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/classes/Bio/DB/SAM/Library.html DELETED
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- <td><strong>In:</strong></td>
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- <a href="../../../../files/lib/bio/db/sam/library_rb.html">
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data/doc/classes/Bio/DB/SAM/Library.src/M000006.html DELETED
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data/doc/classes/Bio/DB/SAM/Tools.html DELETED
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- <a href="../../../../files/lib/bio/db/sam/bam_rb.html">
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- Class <a href="Tools/Bam1T.html" class="link">Bio::DB::SAM::Tools::Bam1T</a><br />
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- Class <a href="Tools/BamHeaderT.html" class="link">Bio::DB::SAM::Tools::BamHeaderT</a><br />
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- Class <a href="Tools/BamPileup1T.html" class="link">Bio::DB::SAM::Tools::BamPileup1T</a><br />
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- Class <a href="Tools/SamfileT.html" class="link">Bio::DB::SAM::Tools::SamfileT</a><br />
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- <tr class="top-aligned-row context-row">
130
- <td class="context-item-name">BAM_FUNMAP</td>
131
- <td>=</td>
132
- <td class="context-item-value">4</td>
133
- </tr>
134
- <tr class="top-aligned-row context-row">
135
- <td class="context-item-name">BAM_FMUNMAP</td>
136
- <td>=</td>
137
- <td class="context-item-value">8</td>
138
- </tr>
139
- <tr class="top-aligned-row context-row">
140
- <td class="context-item-name">BAM_FREVERSE</td>
141
- <td>=</td>
142
- <td class="context-item-value">16</td>
143
- </tr>
144
- <tr class="top-aligned-row context-row">
145
- <td class="context-item-name">BAM_FMREVERSE</td>
146
- <td>=</td>
147
- <td class="context-item-value">32</td>
148
- </tr>
149
- <tr class="top-aligned-row context-row">
150
- <td class="context-item-name">BAM_FREAD1</td>
151
- <td>=</td>
152
- <td class="context-item-value">64</td>
153
- </tr>
154
- <tr class="top-aligned-row context-row">
155
- <td class="context-item-name">BAM_FREAD2</td>
156
- <td>=</td>
157
- <td class="context-item-value">128</td>
158
- </tr>
159
- <tr class="top-aligned-row context-row">
160
- <td class="context-item-name">BAM_FSECONDARY</td>
161
- <td>=</td>
162
- <td class="context-item-value">256</td>
163
- </tr>
164
- <tr class="top-aligned-row context-row">
165
- <td class="context-item-name">BAM_FQCFAIL</td>
166
- <td>=</td>
167
- <td class="context-item-value">512</td>
168
- </tr>
169
- <tr class="top-aligned-row context-row">
170
- <td class="context-item-name">BAM_FDUP</td>
171
- <td>=</td>
172
- <td class="context-item-value">1024</td>
173
- </tr>
174
- <tr class="top-aligned-row context-row">
175
- <td class="context-item-name">BAM_OFDEC</td>
176
- <td>=</td>
177
- <td class="context-item-value">0</td>
178
- </tr>
179
- <tr class="top-aligned-row context-row">
180
- <td class="context-item-name">BAM_OFHEX</td>
181
- <td>=</td>
182
- <td class="context-item-value">1</td>
183
- </tr>
184
- <tr class="top-aligned-row context-row">
185
- <td class="context-item-name">BAM_OFSTR</td>
186
- <td>=</td>
187
- <td class="context-item-value">2</td>
188
- </tr>
189
- <tr class="top-aligned-row context-row">
190
- <td class="context-item-name">BAM_DEF_MASK</td>
191
- <td>=</td>
192
- <td class="context-item-value">(4|256|512|1024)</td>
193
- </tr>
194
- <tr class="top-aligned-row context-row">
195
- <td class="context-item-name">BAM_CIGAR_SHIFT</td>
196
- <td>=</td>
197
- <td class="context-item-value">4</td>
198
- </tr>
199
- <tr class="top-aligned-row context-row">
200
- <td class="context-item-name">BAM_CIGAR_MASK</td>
201
- <td>=</td>
202
- <td class="context-item-value">((1 &lt;&lt; 4) -1)</td>
203
- </tr>
204
- <tr class="top-aligned-row context-row">
205
- <td class="context-item-name">BAM_CMATCH</td>
206
- <td>=</td>
207
- <td class="context-item-value">0</td>
208
- </tr>
209
- <tr class="top-aligned-row context-row">
210
- <td class="context-item-name">BAM_CINS</td>
211
- <td>=</td>
212
- <td class="context-item-value">1</td>
213
- </tr>
214
- <tr class="top-aligned-row context-row">
215
- <td class="context-item-name">BAM_CDEL</td>
216
- <td>=</td>
217
- <td class="context-item-value">2</td>
218
- </tr>
219
- <tr class="top-aligned-row context-row">
220
- <td class="context-item-name">BAM_CREF_SKIP</td>
221
- <td>=</td>
222
- <td class="context-item-value">3</td>
223
- </tr>
224
- <tr class="top-aligned-row context-row">
225
- <td class="context-item-name">BAM_CSOFT_CLIP</td>
226
- <td>=</td>
227
- <td class="context-item-value">4</td>
228
- </tr>
229
- <tr class="top-aligned-row context-row">
230
- <td class="context-item-name">BAM_CHARD_CLIP</td>
231
- <td>=</td>
232
- <td class="context-item-value">5</td>
233
- </tr>
234
- <tr class="top-aligned-row context-row">
235
- <td class="context-item-name">BAM_CPAD</td>
236
- <td>=</td>
237
- <td class="context-item-value">6</td>
238
- </tr>
239
- </table>
240
- </div>
241
- </div>
242
-
243
-
244
-
245
-
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-
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-
248
- <!-- if method_list -->
249
- <div id="methods">
250
- <h3 class="section-bar">Public Class methods</h3>
251
-
252
- <div id="method-M000007" class="method-detail">
253
- <a name="M000007"></a>
254
-
255
- <div class="method-heading">
256
- <a href="Tools.src/M000007.html" target="Code" class="method-signature"
257
- onclick="popupCode('Tools.src/M000007.html');return false;">
258
- <span class="method-name">bam_sort</span><span class="method-args">(bam_filename, bam_output_prefix)</span>
259
- </a>
260
- </div>
261
-
262
- <div class="method-description">
263
- </div>
264
- </div>
265
-
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-
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- </div>
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-
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-
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- </div>
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-
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-
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- <div id="validator-badges">
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- <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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- </div>
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-
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- </body>
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- </html>
data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html DELETED
@@ -1,20 +0,0 @@
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- <?xml version="1.0" encoding="iso-8859-1"?>
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- <!DOCTYPE html
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- PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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-
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- <html>
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- <head>
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- <title>bam_sort (Bio::DB::SAM::Tools)</title>
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- <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
- <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
11
- </head>
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- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/bam.rb, line 172</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">bam_sort</span>(<span class="ruby-identifier">bam_filename</span>, <span class="ruby-identifier">bam_output_prefix</span>)
15
- <span class="ruby-identifier">is_by_name</span> = <span class="ruby-value">0</span>
16
- <span class="ruby-identifier">max_mem</span> = <span class="ruby-value">500000000</span>
17
- <span class="ruby-identifier">bam_sort_core</span>(<span class="ruby-identifier">is_by_name</span>, <span class="ruby-identifier">bam_filename</span>, <span class="ruby-identifier">bam_output_prefix</span>, <span class="ruby-identifier">max_mem</span>)
18
- <span class="ruby-keyword kw">end</span></pre>
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- </body>
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- </html>