a href="#method-c-new">::new</a>
76
79
 
77
- <li><a href="#method-c-new">::new</a>
80
+ <li ><a href="#method-i-average_coverage">#average_coverage</a>
78
81
 
79
- <li><a href="#method-i-average_coverage">#average_coverage</a>
82
+ <li ><a href="#method-i-calmd">#calmd</a>
80
83
 
81
- <li><a href="#method-i-chromosome_coverage">#chromosome_coverage</a>
84
+ <li ><a href="#method-i-cat">#cat</a>
82
85
 
83
- <li><a href="#method-i-close">#close</a>
86
+ <li ><a href="#method-i-chromosome_coverage">#chromosome_coverage</a>
84
87
 
85
- <li><a href="#method-i-deprecated_pileup">#deprecated_pileup</a>
88
+ <li ><a href="#method-i-depth">#depth</a>
86
89
 
87
- <li><a href="#method-i-each_reference">#each_reference</a>
90
+ <li ><a href="#method-i-faidx">#faidx</a>
88
91
 
89
- <li><a href="#method-i-fetch">#fetch</a>
92
+ <li ><a href="#method-i-fetch">#fetch</a>
90
93
 
91
- <li><a href="#method-i-fetch_reference">#fetch_reference</a>
94
+ <li ><a href="#method-i-fetch_reference">#fetch_reference</a>
92
95
 
93
- <li><a href="#method-i-fetch_with_function">#fetch_with_function</a>
96
+ <li ><a href="#method-i-fetch_with_function">#fetch_with_function</a>
94
97
 
95
- <li><a href="#method-i-index_stats">#index_stats</a>
98
+ <li ><a href="#method-i-fix_mates">#fix_mates</a>
96
99
 
97
- <li><a href="#method-i-load_index">#load_index</a>
100
+ <li ><a href="#method-i-fixmate">#fixmate</a>
98
101
 
99
- <li><a href="#method-i-load_reference">#load_reference</a>
102
+ <li ><a href="#method-i-flag_stats">#flag_stats</a>
100
103
 
101
- <li><a href="#method-i-mpileup">#mpileup</a>
104
+ <li ><a href="#method-i-flagstat">#flagstat</a>
102
105
 
103
- <li><a href="#method-i-mpileup_plus">#mpileup_plus</a>
106
+ <li ><a href="#method-i-idxstats">#idxstats</a>
104
107
 
105
- <li><a href="#method-i-open">#open</a>
108
+ <li ><a href="#method-i-index">#index</a>
106
109
 
107
- <li><a href="#method-i-query_string">#query_string</a>
110
+ <li ><a href="#method-i-index_stats">#index_stats</a>
108
111
 
109
- <li><a href="#method-i-to_s">#to_s</a>
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>
110
135
 
111
136
  </ul>
112
- </nav>
113
-
114
- </div>
115
-
116
- <div id="project-metadata">
117
- <nav id="fileindex-section" class="section project-section">
118
- <h3 class="section-header">Pages</h3>
119
-
120
- <ul>
121
-
122
- <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
123
-
124
- </ul>
125
- </nav>
126
-
127
- <nav id="classindex-section" class="section project-section">
128
- <h3 class="section-header">Class and Module Index</h3>
129
-
130
- <ul class="link-list">
131
-
132
- <li><a href="../../Bio.html">Bio</a>
133
-
134
- <li><a href="../../Bio/DB.html">Bio::DB</a>
135
-
136
- <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
137
-
138
- <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
139
-
140
- <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
141
-
142
- <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
143
-
144
- <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
145
-
146
- <li><a href="../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
147
-
148
- <li><a href="../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
149
-
150
- <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
151
-
152
- <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
153
-
154
- <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
155
-
156
- <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
157
-
158
- <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
159
-
160
- <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
161
-
162
- <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
163
-
164
- <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
165
-
166
- <li><a href="../../LibC.html">LibC</a>
167
-
168
- </ul>
169
- </nav>
137
+ </div>
170
138
 
171
139
  </div>
172
140
  </nav>
173
141
 
174
- <div id="documentation">
175
- <h1 class="class">class Bio::DB::Sam</h1>
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>
176
146
 
177
- <div id="description" class="description">
147
+ <section class="description">
178
148
 
179
- </div><!-- description -->
149
+ </section>
180
150
 
181
151
 
182
152
 
@@ -189,15 +159,16 @@
189
159
 
190
160
 
191
161
 
192
- <!-- Attributes -->
193
- <section id="attribute-method-details" class="method-section section">
194
- <h3 class="section-header">Attributes</h3>
162
+ <section class="attribute-method-details" class="method-section">
163
+ <header>
164
+ <h3>Attributes</h3>
165
+ </header>
195
166
 
196
167
 
197
- <div id="attribute-i-sam_file" class="method-detail">
168
+ <div id="attribute-i-bam" class="method-detail">
198
169
  <div class="method-heading attribute-method-heading">
199
- <span class="method-name">sam_file</span><span
200
- class="attribute-access-type">[R]</span>
170
+ <span class="method-name">bam</span><span
171
+ class="attribute-access-type">[RW]</span>
201
172
  </div>
202
173
 
203
174
  <div class="method-description">
@@ -207,941 +178,1093 @@
207
178
  </div>
208
179
  </div>
209
180
 
210
- </section><!-- attribute-method-details -->
211
-
212
-
213
- <!-- Methods -->
214
-
215
- <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
216
- <h3 class="section-header">Public Class Methods</h3>
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>
217
186
 
218
-
219
- <div id="method-c-finalize" class="method-detail ">
187
+ <div class="method-description">
220
188
 
221
- <div class="method-heading">
222
- <span class="method-name">finalize</span><span
223
- class="method-args">(id)</span>
224
- <span class="method-click-advice">click to toggle source</span>
225
- </div>
226
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>
227
199
 
228
200
  <div class="method-description">
229
-
230
- <p>Destructor method that closes the file before letting the object be garbage
231
- collected.</p>
232
-
233
-
234
-
235
- <div class="method-source-code" id="finalize-source">
236
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 104</span>
237
- <span class="ruby-keyword">def</span> <span class="ruby-constant">Sam</span>.<span class="ruby-identifier">finalize</span>(<span class="ruby-identifier">id</span>)
238
- <span class="ruby-identifier">id</span>.<span class="ruby-identifier">close</span>()
239
- <span class="ruby-identifier">puts</span> <span class="ruby-node">&quot;Finalizing #{id} at #{Time.new}&quot;</span>
240
- <span class="ruby-keyword">end</span></pre>
241
- </div><!-- finalize-source -->
242
-
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>
243
211
  </div>
244
212
 
213
+ <div class="method-description">
214
+
215
+
245
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>
246
225
 
226
+ <div class="method-description">
227
+
228
+
247
229
 
248
- </div><!-- finalize-method -->
230
+ </div>
231
+ </div>
232
+
233
+ </section>
234
+
249
235
 
250
236
 
251
- <div id="method-c-merge" class="method-detail ">
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 ">
252
244
 
253
245
  <div class="method-heading">
254
- <span class="method-name">merge</span><span
255
- class="method-args">(files, merged_file, headers, add_RG, by_qname)</span>
246
+ <span class="method-name">docs</span><span
247
+ class="method-args">(program, command)</span>
248
+
256
249
  <span class="method-click-advice">click to toggle source</span>
250
+
257
251
  </div>
258
252
 
259
253
 
260
254
  <div class="method-description">
261
255
 
262
- <p>Merges n BAM files. This doesn’t require to create a <a
263
- href="SAM.html">SAM</a> object</p>
264
- <dl class="rdoc-list note-list"><dt>files
265
- <dd>
266
- <p>An array with the paths to the files.</p>
267
- </dd><dt>merged_file
268
- <dd>
269
- <p>The path to the merged file</p>
270
- </dd><dt>headers
271
- <dd>
272
- <p>The BAM file containing the header</p>
273
- </dd><dt>add_RG
274
- <dd>
275
- <p>If true, the RG tag is added (infered from the filenames)</p>
276
- </dd><dt>by_qname
277
- <dd>
278
- <p>If true, the bamfiles should by ordered by query name, if false, by
279
- coordinates.</p>
280
- </dd></dl>
256
+ <ul><li>
257
+ <p>program - one of &#39;samtools&#39; &#39;bcftools&#39;</p>
258
+ </li><li>
259
+ <p>command - one of the commands relevant to the program</p>
260
+ </li></ul>
281
261
 
282
-
283
262
 
284
- <div class="method-source-code" id="merge-source">
285
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 259</span>
286
- <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">files</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">add_RG</span>, <span class="ruby-identifier">by_qname</span>)
287
- <span class="ruby-identifier">strptrs</span> = []
288
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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-string">&quot;merge&quot;</span>)
289
- <span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
290
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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">file</span>)
291
- <span class="ruby-keyword">end</span>
292
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword">nil</span>
293
263
 
294
- <span class="ruby-comment"># Now load all the pointers into a native memory block</span>
295
- <span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
296
- <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
297
- <span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
298
- <span class="ruby-keyword">end</span>
299
- <span class="ruby-comment">#void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)</span>
300
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_merge_core</span>(<span class="ruby-identifier">by_qname</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">argv</span>, <span class="ruby-identifier">add_RG</span>)
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">&quot;program must be &#39;samtools&#39; or &#39;bcftools&#39;&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">not</span> [<span class="ruby-string">&#39;samtools&#39;</span>, <span class="ruby-string">&#39;bcftools&#39;</span>].<span class="ruby-identifier">include?</span> <span class="ruby-identifier">program</span>
269
+ <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{program} #{command}&quot;</span>
270
+ <span class="ruby-node">%x#{command}`</span>
301
271
  <span class="ruby-keyword">end</span></pre>
302
- </div><!-- merge-source -->
272
+ </div>
303
273
 
304
274
  </div>
305
275
 
306
276
 
307
277
 
308
278
 
309
- </div><!-- merge-method -->
279
+ </div>
310
280
 
311
281
 
312
282
  <div id="method-c-new" class="method-detail ">
313
283
 
314
284
  <div class="method-heading">
315
285
  <span class="method-name">new</span><span
316
- class="method-args">(optsa={})</span>
286
+ class="method-args">(args)</span>
287
+
317
288
  <span class="method-click-advice">click to toggle source</span>
289
+
318
290
  </div>
319
291
 
320
292
 
321
293
  <div class="method-description">
322
294
 
323
- <p>To make a new sam object. Initialize expects a hash optsa with the
324
- following elemets:</p>
325
- <dl class="rdoc-list note-list"><dt>fasta
326
- <dd>
327
- <p>The fasta file with the reference. (nil)</p>
328
- </dd><dt>bam
329
- <dd>
330
- <p>path to a binary <a href="SAM.html">SAM</a> file (nil)</p>
331
- </dd><dt>tam
332
- <dd>
333
- <p>path to a text <a href="SAM.html">SAM</a> file (nil)</p>
334
- </dd><dt>compressed
335
- <dd>
336
- <p>If the binary file is compressed (true)</p>
337
- </dd><dt>write
338
- <dd>
339
- <p>If the file is to be writen (false). Not supported yet.</p>
340
- </dd></dl>
341
-
342
- <p><strong>NOTE:</strong> you can’t use binary and text formats
343
- simultaneusly. To make queries, the file has to be a sorted binary. This
344
- function doesn’t actually open the file, it just prepares the object to
345
- be opened in a later stage.</p>
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
+
346
308
 
347
309
 
348
310
 
349
311
  <div class="method-source-code" id="new-source">
350
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 29</span>
351
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">optsa</span>={})
352
- <span class="ruby-identifier">opts</span> = { <span class="ruby-value">:fasta</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">nil</span>, <span class="ruby-value">:bam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">nil</span>,<span class="ruby-value">:tam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">nil</span>, <span class="ruby-value">:compressed</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">true</span>, <span class="ruby-value">:write</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">false</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">optsa</span>)
353
-
354
-
355
-
356
- <span class="ruby-ivar">@fasta_path</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:fasta</span>]
357
- <span class="ruby-ivar">@compressed</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:compressed</span>]
358
- <span class="ruby-ivar">@write</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:write</span>]
359
- <span class="ruby-identifier">bam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:bam</span>]
360
- <span class="ruby-identifier">tam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-value">:tam</span>]
361
-
362
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
363
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No alignment or reference file&quot;</span>
364
- <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
365
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Alignment has to be in either text or binary format, not both&quot;</span>
366
- <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
367
- <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword">true</span>
368
- <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">bam</span>
369
- <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span> <span class="ruby-keyword">then</span>
370
- <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">tam</span>
371
- <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword">false</span>
372
-
373
- <span class="ruby-keyword">end</span>
374
- <span class="ruby-ivar">@fasta_file</span> = <span class="ruby-keyword">nil</span>
375
- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
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">&#39;sam&#39;</span>,<span class="ruby-string">&#39;external&#39;</span>,<span class="ruby-string">&#39;samtools&#39;</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">&#39;sam&#39;</span>,<span class="ruby-string">&#39;external&#39;</span>,<span class="ruby-string">&#39;bcftools&#39;</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>)
376
320
 
377
- <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-value">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
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">&quot;Need Fasta and at least one BAM or SAM&quot;</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">&quot;File not found&quot;</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
+
378
326
  <span class="ruby-keyword">end</span></pre>
379
- </div><!-- new-source -->
327
+ </div>
380
328
 
381
329
  </div>
382
330
 
383
331
 
384
332
 
385
333
 
386
- </div><!-- new-method -->
334
+ </div>
387
335
 
388
336
 
389
- </section><!-- public-class-method-details -->
337
+ </section>
390
338
 
391
- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
392
- <h3 class="section-header">Public Instance Methods</h3>
339
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
340
+ <header>
341
+ <h3>Public Instance Methods</h3>
342
+ </header>
393
343
 
394
344
 
395
345
  <div id="method-i-average_coverage" class="method-detail ">
396
346
 
397
347
  <div class="method-heading">
398
348
  <span class="method-name">average_coverage</span><span
399
- class="method-args">(chromosome, qstart, len)</span>
349
+ class="method-args">(chr,start,length)</span>
350
+
400
351
  <span class="method-click-advice">click to toggle source</span>
352
+
401
353
  </div>
402
354
 
403
355
 
404
356
  <div class="method-description">
405
357
 
406
- <p>Returns the average coverage of a region in a bam file.</p>
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
+
407
367
 
408
368
 
409
369
 
410
370
  <div class="method-source-code" id="average_coverage-source">
411
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 143</span>
412
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">average_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
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
+
413
381
 
414
- <span class="ruby-comment">#reference = fetch_reference(chromosome, qstart,len)</span>
415
- <span class="ruby-comment"># len = reference.length if len &gt; reference.length</span>
382
+
383
+ </div>
416
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
+
417
396
 
418
- <span class="ruby-identifier">coverages</span> = <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
419
- <span class="ruby-identifier">total</span> = <span class="ruby-value">0</span>
420
- <span class="ruby-identifier">len</span>.<span class="ruby-identifier">times</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">total</span>= <span class="ruby-identifier">total</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span>] }
421
- <span class="ruby-identifier">avg_cov</span> = <span class="ruby-identifier">total</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">len</span>
422
- <span class="ruby-comment">#LibC.free reference</span>
423
- <span class="ruby-identifier">avg_cov</span>
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">&amp;</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">&quot;calmd&quot;</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">&quot; &quot;</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">&quot;@&quot;</span>,<span class="ruby-operator">&amp;</span><span class="ruby-identifier">block</span>)
424
435
  <span class="ruby-keyword">end</span></pre>
425
- </div><!-- average_coverage-source -->
436
+ </div>
426
437
 
427
438
  </div>
428
439
 
429
440
 
430
441
 
431
442
 
432
- </div><!-- average_coverage-method -->
443
+ </div>
433
444
 
434
445
 
435
- <div id="method-i-chromosome_coverage" class="method-detail ">
446
+ <div id="method-i-cat" class="method-detail ">
436
447
 
437
448
  <div class="method-heading">
438
- <span class="method-name">chromosome_coverage</span><span
439
- class="method-args">(chromosome, qstart, len)</span>
449
+ <span class="method-name">cat</span><span
450
+ class="method-args">(opts={})</span>
451
+
440
452
  <span class="method-click-advice">click to toggle source</span>
453
+
441
454
  </div>
442
455
 
443
456
 
444
457
  <div class="method-description">
445
458
 
446
- <p>Returns an array with the coverage at each possition in the queried region
447
- This is a simple average coverage just calculated with the first and last
448
- possition of the alignment, ignoring the gaps.</p>
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>
449
469
 
450
-
451
470
 
452
- <div class="method-source-code" id="chromosome_coverage-source">
453
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 160</span>
454
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
455
- <span class="ruby-comment"># reference = fetch_reference(chromosome, qstart,len)</span>
456
- <span class="ruby-comment"># len = reference.length if len &gt; reference.length</span>
457
- <span class="ruby-comment">#p qend.to_s + &quot;-&quot; + qstart.to_s + &quot;framesize &quot; + (qend - qstart).to_s</span>
458
- <span class="ruby-identifier">coverages</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">len</span>, <span class="ruby-value">0</span>)
459
-
460
- <span class="ruby-identifier">chr_cov_proc</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
461
- <span class="ruby-comment">#last = qstart + len</span>
462
- <span class="ruby-comment">#first = qstart</span>
463
- <span class="ruby-comment">#last = alignment.calend if last &gt; alignment.calend</span>
464
- <span class="ruby-comment">#first = alignment.pos if first &lt; alignment.pos</span>
465
- <span class="ruby-comment"># p first</span>
466
- <span class="ruby-identifier">last</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">calend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
467
- <span class="ruby-identifier">first</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
468
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">last</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">first</span>
469
- <span class="ruby-identifier">tmp</span> = <span class="ruby-identifier">last</span>
470
- <span class="ruby-identifier">last</span> = <span class="ruby-identifier">first</span>
471
- <span class="ruby-identifier">first</span> = <span class="ruby-identifier">last</span>
472
- <span class="ruby-keyword">end</span>
473
471
 
474
- <span class="ruby-comment"># STDERR.puts &quot;#{first} #{last}\n&quot;</span>
475
- <span class="ruby-identifier">first</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">last</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
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>)
476
478
 
477
- <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] = <span class="ruby-value">1</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] <span class="ruby-keyword">if</span> <span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">len</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
478
- }
479
- <span class="ruby-keyword">end</span>
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">&#39; &#39;</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">&quot;#{@samtools} cat #{options} -o #{out} #{bam_list}&quot;</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>)
480
488
 
481
- <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qstart</span><span class="ruby-operator">+</span><span class="ruby-identifier">len</span>, <span class="ruby-identifier">chr_cov_proc</span>)
482
- <span class="ruby-comment">#p coverages</span>
483
- <span class="ruby-identifier">coverages</span>
484
489
  <span class="ruby-keyword">end</span></pre>
485
- </div><!-- chromosome_coverage-source -->
490
+ </div>
486
491
 
487
492
  </div>
488
493
 
489
494
 
490
495
 
491
496
 
492
- </div><!-- chromosome_coverage-method -->
497
+ </div>
493
498
 
494
499
 
495
- <div id="method-i-close" class="method-detail ">
500
+ <div id="method-i-chromosome_coverage" class="method-detail ">
496
501
 
497
502
  <div class="method-heading">
498
- <span class="method-name">close</span><span
499
- class="method-args">()</span>
503
+ <span class="method-name">chromosome_coverage</span><span
504
+ class="method-args">(chr,start,length)</span>
505
+
500
506
  <span class="method-click-advice">click to toggle source</span>
507
+
501
508
  </div>
502
509
 
503
510
 
504
511
  <div class="method-description">
505
512
 
506
- <p>Closes the sam file and destroys the C pointers using the functions
507
- provided by libbam</p>
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
+
508
523
 
509
524
 
510
525
 
511
- <div class="method-source-code" id="close-source">
512
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 95</span>
513
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">close</span>()
514
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_destroy</span>(<span class="ruby-ivar">@fasta_index</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
515
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_destroy</span>(<span class="ruby-ivar">@sam_index</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
516
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samclose</span>(<span class="ruby-ivar">@sam_file</span>) <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam_file</span>.<span class="ruby-identifier">nil?</span>
517
- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
518
- <span class="ruby-ivar">@fasta_index</span> = <span class="ruby-keyword">nil</span>
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">&quot;#{chr}:#{start}-#{start + length}&quot;</span>
531
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mpileup</span>(<span class="ruby-value">:r</span> =<span class="ruby-operator">&gt;</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">&lt;&lt;</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>
519
535
  <span class="ruby-keyword">end</span></pre>
520
- </div><!-- close-source -->
536
+ </div>
521
537
 
522
538
  </div>
523
539
 
524
540
 
525
541
 
526
542
 
527
- </div><!-- close-method -->
543
+ </div>
528
544
 
529
545
 
530
- <div id="method-i-deprecated_pileup" class="method-detail ">
546
+ <div id="method-i-depth" class="method-detail ">
531
547
 
532
548
  <div class="method-heading">
533
- <span class="method-name">deprecated_pileup</span><span
534
- class="method-args">( cmd ) { |pileup| ... }</span>
549
+ <span class="method-name">depth</span><span
550
+ class="method-args">(opts={}) { |split(/\t/)| ... }</span>
551
+
535
552
  <span class="method-click-advice">click to toggle source</span>
553
+
536
554
  </div>
537
555
 
538
556
 
539
557
  <div class="method-description">
540
558
 
541
- <p>utility method that does not use the samtools API, it calls samtools
542
- directly as if on the command line and catches the output, to use this
543
- method you must have a version of samtools that supports the pileup command
544
- (&lt; 0.1.17) otherwise the command will fail. mpileup is the preferred
545
- method for getting pileups. With this method the sam object should be
546
- created as usual, but you need to pass this method a string of options for
547
- samtools you don’t need to provide the call to samtools pileup itself or
548
- -f &lt;fasta file&gt; or the bam file itself, these are taken from the sam
549
- object</p>
550
-
551
-
552
-
553
- <div class="method-source-code" id="deprecated_pileup-source">
554
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 473</span>
555
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">deprecated_pileup</span>( <span class="ruby-identifier">cmd</span> )
556
-
557
- <span class="ruby-identifier">system</span>(<span class="ruby-string">'samtools pileup &gt; /dev/null 2&gt;&amp;1'</span>)
558
- <span class="ruby-comment">##assumes samtools is in the path...</span>
559
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">$?</span>.<span class="ruby-identifier">exitstatus</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>
560
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">RuntimeError</span>, <span class="ruby-string">&quot;samtools is required on the path. A version of samtools with the pileup function is required&quot;</span>
561
- <span class="ruby-keyword">end</span>
562
-
563
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No BAMFile provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
564
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No FastA provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
565
-
566
- <span class="ruby-identifier">command</span> = <span class="ruby-string">'samtools pileup '</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">cmd</span> <span class="ruby-operator">+</span> <span class="ruby-node">&quot; -f #{@fasta_path}&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-node">&quot; #{@sam}&quot;</span>
567
-
568
- <span class="ruby-identifier">pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">command</span>)
569
- <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
570
- <span class="ruby-keyword">yield</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
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">&quot;depth&quot;</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>)
571
583
  <span class="ruby-keyword">end</span>
572
- <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>
584
+
573
585
  <span class="ruby-keyword">end</span></pre>
574
- </div><!-- deprecated_pileup-source -->
586
+ </div>
575
587
 
576
588
  </div>
577
589
 
578
590
 
579
591
 
580
592
 
581
- </div><!-- deprecated_pileup-method -->
593
+ </div>
582
594
 
583
595
 
584
- <div id="method-i-each_reference" class="method-detail ">
596
+ <div id="method-i-faidx" class="method-detail ">
585
597
 
586
598
  <div class="method-heading">
587
- <span class="method-name">each_reference</span><span
588
- class="method-args">() { |k, v| ... }</span>
599
+ <span class="method-name">faidx</span><span
600
+ class="method-args">(opts={})</span>
601
+
589
602
  <span class="method-click-advice">click to toggle source</span>
603
+
590
604
  </div>
591
605
 
592
606
 
593
607
  <div class="method-description">
594
608
 
595
- <p>yields each reference name and its length</p>
596
-
597
-
598
-
599
- <div class="method-source-code" id="each_reference-source">
600
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 535</span>
601
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">each_reference</span>
602
- <span class="ruby-identifier">refs</span> = <span class="ruby-identifier">index_stats</span>
603
- <span class="ruby-identifier">refs</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>
604
- <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span>[<span class="ruby-value">:length</span>]
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 &lt;ref.fasta&gt;.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">&gt;</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">&quot;#{@samtools} faidx #{@fasta}&quot;</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>)
605
635
  <span class="ruby-keyword">end</span>
606
636
  <span class="ruby-keyword">end</span></pre>
607
- </div><!-- each_reference-source -->
637
+ </div>
608
638
 
609
639
  </div>
610
640
 
611
641
 
612
642
 
613
643
 
614
- </div><!-- each_reference-method -->
644
+ </div>
615
645
 
616
646
 
617
647
  <div id="method-i-fetch" class="method-detail ">
618
648
 
619
649
  <div class="method-heading">
620
650
  <span class="method-name">fetch</span><span
621
- class="method-args">(chromosome, qstart, qend)</span>
651
+ class="method-args">(chr, start,stop, &block)</span>
652
+
622
653
  <span class="method-click-advice">click to toggle source</span>
654
+
623
655
  </div>
624
656
 
625
657
 
626
658
  <div class="method-description">
627
659
 
628
- <p>Returns an array of Alignments on a given region.</p>
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>&amp;block - the the block of code to execute</p>
669
+ </li></ul>
670
+
629
671
 
630
672
 
631
673
 
632
674
  <div class="method-source-code" id="fetch-source">
633
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 211</span>
634
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>)
635
- <span class="ruby-identifier">als</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
636
- <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
637
- <span class="ruby-identifier">als</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">clone</span>)
638
- <span class="ruby-value">0</span>
639
- <span class="ruby-keyword">end</span>
640
- <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">fetchAlignment</span>)
641
- <span class="ruby-identifier">als</span>
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">&amp;</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">&gt;</span> <span class="ruby-identifier">chr</span>,
679
+ <span class="ruby-value">:start</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">start</span>,
680
+ <span class="ruby-value">:stop</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-identifier">stop</span>,
681
+ <span class="ruby-operator">&amp;</span><span class="ruby-identifier">block</span>
682
+ )
642
683
  <span class="ruby-keyword">end</span></pre>
643
- </div><!-- fetch-source -->
684
+ </div>
644
685
 
645
686
  </div>
646
687
 
647
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
+
648
693
 
649
694
 
650
- </div><!-- fetch-method -->
695
+ </div>
651
696
 
652
697
 
653
698
  <div id="method-i-fetch_reference" class="method-detail ">
654
699
 
655
700
  <div class="method-heading">
656
701
  <span class="method-name">fetch_reference</span><span
657
- class="method-args">(chromosome, qstart,qend)</span>
702
+ class="method-args">(chr,start,stop, opts={:as_bio => false})</span>
703
+
658
704
  <span class="method-click-advice">click to toggle source</span>
705
+
659
706
  </div>
660
707
 
661
708
 
662
709
  <div class="method-description">
663
710
 
664
- <p>Returns the sequence for a given region.</p>
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
+
665
724
 
666
725
 
667
726
 
668
727
  <div class="method-source-code" id="fetch_reference-source">
669
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 193</span>
670
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch_reference</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
671
- <span class="ruby-identifier">load_reference</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
672
- <span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
673
- <span class="ruby-identifier">len</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
674
- <span class="ruby-identifier">reference</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_fetch</span>(<span class="ruby-ivar">@fasta_index</span>, <span class="ruby-identifier">query</span>, <span class="ruby-identifier">len</span>)
675
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Unable to get sequence for reference: &quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">query</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">reference</span>.<span class="ruby-identifier">nil?</span>
676
-
677
- <span class="ruby-identifier">reference</span>
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">&gt;</span> <span class="ruby-keyword">false</span>})
730
+ <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{@samtools} faidx #{@fasta} #{chr}:#{start}-#{stop}&quot;</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">&quot;&quot;</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">/^&gt;/</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">&quot;#{chr}:#{start}-#{stop}&quot;</span>)
737
+ <span class="ruby-keyword">end</span>
738
+ <span class="ruby-identifier">seq</span>
678
739
  <span class="ruby-keyword">end</span></pre>
679
- </div><!-- fetch_reference-source -->
740
+ </div>
680
741
 
681
742
  </div>
682
743
 
683
744
 
684
745
 
685
746
 
686
- </div><!-- fetch_reference-method -->
747
+ </div>
687
748
 
688
749
 
689
- <div id="method-i-fetch_with_function" class="method-detail ">
750
+ <div id="method-i-fetch_with_function" class="method-detail method-alias">
690
751
 
691
752
  <div class="method-heading">
692
753
  <span class="method-name">fetch_with_function</span><span
693
- class="method-args">(chromosome, qstart, qend, function)</span>
694
- <span class="method-click-advice">click to toggle source</span>
754
+ class="method-args">(chr, start,stop, &block)</span>
755
+
695
756
  </div>
696
757
 
697
758
 
698
759
  <div class="method-description">
699
760
 
700
- <p>Executes a function on each <a href="Alignment.html">Alignment</a> inside
701
- the queried region of the chromosome. The chromosome can be either the
702
- textual name or a FixNum with the internal index. However, you need to get
703
- the internal index with the provided API, otherwise the pointer is outside
704
- the scope of the C library. Returns the count of alignments in the region.
705
- WARNING: Accepts an index already parsed by the library. It fails when you
706
- use your own FixNum (FFI-bug?)</p>
707
-
708
-
709
-
710
- <div class="method-source-code" id="fetch_with_function-source">
711
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 226</span>
712
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">function</span>)
713
- <span class="ruby-identifier">load_index</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
714
- <span class="ruby-identifier">chr</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
715
- <span class="ruby-identifier">beg</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
716
- <span class="ruby-identifier">last</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-value">:int</span>
717
- <span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
718
- <span class="ruby-identifier">qpointer</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">query</span>)
719
- <span class="ruby-identifier">header</span> = <span class="ruby-ivar">@sam_file</span>[<span class="ruby-value">:header</span>]
720
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_parse_region</span>(<span class="ruby-identifier">header</span>,<span class="ruby-identifier">qpointer</span>, <span class="ruby-identifier">chr</span>, <span class="ruby-identifier">beg</span>, <span class="ruby-identifier">last</span>)
721
- <span class="ruby-comment">#raise SAMException.new(), &quot;invalid query: &quot; + query if(chr.read_int &lt; 0)</span>
722
- <span class="ruby-identifier">count</span> = <span class="ruby-value">0</span>;
723
-
724
- <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">data</span><span class="ruby-operator">|</span>
725
- <span class="ruby-identifier">alignment</span> = <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">new</span>
726
- <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
727
- <span class="ruby-identifier">function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">alignment</span>)
728
- <span class="ruby-identifier">count</span> = <span class="ruby-identifier">count</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
729
- <span class="ruby-value">0</span>
730
- <span class="ruby-keyword">end</span>
731
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_fetch</span>(<span class="ruby-ivar">@sam_file</span>[<span class="ruby-value">:x</span>][<span class="ruby-value">:bam</span>], <span class="ruby-ivar">@sam_index</span>,<span class="ruby-identifier">chr</span>.<span class="ruby-identifier">read_int</span>,<span class="ruby-identifier">beg</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-identifier">last</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-keyword">nil</span>, <span class="ruby-identifier">fetchAlignment</span>)
732
- <span class="ruby-comment">#LibC.free chr</span>
733
- <span class="ruby-comment">#LibC.free beg</span>
734
- <span class="ruby-comment">#LibC.free last</span>
735
- <span class="ruby-comment">#LibC.free qpointer</span>
736
- <span class="ruby-identifier">count</span>
737
- <span class="ruby-keyword">end</span></pre>
738
- </div><!-- fetch_with_function-source -->
761
+
762
+
763
+
764
+
739
765
 
740
766
  </div>
741
767
 
742
768
 
743
769
 
744
770
 
745
- </div><!-- fetch_with_function-method -->
771
+ <div class="aliases">
772
+ Alias for: <a href="Sam.html#method-i-fetch">fetch</a>
773
+ </div>
774
+
775
+ </div>
746
776
 
747
777
 
748
- <div id="method-i-index_stats" class="method-detail ">
778
+ <div id="method-i-fix_mates" class="method-detail ">
749
779
 
750
780
  <div class="method-heading">
751
- <span class="method-name">index_stats</span><span
752
- class="method-args">()</span>
781
+ <span class="method-name">fix_mates</span><span
782
+ class="method-args">(opts={})</span>
783
+
753
784
  <span class="method-click-advice">click to toggle source</span>
785
+
754
786
  </div>
755
787
 
756
788
 
757
789
  <div class="method-description">
758
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>
759
798
 
760
799
 
761
800
 
762
801
 
763
- <div class="method-source-code" id="index_stats-source">
764
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 494</span>
765
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">index_stats</span>
766
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No BAMFile provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
767
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No FastA provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
768
- <span class="ruby-identifier">strptrs</span> = []
769
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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-string">&quot;idxstats&quot;</span>)
770
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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-ivar">@sam</span>)
771
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword">nil</span>
772
-
773
- <span class="ruby-comment"># Now load all the pointers into a native memory block</span>
774
- <span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
775
- <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
776
- <span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
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=&gt;nil})</span>
806
+ <span class="ruby-identifier">remove_reads</span> = <span class="ruby-string">&quot;&quot;</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">&quot;-r&quot;</span>
777
809
  <span class="ruby-keyword">end</span>
778
-
779
- <span class="ruby-identifier">index_stats</span> = {}
780
-
781
- <span class="ruby-identifier">old_stdout</span> = <span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">clone</span>
782
- <span class="ruby-identifier">read_pipe</span>, <span class="ruby-identifier">write_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">pipe</span>()
783
- <span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">write_pipe</span>)
784
-
785
- <span class="ruby-comment">#int bam_idxstats(int argc, char *argv[])</span>
786
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_idxstats</span>(<span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span>,<span class="ruby-identifier">argv</span>)
787
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">fork</span>
788
- <span class="ruby-identifier">write_pipe</span>.<span class="ruby-identifier">close</span>
789
- <span class="ruby-constant">STDOUT</span>.<span class="ruby-identifier">reopen</span>(<span class="ruby-identifier">old_stdout</span>) <span class="ruby-comment">#beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
790
- <span class="ruby-keyword">begin</span>
791
-
792
- <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">readline</span> <span class="ruby-comment">#TAB delimited with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads.</span>
793
- <span class="ruby-identifier">info</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r\t/</span>)
794
- <span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">info</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">4</span>
795
- <span class="ruby-identifier">index_stats</span>[ <span class="ruby-identifier">info</span>[<span class="ruby-value">0</span>] ] = {<span class="ruby-value">:length</span> =<span class="ruby-operator">&gt;</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">&gt;</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">&gt;</span> <span class="ruby-identifier">info</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span> }
796
- <span class="ruby-keyword">end</span>
797
- <span class="ruby-keyword">rescue</span> <span class="ruby-constant">EOFError</span>
798
- <span class="ruby-identifier">read_pipe</span>.<span class="ruby-identifier">close</span>
799
- <span class="ruby-constant">Process</span>.<span class="ruby-identifier">wait</span>
800
- <span class="ruby-keyword">end</span>
801
- <span class="ruby-keyword">end</span> <span class="ruby-comment">#fork</span>
802
- <span class="ruby-identifier">index_stats</span>
810
+ <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{@samtools} fixmate #{remove_reads} #{@bam} #{opts[:out_bam]}&quot;</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>)
803
814
  <span class="ruby-keyword">end</span></pre>
804
- </div><!-- index_stats-source -->
815
+ </div>
805
816
 
806
817
  </div>
807
818
 
808
819
 
820
+ <div class="aliases">
821
+ Also aliased as: <a href="Sam.html#method-i-fixmate">fixmate</a>
822
+ </div>
823
+
809
824
 
810
825
 
811
- </div><!-- index_stats-method -->
826
+ </div>
812
827
 
813
828
 
814
- <div id="method-i-load_index" class="method-detail ">
829
+ <div id="method-i-fixmate" class="method-detail method-alias">
815
830
 
816
831
  <div class="method-heading">
817
- <span class="method-name">load_index</span><span
818
- class="method-args">()</span>
819
- <span class="method-click-advice">click to toggle source</span>
832
+ <span class="method-name">fixmate</span><span
833
+ class="method-args">(opts={})</span>
834
+
820
835
  </div>
821
836
 
822
837
 
823
838
  <div class="method-description">
824
839
 
825
- <p>Loads the bam index to be used for fetching. If the index doesn’t exists
826
- the index is built provided that the user has writing access to the folder
827
- where the BAM file is located. If the creation of the file fails a <a
828
- href="SAMException.html">SAMException</a> is thrown. If the index
829
- doesn’t exist, loading it will take more time. It is suggested to
830
- generate the index separatedly if the bam file sits on a server where the
831
- executing user may not have writing permissions in the server.</p>
832
-
833
-
834
-
835
- <div class="method-source-code" id="load_index-source">
836
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 114</span>
837
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">load_index</span>()
838
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Indexes are only supported by BAM files, please use samtools to convert your SAM file&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@binary</span>
839
- <span class="ruby-ivar">@sam_index</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
840
- <span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
841
- <span class="ruby-identifier">p</span> <span class="ruby-string">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
842
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_build</span>(<span class="ruby-ivar">@sam</span>)
843
- <span class="ruby-ivar">@sam_index</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
844
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Unable to generate bam index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
845
- <span class="ruby-keyword">end</span>
846
- <span class="ruby-keyword">end</span></pre>
847
- </div><!-- load_index-source -->
840
+
841
+
842
+
843
+
848
844
 
849
845
  </div>
850
846
 
851
847
 
852
848
 
853
849
 
854
- </div><!-- load_index-method -->
850
+ <div class="aliases">
851
+ Alias for: <a href="Sam.html#method-i-fix_mates">fix_mates</a>
852
+ </div>
853
+
854
+ </div>
855
855
 
856
856
 
857
- <div id="method-i-load_reference" class="method-detail ">
857
+ <div id="method-i-flag_stats" class="method-detail ">
858
858
 
859
859
  <div class="method-heading">
860
- <span class="method-name">load_reference</span><span
861
- class="method-args">()</span>
860
+ <span class="method-name">flag_stats</span><span
861
+ class="method-args">(opts={})</span>
862
+
862
863
  <span class="method-click-advice">click to toggle source</span>
864
+
863
865
  </div>
864
866
 
865
867
 
866
868
  <div class="method-description">
867
869
 
868
- <p>Loads the reference file to be able to query regions of it. This requires
869
- the fai index to exist in the same folder than the reference. If it
870
- doesn’t exisits, this functions attempts to generate it. If user
871
- doesn’t have writing permissions on the folder, or the creation of the
872
- fai fails for any reason, a <a href="SAMException.html">SAMException</a> is
873
- thrown.</p>
870
+ <p>generate simple stats with regard to the number and pairing of reads mapped
871
+ to a reference</p>
874
872
 
875
-
876
873
 
877
- <div class="method-source-code" id="load_reference-source">
878
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 128</span>
879
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">load_reference</span>()
880
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No path for the refernce fasta file. &quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_path</span>.<span class="ruby-identifier">nil?</span>
881
-
882
- <span class="ruby-ivar">@fasta_index</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
883
-
884
- <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
885
- <span class="ruby-identifier">p</span> <span class="ruby-string">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
886
- <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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_build</span>(<span class="ruby-ivar">@fasta_path</span>)
887
- <span class="ruby-ivar">@fasta_index</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
888
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Unable to generate fasta index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
889
- <span class="ruby-keyword">end</span>
890
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">&quot;flagstat&quot;</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">&lt;&lt;</span> <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>}
884
+ <span class="ruby-identifier">strings</span>
891
885
  <span class="ruby-keyword">end</span></pre>
892
- </div><!-- load_reference-source -->
886
+ </div>
893
887
 
894
888
  </div>
895
889
 
896
890
 
891
+ <div class="aliases">
892
+ Also aliased as: <a href="Sam.html#method-i-flagstat">flagstat</a>
893
+ </div>
894
+
897
895
 
898
896
 
899
- </div><!-- load_reference-method -->
897
+ </div>
900
898
 
901
899
 
902
- <div id="method-i-mpileup" class="method-detail ">
900
+ <div id="method-i-flagstat" class="method-detail method-alias">
903
901
 
904
902
  <div class="method-heading">
905
- <span class="method-name">mpileup</span><span
906
- class="method-args">( opts={}) { |pileup| ... }</span>
907
- <span class="method-click-advice">click to toggle source</span>
903
+ <span class="method-name">flagstat</span><span
904
+ class="method-args">(opts={})</span>
905
+
908
906
  </div>
909
907
 
910
908
 
911
909
  <div class="method-description">
912
910
 
913
- <p>calls the mpileup function, opts is a hash of options identical to the
914
- command line options for mpileup. is an iterator that yields a <a
915
- href="Pileup.html">Pileup</a> object for each postion the command line
916
- options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p) call
917
- the option as a symbol of the flag, eg -r for region is called :r =&gt;
918
- “some <a href="SAM.html">SAM</a> compatible region” eg bam.mpileup(:r
919
- =&gt; “chr1:1000-2000”, :q =&gt; 50) gets the bases with quality &gt;
920
- 50 on chr1 between 1000-5000</p>
911
+
912
+
921
913
 
922
914
 
923
915
 
924
- <div class="method-source-code" id="mpileup-source">
925
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 281</span>
926
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup</span>( <span class="ruby-identifier">opts</span>={})
927
-
928
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No BAMFile provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
929
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No FastA provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
930
- <span class="ruby-comment">#long option form to short samtools form..</span>
931
- <span class="ruby-identifier">long_opts</span> = {
932
- <span class="ruby-value">:region</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:r</span>,
933
- <span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:six</span>,
934
- <span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:A</span>,
935
- <span class="ruby-value">:no_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:B</span>,
936
- <span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:C</span>,
937
- <span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:d</span>,
938
- <span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:E</span>,
939
- <span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:G</span>,
940
- <span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:l</span>,
941
- <span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:M</span>,
942
- <span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:R</span>,
943
- <span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:q</span>,
944
- <span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:Q</span>
945
- }
946
- <span class="ruby-comment">##convert any long_opts to short opts </span>
947
- <span class="ruby-identifier">temp_opts</span> = <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">dup</span>
948
- <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>
949
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
950
- <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>
951
- <span class="ruby-identifier">temp_opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
952
- <span class="ruby-keyword">end</span>
953
- <span class="ruby-keyword">end</span>
954
- <span class="ruby-identifier">opts</span> = <span class="ruby-identifier">temp_opts</span>
955
- <span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
956
- <span class="ruby-comment">##and also associated output options</span>
957
- [<span class="ruby-value">:g</span>, <span class="ruby-value">:u</span>, <span class="ruby-value">:e</span>, <span class="ruby-value">:h</span>, <span class="ruby-value">:I</span>, <span class="ruby-value">:L</span>, <span class="ruby-value">:o</span>, <span class="ruby-value">:p</span>].<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">x</span>) }
958
-
959
- <span class="ruby-identifier">sam_opts</span> = []
960
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(&quot;mpileup&quot;)</span>
961
- <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each</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>
962
- <span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">k</span>] <span class="ruby-comment">##dont bother unless the values provided are true.. </span>
963
- <span class="ruby-identifier">k</span> = <span class="ruby-string">'6'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">k</span> <span class="ruby-operator">==</span> <span class="ruby-value">:six</span>
964
- <span class="ruby-identifier">k</span> = <span class="ruby-string">'-'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span>
965
- <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">k</span> <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(k)</span>
966
- <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-keyword">unless</span> [<span class="ruby-string">&quot;-R&quot;</span>, <span class="ruby-string">&quot;-B&quot;</span>, <span class="ruby-string">&quot;-E&quot;</span>, <span class="ruby-string">&quot;-6&quot;</span>, <span class="ruby-string">&quot;-A&quot;</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">k</span>) <span class="ruby-comment">#these are just flags so don't pass a value... strptrs &lt;&lt; FFI::MemoryPointer.from_string(v.to_s)</span>
967
- <span class="ruby-keyword">end</span>
968
- <span class="ruby-identifier">sam_opts</span> = <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">+</span> [<span class="ruby-string">'-f'</span>, <span class="ruby-ivar">@fasta_path</span>, <span class="ruby-ivar">@sam</span>]
969
- <span class="ruby-identifier">sam_command</span> = <span class="ruby-node">&quot;#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2&gt; /dev/null&quot;</span>
970
-
971
- <span class="ruby-identifier">sam_pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">sam_command</span>)
972
- <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">gets</span>
973
- <span class="ruby-keyword">yield</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>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
974
- <span class="ruby-keyword">end</span>
975
- <span class="ruby-identifier">sam_pipe</span>.<span class="ruby-identifier">close</span>
976
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string('-f')</span>
977
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(@fasta_path)</span>
978
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(@sam)</span>
979
- <span class="ruby-comment">#strptrs &lt;&lt; nil</span>
980
-
981
- <span class="ruby-comment"># Now load all the pointers into a native memory block</span>
982
- <span class="ruby-comment">#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)</span>
983
- <span class="ruby-comment">#strptrs.each_with_index do |p, i|</span>
984
- <span class="ruby-comment"># argv[i].put_pointer(0, p)</span>
985
- <span class="ruby-comment">#end</span>
986
-
987
- <span class="ruby-comment">#old_stdout = STDOUT.clone</span>
988
- <span class="ruby-comment">#read_pipe, write_pipe = IO.pipe()</span>
989
- <span class="ruby-comment">#STDOUT.reopen(write_pipe)</span>
990
- <span class="ruby-comment">#int bam_mpileup(int argc, char *argv[])</span>
991
- <span class="ruby-comment"># Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)</span>
992
- <span class="ruby-comment">#if fork</span>
993
- <span class="ruby-comment"># write_pipe.close</span>
994
- <span class="ruby-comment"># STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
995
- <span class="ruby-comment"># begin</span>
996
- <span class="ruby-comment"># while line = read_pipe.readline</span>
997
- <span class="ruby-comment"># yield Pileup.new(line)</span>
998
- <span class="ruby-comment"># end</span>
999
- <span class="ruby-comment"># rescue EOFError</span>
1000
- <span class="ruby-comment"># read_pipe.close</span>
1001
- <span class="ruby-comment"># Process.wait</span>
1002
- <span class="ruby-comment"># end</span>
1003
- <span class="ruby-comment">#end</span>
1004
- <span class="ruby-keyword">end</span></pre>
1005
- </div><!-- mpileup-source -->
1006
-
1007
- </div>
1008
-
1009
-
1010
-
1011
-
1012
- </div><!-- mpileup-method -->
1013
-
1014
-
1015
- <div id="method-i-mpileup_plus" class="method-detail ">
1016
-
1017
- <div class="method-heading">
1018
- <span class="method-name">mpileup_plus</span><span
1019
- class="method-args">( opts ) { |vcf| ... }</span>
1020
- <span class="method-click-advice">click to toggle source</span>
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
+ &lt;aln.bam&gt;.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">&quot;#{@samtools} index #{@bam} #{opts[:out_index]}&quot;</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
+
1021
1004
  </div>
1022
1005
 
1023
1006
 
1024
1007
  <div class="method-description">
1025
1008
 
1026
- <p>experimental method that spawns a samtools mpileup | bcftools view process
1027
- and supports returning of pileup vcf</p>
1028
-
1029
- <pre>otherwise works like mpileup</pre>
1030
-
1031
-
1032
-
1033
- <div class="method-source-code" id="mpileup_plus-source">
1034
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 363</span>
1035
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">mpileup_plus</span>( <span class="ruby-identifier">opts</span> )
1036
-
1037
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No BAMFile provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword">and</span> <span class="ruby-ivar">@binary</span>
1038
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No FastA provided&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@fasta_path</span>
1039
- <span class="ruby-comment">#long option form to short samtools form..</span>
1040
- <span class="ruby-identifier">long_opts</span> = {
1041
- <span class="ruby-value">:region</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:r</span>,
1042
- <span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:six</span>,
1043
- <span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:A</span>,
1044
- <span class="ruby-value">:no_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:B</span>,
1045
- <span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:C</span>,
1046
- <span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:d</span>,
1047
- <span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:E</span>,
1048
- <span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:G</span>,
1049
- <span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:l</span>,
1050
- <span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:M</span>,
1051
- <span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:R</span>,
1052
- <span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:q</span>,
1053
- <span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:Q</span>,
1054
- <span class="ruby-comment">###following options are for the -g -u option</span>
1055
- <span class="ruby-value">:genotype_calling</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:g</span>,
1056
- <span class="ruby-value">:uncompressed_bcf</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:u</span>,
1057
- <span class="ruby-value">:extension_sequencing_probability</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:e</span>,
1058
- <span class="ruby-value">:homopolymer_error_coefficient</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:h</span>,
1059
- <span class="ruby-value">:no_indels</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:I</span>,
1060
- <span class="ruby-value">:skip_indel_over_average_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:L</span>,
1061
- <span class="ruby-value">:gap_open_sequencing_error_probability</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:o</span>,
1062
- <span class="ruby-value">:platforms</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:P</span>
1063
- }
1064
-
1065
- <span class="ruby-comment">##convert any long_opts to short opts </span>
1066
- <span class="ruby-identifier">temp_opts</span> = <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">dup</span>
1067
- <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>
1068
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">long_opts</span>[<span class="ruby-identifier">k</span>]
1069
- <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>
1070
- <span class="ruby-identifier">temp_opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-identifier">k</span>)
1071
- <span class="ruby-keyword">end</span>
1072
- <span class="ruby-keyword">end</span>
1073
- <span class="ruby-identifier">opts</span> = <span class="ruby-identifier">temp_opts</span>
1074
- <span class="ruby-comment">##remove any calls to -g or -u for mpileup, bcf output is not yet supported</span>
1075
- <span class="ruby-comment">##and also associated output options</span>
1076
- <span class="ruby-comment">#[:g, :u, :e, :h, :I, :L, :o, :p].each {|x| opts.delete(x) }</span>
1077
- <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>
1078
- <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">delete</span>(<span class="ruby-value">:g</span>)
1079
-
1080
- <span class="ruby-identifier">sam_opts</span> = []
1081
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(&quot;mpileup&quot;)</span>
1082
- <span class="ruby-identifier">opts</span>.<span class="ruby-identifier">each</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>
1083
- <span class="ruby-keyword">next</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">k</span>] <span class="ruby-comment">##dont bother unless the values provided are true.. </span>
1084
- <span class="ruby-identifier">k</span> = <span class="ruby-string">'6'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">k</span> <span class="ruby-operator">==</span> <span class="ruby-value">:six</span>
1085
- <span class="ruby-identifier">k</span> = <span class="ruby-string">'-'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span>
1086
- <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">k</span> <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(k)</span>
1087
- <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-keyword">unless</span> [<span class="ruby-string">&quot;-R&quot;</span>, <span class="ruby-string">&quot;-B&quot;</span>, <span class="ruby-string">&quot;-E&quot;</span>, <span class="ruby-string">&quot;-6&quot;</span>, <span class="ruby-string">&quot;-A&quot;</span>, <span class="ruby-string">&quot;-g&quot;</span>, <span class="ruby-string">&quot;-u&quot;</span>, <span class="ruby-string">&quot;-I&quot;</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">k</span>) <span class="ruby-comment">#these are just flags so don't pass a value... strptrs &lt;&lt; FFI::MemoryPointer.from_string(v.to_s)</span>
1088
- <span class="ruby-keyword">end</span>
1089
- <span class="ruby-identifier">sam_opts</span> = <span class="ruby-identifier">sam_opts</span> <span class="ruby-operator">+</span> [<span class="ruby-string">'-f'</span>, <span class="ruby-ivar">@fasta_path</span>, <span class="ruby-ivar">@sam</span>]
1090
-
1091
- <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')} mpileup #{sam_opts.join(' ')} 2&gt; /dev/null&quot;</span>
1092
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
1093
- <span class="ruby-identifier">command</span> = <span class="ruby-identifier">command</span> <span class="ruby-operator">+</span> <span class="ruby-node">&quot; | #{File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','bcftools')} view -cg -&quot;</span>
1094
- <span class="ruby-keyword">end</span>
1095
- <span class="ruby-identifier">pipe</span> = <span class="ruby-constant">IO</span>.<span class="ruby-identifier">popen</span>(<span class="ruby-identifier">command</span>)
1096
- <span class="ruby-identifier">$stderr</span>.<span class="ruby-identifier">puts</span> <span class="ruby-identifier">command</span>
1097
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:u</span>]
1098
- <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
1099
- <span class="ruby-keyword">next</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span> <span class="ruby-comment">#skip any header or meta-lines, we dont do anything with those </span>
1100
- <span class="ruby-keyword">yield</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-identifier">new</span>(<span class="ruby-identifier">line</span>)
1101
- <span class="ruby-keyword">end</span>
1102
- <span class="ruby-keyword">else</span>
1103
- <span class="ruby-keyword">while</span> <span class="ruby-identifier">line</span> = <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">gets</span>
1104
- <span class="ruby-keyword">yield</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>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">line</span>)
1105
- <span class="ruby-keyword">end</span>
1106
- <span class="ruby-keyword">end</span>
1107
- <span class="ruby-identifier">pipe</span>.<span class="ruby-identifier">close</span>
1108
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string('-f')</span>
1109
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(@fasta_path)</span>
1110
- <span class="ruby-comment">#strptrs &lt;&lt; FFI::MemoryPointer.from_string(@sam)</span>
1111
- <span class="ruby-comment">#strptrs &lt;&lt; nil</span>
1112
-
1113
- <span class="ruby-comment"># Now load all the pointers into a native memory block</span>
1114
- <span class="ruby-comment">#argv = FFI::MemoryPointer.new(:pointer, strptrs.length)</span>
1115
- <span class="ruby-comment">#strptrs.each_with_index do |p, i|</span>
1116
- <span class="ruby-comment"># argv[i].put_pointer(0, p)</span>
1117
- <span class="ruby-comment">#end</span>
1118
-
1119
- <span class="ruby-comment">#old_stdout = STDOUT.clone</span>
1120
- <span class="ruby-comment">#read_pipe, write_pipe = IO.pipe()</span>
1121
- <span class="ruby-comment">#STDOUT.reopen(write_pipe)</span>
1122
- <span class="ruby-comment">#int bam_mpileup(int argc, char *argv[])</span>
1123
- <span class="ruby-comment"># Bio::DB::SAM::Tools.bam_mpileup(strptrs.length - 1,argv)</span>
1124
- <span class="ruby-comment">#if fork</span>
1125
- <span class="ruby-comment"># write_pipe.close</span>
1126
- <span class="ruby-comment"># STDOUT.reopen(old_stdout) #beware .. stdout from other processes eg tests calling this method can get mixed in...</span>
1127
- <span class="ruby-comment"># begin</span>
1128
- <span class="ruby-comment"># while line = read_pipe.readline</span>
1129
- <span class="ruby-comment"># yield Pileup.new(line)</span>
1130
- <span class="ruby-comment"># end</span>
1131
- <span class="ruby-comment"># rescue EOFError</span>
1132
- <span class="ruby-comment"># read_pipe.close</span>
1133
- <span class="ruby-comment"># Process.wait</span>
1134
- <span class="ruby-comment"># end</span>
1135
- <span class="ruby-comment">#end</span>
1136
- <span class="ruby-keyword">end</span></pre>
1137
- </div><!-- mpileup_plus-source -->
1138
-
1139
- </div>
1140
-
1141
-
1142
-
1143
-
1144
- </div><!-- mpileup_plus-method -->
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">&quot;idxstats #{@bam}&quot;</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">&quot;#&quot;</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">&gt;</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">&gt;</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">&gt;</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 &lt;out.bam&gt; [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">&#39;1&#39;</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">&#39;@&#39;</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">&#39; &#39;</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">&#39;1&#39;</span>] )
1106
+ <span class="ruby-comment">#command = &quot;#{form_opt_string(@samtools, &quot;merge&quot;, opts, [:n, :r, :u, :f, &#39;1&#39;] )} #{out} #{bam_list}&quot;</span>
1107
+ <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{@samtools} merge #{options} #{out} #{bam_list}&quot;</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">&amp;</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">&gt;</span> <span class="ruby-value">:r</span>,
1207
+ <span class="ruby-value">:illumina_quals</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:six</span>,
1208
+ <span class="ruby-value">:count_anomalous</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:A</span>,
1209
+ <span class="ruby-value">:no_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:B</span>,
1210
+ <span class="ruby-value">:adjust_mapq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:C</span>,
1211
+ <span class="ruby-value">:max_per_bam_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:d</span>,
1212
+ <span class="ruby-value">:extended_baq</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:E</span>,
1213
+ <span class="ruby-value">:exclude_reads_file</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:G</span>,
1214
+ <span class="ruby-value">:list_of_positions</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:l</span>,
1215
+ <span class="ruby-value">:mapping_quality_cap</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:M</span>,
1216
+ <span class="ruby-value">:ignore_rg</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:R</span>,
1217
+ <span class="ruby-value">:min_mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:q</span>,
1218
+ <span class="ruby-value">:min_base_quality</span> =<span class="ruby-operator">&gt;</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">&gt;</span> <span class="ruby-value">:g</span>,
1221
+ <span class="ruby-value">:uncompressed_bcf</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:u</span>,
1222
+ <span class="ruby-value">:extension_sequencing_probability</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:e</span>,
1223
+ <span class="ruby-value">:homopolymer_error_coefficient</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:h</span>,
1224
+ <span class="ruby-value">:no_indels</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:I</span>,
1225
+ <span class="ruby-value">:skip_indel_over_average_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:L</span>,
1226
+ <span class="ruby-value">:gap_open_sequencing_error_probability</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">:o</span>,
1227
+ <span class="ruby-value">:platforms</span> =<span class="ruby-operator">&gt;</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">&quot;6&quot;</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">&quot;mpileup&quot;</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">&quot;6&quot;</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">&quot; | #{@bcftools} view -cg -&quot;</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">&amp;</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>
1145
1268
 
1146
1269
 
1147
1270
  <div id="method-i-open" class="method-detail ">
@@ -1149,129 +1272,582 @@ and supports returning of pileup vcf</p>
1149
1272
  <div class="method-heading">
1150
1273
  <span class="method-name">open</span><span
1151
1274
  class="method-args">()</span>
1275
+
1152
1276
  <span class="method-click-advice">click to toggle source</span>
1277
+
1153
1278
  </div>
1154
1279
 
1155
1280
 
1156
1281
  <div class="method-description">
1157
1282
 
1158
- <p>Function that actually opens the sam file Throws a <a
1159
- href="SAMException.html">SAMException</a> if the file can’t be open.</p>
1283
+ <p>backward compatibility method, returns true if file exists otherwise,
1284
+ complains and quits.</p>
1285
+
1160
1286
 
1161
1287
 
1162
1288
 
1163
1289
  <div class="method-source-code" id="open-source">
1164
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 60</span>
1165
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">open</span>()
1166
-
1167
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Writing not supported yet&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-ivar">@write</span>
1168
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;No SAM file specified&quot;</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sam</span>
1169
-
1170
- <span class="ruby-identifier">opts</span> = <span class="ruby-ivar">@write</span> <span class="ruby-operator">?</span> <span class="ruby-string">&quot;w&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-string">&quot;r&quot;</span>
1171
- <span class="ruby-keyword">if</span> <span class="ruby-ivar">@binary</span> <span class="ruby-keyword">then</span>
1172
- <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-string">&quot;b&quot;</span>
1173
- <span class="ruby-keyword">if</span> <span class="ruby-ivar">@write</span> <span class="ruby-keyword">then</span>
1174
- <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@compressed</span> <span class="ruby-keyword">then</span>
1175
- <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-string">&quot;u&quot;</span>
1176
- <span class="ruby-keyword">end</span>
1177
- <span class="ruby-keyword">end</span>
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">&quot;#{form_opt_string(@samtools, &quot;phase&quot;, opts, [:A, :F] )}&quot;</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>
1178
1397
  <span class="ruby-keyword">end</span>
1179
- <span class="ruby-identifier">valid</span> = [<span class="ruby-string">&quot;r&quot;</span>, <span class="ruby-string">&quot;w&quot;</span>, <span class="ruby-string">&quot;wh&quot;</span>, <span class="ruby-string">&quot;rb&quot;</span>, <span class="ruby-string">&quot;wb&quot;</span> , <span class="ruby-string">&quot;wbu&quot;</span>]
1180
- <span class="ruby-keyword">unless</span> <span class="ruby-identifier">valid</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-keyword">then</span>
1181
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;Invalid options for samopen: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">opts</span>
1398
+ <span class="ruby-identifier">result</span> = []
1399
+ <span class="ruby-identifier">region</span> = <span class="ruby-node">&quot;#{chr}:#{start}-#{start + length}&quot;</span>
1400
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mpileup</span>(<span class="ruby-value">:r</span> =<span class="ruby-operator">&gt;</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">&lt;&lt;</span> <span class="ruby-identifier">p</span>.<span class="ruby-identifier">coverage</span>
1182
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">&gt;</span> <span class="ruby-value">1000</span>,
1404
+ <span class="ruby-value">:height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">200</span>,
1405
+ <span class="ruby-value">:number_of_intervals</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">10</span>,
1406
+ <span class="ruby-value">:font_size</span> =<span class="ruby-operator">&gt;</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">&gt;</span> <span class="ruby-value">:histogram</span>,
1409
+ <span class="ruby-value">:stroke_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&#39;black&#39;</span>,
1410
+ <span class="ruby-value">:fill_color</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&#39;gold&#39;</span>,
1411
+ <span class="ruby-value">:track_height</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">150</span>,
1412
+ <span class="ruby-value">:name</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&#39;read coverage&#39;</span>,
1413
+ <span class="ruby-value">:label</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">true</span>,
1414
+ <span class="ruby-value">:stroke_width</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-string">&#39;1&#39;</span>,
1415
+ <span class="ruby-value">:x_round</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">1</span>,
1416
+ <span class="ruby-value">:y_round</span> =<span class="ruby-operator">&gt;</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">&gt;</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">&gt;</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">&gt;</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
+
1183
1455
 
1184
- <span class="ruby-identifier">samFile</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samopen</span>(<span class="ruby-ivar">@sam</span>, <span class="ruby-identifier">opts</span>, <span class="ruby-keyword">nil</span>)
1185
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">samFile</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword">then</span>
1186
- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword">nil</span>
1187
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-string">&quot;File not opened: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
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">&quot;#{@samtools} reheader #{header_sam} #{@bam} &gt; #{out}&quot;</span>
1474
+ <span class="ruby-keyword">else</span>
1475
+ <span class="ruby-identifier">command</span> = <span class="ruby-node">&quot;#{@samtools} reheader #{header_sam} #{@bam}&quot;</span>
1188
1476
  <span class="ruby-keyword">end</span>
1189
- <span class="ruby-ivar">@sam_file</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">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span><span class="ruby-operator">::</span><span class="ruby-constant">SamfileT</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">samFile</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>
1190
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">&quot;#{form_opt_string(@samtools, &quot;rmdup&quot;, opts, [:s, :S])} #{out} #{@bam}&quot;</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>)
1191
1525
  <span class="ruby-keyword">end</span></pre>
1192
- </div><!-- open-source -->
1526
+ </div>
1193
1527
 
1194
1528
  </div>
1195
1529
 
1196
1530
 
1531
+ <div class="aliases">
1532
+ Also aliased as: <a href="Sam.html#method-i-rmdup">rmdup</a>
1533
+ </div>
1534
+
1197
1535
 
1198
1536
 
1199
- </div><!-- open-method -->
1537
+ </div>
1200
1538
 
1201
1539
 
1202
- <div id="method-i-query_string" class="method-detail ">
1540
+ <div id="method-i-rmdup" class="method-detail method-alias">
1203
1541
 
1204
1542
  <div class="method-heading">
1205
- <span class="method-name">query_string</span><span
1206
- class="method-args">(chromosome, qstart,qend)</span>
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
+
1207
1574
  <span class="method-click-advice">click to toggle source</span>
1575
+
1208
1576
  </div>
1209
1577
 
1210
1578
 
1211
1579
  <div class="method-description">
1212
1580
 
1213
- <p>Generates a query sting to be used by the region parser in samtools. In
1214
- principle, you shouldn’t need to use this function.</p>
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 &lt;out.prefix&gt; 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">&gt;</span> <span class="ruby-string">&quot;sorted&quot;</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">&quot;sort&quot;</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">&quot; &quot;</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>
1215
1620
 
1621
+ </div>
1216
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>
1217
1636
 
1218
- <div class="method-source-code" id="query_string-source">
1219
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 205</span>
1220
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
1221
- <span class="ruby-identifier">query</span> = <span class="ruby-identifier">chromosome</span> <span class="ruby-operator">+</span> <span class="ruby-string">&quot;:&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qstart</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-string">&quot;-&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qend</span>.<span class="ruby-identifier">to_s</span>
1222
- <span class="ruby-identifier">query</span>
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">&#39;f&#39;</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">&quot;#{form_opt_string(@samtools, &quot;targetcut&quot;, opts, [] )}&quot;</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>)
1223
1674
  <span class="ruby-keyword">end</span></pre>
1224
- </div><!-- query_string-source -->
1675
+ </div>
1225
1676
 
1226
1677
  </div>
1227
1678
 
1228
1679
 
1229
1680
 
1230
1681
 
1231
- </div><!-- query_string-method -->
1682
+ </div>
1232
1683
 
1233
1684
 
1234
- <div id="method-i-to_s" class="method-detail ">
1685
+ <div id="method-i-tview" class="method-detail ">
1235
1686
 
1236
1687
  <div class="method-heading">
1237
- <span class="method-name">to_s</span><span
1238
- class="method-args">()</span>
1688
+ <span class="method-name">tview</span><span
1689
+ class="method-args">(opts={})</span>
1690
+
1239
1691
  <span class="method-click-advice">click to toggle source</span>
1692
+
1240
1693
  </div>
1241
1694
 
1242
1695
 
1243
1696
  <div class="method-description">
1244
1697
 
1245
- <p>Prints a description of the sam file in a text format containg if it is
1246
- binary or text, the path and the fasta file of the reference</p>
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
+
1247
1707
 
1248
1708
 
1249
1709
 
1250
- <div class="method-source-code" id="to_s-source">
1251
- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 90</span>
1252
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>()
1253
- (<span class="ruby-ivar">@binary</span> <span class="ruby-operator">?</span> <span class="ruby-string">&quot;Binary&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-string">&quot;Text&quot;</span>) <span class="ruby-operator">+</span> <span class="ruby-string">&quot; file: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-operator">+</span> <span class="ruby-string">&quot; with fasta: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
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">&#39;d&#39;</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">&#39;p&#39;</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">&#39;s&#39;</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">&quot;#{form_opt_string(@samtools, &quot;tview&quot;, opts)}&quot;</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>)
1254
1728
  <span class="ruby-keyword">end</span></pre>
1255
- </div><!-- to_s-source -->
1729
+ </div>
1256
1730
 
1257
1731
  </div>
1258
1732
 
1259
1733
 
1260
1734
 
1261
1735
 
1262
- </div><!-- to_s-method -->
1736
+ </div>
1263
1737
 
1264
1738
 
1265
- </section><!-- public-instance-method-details -->
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">&amp;</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">&quot;#{opts[:chr]}:#{opts[:start]}-#{opts[:stop]}&quot;</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">&#39;@&#39;</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>
1266
1820
 
1267
- </section><!-- 5Buntitled-5D -->
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">&#39;1&#39;</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">&#39;view&#39;</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">&#39;1&#39;</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">&quot; &quot;</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">&amp;</span><span class="ruby-identifier">block</span>)
1831
+ <span class="ruby-keyword">end</span></pre>
1832
+ </div>
1833
+
1834
+ </div>
1835
+
1836
+
1268
1837
 
1269
- </div><!-- documentation -->
1838
+
1839
+ </div>
1840
+
1841
+
1842
+ </section>
1843
+
1844
+ </section>
1845
+ </main>
1270
1846
 
1271
1847
 
1272
- <footer id="validator-badges">
1273
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
1274
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
1275
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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>.
1276
1852
  </footer>
1277
1853