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/Pileup.html CHANGED
@@ -2,159 +2,109 @@
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  <html>
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  <head>
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- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <meta charset="UTF-8">
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  <title>class Bio::DB::Pileup - Pileup</title>
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- <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+ <link href="../../fonts.css" rel="stylesheet">
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  <script type="text/javascript">
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- <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
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+ <script src="../../js/jquery.js"></script>
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+ <script src="../../js/navigation.js"></script>
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+ <script src="../../js/search_index.js"></script>
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+ <script src="../../js/search.js"></script>
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+ <script src="../../js/searcher.js"></script>
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+ <script src="../../js/darkfish.js"></script>
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- <body id="top" class="class">
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- <nav id="metadata">
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- <nav id="home-section" class="section">
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- <h3 class="section-header">
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- <a href="../../index.html">Home</a>
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+ <body id="top" role="document" class="class">
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+ <nav role="navigation">
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+ <div id="project-navigation">
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <h2>
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+ <a href="../../index.html" rel="home">Home</a>
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+ </h2>
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+
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+ <div id="table-of-contents-navigation">
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+ <a href="../../table_of_contents.html#pages">Pages</a>
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  <a href="../../table_of_contents.html#classes">Classes</a>
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  <a href="../../table_of_contents.html#methods">Methods</a>
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- </h3>
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- </nav>
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+ <div id="search-section" role="search" class="project-section initially-hidden">
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- <h3 class="section-header">
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- <input type="text" name="search" placeholder="Search" id="search-field"
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+ <div id="search-field-wrapper">
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+ <input id="search-field" role="combobox" aria-label="Search"
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+ aria-autocomplete="list" aria-controls="search-results"
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+ type="text" name="search" placeholder="Search" spellcheck="false"
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  title="Type to search, Up and Down to navigate, Enter to load">
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- </h3>
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- </form>
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- <ul id="search-results" class="initially-hidden"></ul>
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- </nav>
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+ </div>
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+ <ul id="search-results" aria-label="Search Results"
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+ aria-busy="false" aria-expanded="false"
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+ aria-atomic="false" class="initially-hidden"></ul>
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+ </form>
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+ </div>
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- <div id="file-metadata">
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- <nav id="file-list-section" class="section">
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- <h3 class="section-header">Defined In</h3>
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- <ul>
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- <li>lib/bio/db/pileup.rb
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- </ul>
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- <li><a href="../../Bio.html">Bio</a>
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- <li><a href="../../Bio/DB.html">Bio::DB</a>
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396
351
  <span class="ruby-keyword">def</span> <span class="ruby-constant">Pileup</span>.<span class="ruby-identifier">iupac_to_base</span>(<span class="ruby-identifier">alt_base</span>)
397
352
  <span class="ruby-keyword">case</span> <span class="ruby-identifier">alt_base</span>
398
- <span class="ruby-keyword">when</span> <span class="ruby-string">'K'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'G'</span>,<span class="ruby-string">'T'</span>]
399
- <span class="ruby-keyword">when</span> <span class="ruby-string">'M'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'C'</span>]
400
- <span class="ruby-keyword">when</span> <span class="ruby-string">'S'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'C'</span>,<span class="ruby-string">'G'</span>]
401
- <span class="ruby-keyword">when</span> <span class="ruby-string">'R'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'G'</span>]
402
- <span class="ruby-keyword">when</span> <span class="ruby-string">'W'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'A'</span>,<span class="ruby-string">'T'</span>]
403
- <span class="ruby-keyword">when</span> <span class="ruby-string">'Y'</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">'C'</span>,<span class="ruby-string">'T'</span>]
404
- <span class="ruby-keyword">else</span> <span class="ruby-identifier">alt_base</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r/</span>)
353
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;K&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;G&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
354
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;M&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;C&#39;</span>]
355
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;S&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;C&#39;</span>,<span class="ruby-string">&#39;G&#39;</span>]
356
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;R&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;G&#39;</span>]
357
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;W&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;A&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
358
+ <span class="ruby-keyword">when</span> <span class="ruby-string">&#39;Y&#39;</span> <span class="ruby-keyword">then</span> [<span class="ruby-string">&#39;C&#39;</span>,<span class="ruby-string">&#39;T&#39;</span>]
359
+ <span class="ruby-keyword">else</span> <span class="ruby-identifier">alt_base</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">//</span>)
405
360
  <span class="ruby-keyword">end</span>
406
361
  <span class="ruby-keyword">end</span></pre>
407
- </div><!-- iupac_to_base-source -->
362
+ </div>
408
363
 
409
364
  </div>
410
365
 
411
366
 
412
367
 
413
368
 
414
- </div><!-- iupac_to_base-method -->
369
+ </div>
415
370
 
416
371
 
417
372
  <div id="method-c-new" class="method-detail ">
@@ -419,7 +374,9 @@
419
374
  <div class="method-heading">
420
375
  <span class="method-name">new</span><span
421
376
  class="method-args">(pile_up_line)</span>
377
+
422
378
  <span class="method-click-advice">click to toggle source</span>
379
+
423
380
  </div>
424
381
 
425
382
 
@@ -430,16 +387,17 @@
430
387
  <pre>pile_up_line = &quot;seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;&quot;
431
388
  pile = Bio::DB::Pileup.new(pile_up_line)</pre>
432
389
 
390
+
433
391
 
434
392
 
435
393
  <div class="method-source-code" id="new-source">
436
394
  <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 35</span>
437
395
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
438
- <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r\t/</span>)
396
+ <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
439
397
  <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">6</span> <span class="ruby-comment">##should only be able to get 6 lines from mpileup</span>
440
398
  <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
441
399
  <span class="ruby-keyword">elsif</span> (<span class="ruby-value">10</span><span class="ruby-operator">..</span><span class="ruby-value">13</span>).<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span>) <span class="ruby-comment">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</span>
442
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span> <span class="ruby-comment">#indel</span>
400
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span> <span class="ruby-comment">#indel</span>
443
401
  <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@indel_1</span>, <span class="ruby-ivar">@indel_2</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span> = <span class="ruby-identifier">cols</span>
444
402
  <span class="ruby-keyword">else</span> <span class="ruby-comment">#snp / identity</span>
445
403
  <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
@@ -448,7 +406,7 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
448
406
  <span class="ruby-ivar">@snp_quality</span> = <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_f</span>
449
407
  <span class="ruby-ivar">@rms_mapq</span> = <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_f</span>
450
408
  <span class="ruby-keyword">else</span>
451
- <span class="ruby-comment">#raise RuntimeError, &quot;parsing line '#{pile_up_line.chomp}' failed&quot;</span>
409
+ <span class="ruby-comment">#raise RuntimeError, &quot;parsing line &#39;#{pile_up_line.chomp}&#39; failed&quot;</span>
452
410
  <span class="ruby-keyword">end</span>
453
411
 
454
412
  <span class="ruby-ivar">@pos</span> = <span class="ruby-ivar">@pos</span>.<span class="ruby-identifier">to_i</span>
@@ -457,20 +415,22 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
457
415
  <span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword">nil</span>
458
416
  <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword">nil</span>
459
417
  <span class="ruby-keyword">end</span></pre>
460
- </div><!-- new-source -->
418
+ </div>
461
419
 
462
420
  </div>
463
421
 
464
422
 
465
423
 
466
424
 
467
- </div><!-- new-method -->
425
+ </div>
468
426
 
469
427
 
470
- </section><!-- public-class-method-details -->
428
+ </section>
471
429
 
472
- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
473
- <h3 class="section-header">Public Instance Methods</h3>
430
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
431
+ <header>
432
+ <h3>Public Instance Methods</h3>
433
+ </header>
474
434
 
475
435
 
476
436
  <div id="method-i-genotype_list" class="method-detail ">
@@ -478,33 +438,37 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
478
438
  <div class="method-heading">
479
439
  <span class="method-name">genotype_list</span><span
480
440
  class="method-args">()</span>
441
+
481
442
  <span class="method-click-advice">click to toggle source</span>
443
+
482
444
  </div>
483
445
 
484
446
 
485
447
  <div class="method-description">
486
448
 
449
+ <p>identifies the reference base and returns the indel or snp genotype as
450
+ applicable</p>
487
451
 
488
452
 
489
453
 
490
454
 
491
455
  <div class="method-source-code" id="genotype_list-source">
492
- <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 174</span>
456
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 167</span>
493
457
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">genotype_list</span>
494
- <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
458
+ <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
495
459
  <span class="ruby-keyword">return</span> <span class="ruby-identifier">indel_gt</span>
496
460
  <span class="ruby-keyword">else</span>
497
461
  <span class="ruby-keyword">return</span> <span class="ruby-identifier">snp_gt</span>
498
- <span class="ruby-keyword">end</span>
462
+ <span class="ruby-keyword">end</span>
499
463
  <span class="ruby-keyword">end</span></pre>
500
- </div><!-- genotype_list-source -->
464
+ </div>
501
465
 
502
466
  </div>
503
467
 
504
468
 
505
469
 
506
470
 
507
- </div><!-- genotype_list-method -->
471
+ </div>
508
472
 
509
473
 
510
474
  <div id="method-i-non_ref_count" class="method-detail ">
@@ -512,7 +476,9 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
512
476
  <div class="method-heading">
513
477
  <span class="method-name">non_ref_count</span><span
514
478
  class="method-args">()</span>
479
+
515
480
  <span class="method-click-advice">click to toggle source</span>
481
+
516
482
  </div>
517
483
 
518
484
 
@@ -520,6 +486,7 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
520
486
 
521
487
  <p>returns the total non-reference bases in the reads at this position</p>
522
488
 
489
+
523
490
 
524
491
 
525
492
  <div class="method-source-code" id="non_ref_count-source">
@@ -530,14 +497,14 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
530
497
  <span class="ruby-keyword">end</span>
531
498
  <span class="ruby-ivar">@non_ref_count</span>
532
499
  <span class="ruby-keyword">end</span></pre>
533
- </div><!-- non_ref_count-source -->
500
+ </div>
534
501
 
535
502
  </div>
536
503
 
537
504
 
538
505
 
539
506
 
540
- </div><!-- non_ref_count-method -->
507
+ </div>
541
508
 
542
509
 
543
510
  <div id="method-i-non_refs" class="method-detail ">
@@ -545,17 +512,18 @@ pile = Bio::DB::Pileup.new(pile_up_line)</pre>
545
512
  <div class="method-heading">
546
513
  <span class="method-name">non_refs</span><span
547
514
  class="method-args">()</span>
515
+
548
516
  <span class="method-click-advice">click to toggle source</span>
517
+
549
518
  </div>
550
519
 
551
520
 
552
521
  <div class="method-description">
553
522
 
554
523
  <p>Calculate the total count of each non-reference nucleotide and return a
555
- hash of all 4 nt counts, returns a hash</p>
556
-
557
- <pre class="ruby"><span class="ruby-identifier">pile</span>.<span class="ruby-identifier">non_refs</span> <span class="ruby-comment">#{:A =&gt; 1, :C =&gt; 0, :T =&gt; 0, :G =&gt; 0}</span>
558
- </pre>
524
+ hash of all 4 nt counts returns a hash pile.non_refs #{:A =&gt; 1, :C =&gt;
525
+ 0, :T =&gt; 0, :G =&gt; 0}</p>
526
+
559
527
 
560
528
 
561
529
 
@@ -567,14 +535,52 @@ hash of all 4 nt counts, returns a hash</p>
567
535
  <span class="ruby-keyword">end</span>
568
536
  <span class="ruby-ivar">@non_ref_count_hash</span>
569
537
  <span class="ruby-keyword">end</span></pre>
570
- </div><!-- non_refs-source -->
538
+ </div>
571
539
 
572
540
  </div>
573
541
 
574
542
 
575
543
 
576
544
 
577
- </div><!-- non_refs-method -->
545
+ </div>
546
+
547
+
548
+ <div id="method-i-parse_indel" class="method-detail ">
549
+
550
+ <div class="method-heading">
551
+ <span class="method-name">parse_indel</span><span
552
+ class="method-args">(alt)</span>
553
+
554
+ <span class="method-click-advice">click to toggle source</span>
555
+
556
+ </div>
557
+
558
+
559
+ <div class="method-description">
560
+
561
+ <p>identifies if the indel is an insertion or a deletion</p>
562
+
563
+
564
+
565
+
566
+ <div class="method-source-code" id="parse_indel-source">
567
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 190</span>
568
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">parse_indel</span>(<span class="ruby-identifier">alt</span>)
569
+ <span class="ruby-keyword">return</span> <span class="ruby-node">&quot;D#{$&#39;.length}&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">=~</span><span class="ruby-regexp">/^-/</span>
570
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span><span class="ruby-operator">=~</span><span class="ruby-regexp">/^\+/</span>
571
+ <span class="ruby-keyword">return</span> <span class="ruby-node">&quot;I#{$&#39;}&quot;</span>
572
+ <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
573
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">nil</span>
574
+ <span class="ruby-keyword">end</span>
575
+ <span class="ruby-keyword">end</span></pre>
576
+ </div>
577
+
578
+ </div>
579
+
580
+
581
+
582
+
583
+ </div>
578
584
 
579
585
 
580
586
  <div id="method-i-ref_count" class="method-detail ">
@@ -582,7 +588,9 @@ hash of all 4 nt counts, returns a hash</p>
582
588
  <div class="method-heading">
583
589
  <span class="method-name">ref_count</span><span
584
590
  class="method-args">()</span>
591
+
585
592
  <span class="method-click-advice">click to toggle source</span>
593
+
586
594
  </div>
587
595
 
588
596
 
@@ -590,6 +598,7 @@ hash of all 4 nt counts, returns a hash</p>
590
598
 
591
599
  <p>returns the count of reference-bases in the reads at this position</p>
592
600
 
601
+
593
602
 
594
603
 
595
604
  <div class="method-source-code" id="ref_count-source">
@@ -600,14 +609,14 @@ hash of all 4 nt counts, returns a hash</p>
600
609
  <span class="ruby-keyword">end</span>
601
610
  <span class="ruby-ivar">@ref_count</span>
602
611
  <span class="ruby-keyword">end</span></pre>
603
- </div><!-- ref_count-source -->
612
+ </div>
604
613
 
605
614
  </div>
606
615
 
607
616
 
608
617
 
609
618
 
610
- </div><!-- ref_count-method -->
619
+ </div>
611
620
 
612
621
 
613
622
  <div id="method-i-to_s" class="method-detail ">
@@ -615,18 +624,21 @@ hash of all 4 nt counts, returns a hash</p>
615
624
  <div class="method-heading">
616
625
  <span class="method-name">to_s</span><span
617
626
  class="method-args">()</span>
627
+
618
628
  <span class="method-click-advice">click to toggle source</span>
629
+
619
630
  </div>
620
631
 
621
632
 
622
633
  <div class="method-description">
623
634
 
624
- <p>returns pileup format line as</p>
635
+ <p>returns pileup format line</p>
636
+
625
637
 
626
638
 
627
639
 
628
640
  <div class="method-source-code" id="to_s-source">
629
- <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 197</span>
641
+ <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 201</span>
630
642
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
631
643
  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@read_quals</span> <span class="ruby-keyword">and</span> <span class="ruby-operator">!</span><span class="ruby-ivar">@consensus_quality</span> <span class="ruby-comment">#6col</span>
632
644
  [<span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
@@ -637,14 +649,14 @@ hash of all 4 nt counts, returns a hash</p>
637
649
  <span class="ruby-keyword">end</span>
638
650
 
639
651
  <span class="ruby-keyword">end</span></pre>
640
- </div><!-- to_s-source -->
652
+ </div>
641
653
 
642
654
  </div>
643
655
 
644
656
 
645
657
 
646
658
 
647
- </div><!-- to_s-method -->
659
+ </div>
648
660
 
649
661
 
650
662
  <div id="method-i-to_vcf" class="method-detail ">
@@ -652,47 +664,48 @@ hash of all 4 nt counts, returns a hash</p>
652
664
  <div class="method-heading">
653
665
  <span class="method-name">to_vcf</span><span
654
666
  class="method-args">()</span>
667
+
655
668
  <span class="method-click-advice">click to toggle source</span>
669
+
656
670
  </div>
657
671
 
658
672
 
659
673
  <div class="method-description">
660
674
 
661
675
  <p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it
662
- scrimps on the ref for indels, returning a ‘*’ instead of the reference
663
- allele</p>
676
+ scrimps on the ref for indels, returning a &#39;*&#39; instead of the
677
+ reference allele</p>
678
+
664
679
 
665
680
 
666
681
 
667
682
  <div class="method-source-code" id="to_vcf-source">
668
683
  <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 103</span>
669
684
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_vcf</span>
670
-
671
685
  <span class="ruby-identifier">alt</span>,<span class="ruby-identifier">g</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">genotype_list</span>
672
- <span class="ruby-identifier">alt</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">consensus</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">%r/</span>).<span class="ruby-identifier">join</span>(<span class="ruby-string">','</span>) <span class="ruby-keyword">unless</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
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- <span class="ruby-identifier">alt</span> = <span class="ruby-string">'.'</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>
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- [<span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_name</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pos</span>, <span class="ruby-string">'.'</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>, <span class="ruby-identifier">alt</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-string">&quot;0&quot;</span>, <span class="ruby-node">&quot;DP=#{self.coverage.to_i}&quot;</span>, <span class="ruby-string">&quot;GT:GQ:DP&quot;</span>, <span class="ruby-node">&quot;#{g}:#{self.consensus_quality.to_i}:#{self.coverage.to_i}&quot;</span> ].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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+ <span class="ruby-identifier">alt</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">consensus</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">//</span>).<span class="ruby-identifier">join</span>(<span class="ruby-string">&#39;,&#39;</span>) <span class="ruby-keyword">unless</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&#39;*&#39;</span>
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+ <span class="ruby-identifier">alt</span> = <span class="ruby-string">&#39;.&#39;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>
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+ [<span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_name</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pos</span>, <span class="ruby-string">&#39;.&#39;</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span>, <span class="ruby-identifier">alt</span>, <span class="ruby-keyword">self</span>.<span class="ruby-identifier">snp_quality</span>.<span class="ruby-identifier">to_i</span>, <span class="ruby-string">&quot;0&quot;</span>, <span class="ruby-node">&quot;DP=#{self.coverage.to_i}&quot;</span>, <span class="ruby-string">&quot;GT:GQ:DP&quot;</span>, <span class="ruby-node">&quot;#{g}:#{self.consensus_quality.to_i}:#{self.coverage.to_i}&quot;</span> ].<span class="ruby-identifier">join</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- to_vcf-source -->
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+ </div>
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  </div>
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- </div><!-- to_vcf-method -->
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+ </div>
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- </section><!-- public-instance-method-details -->
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+ </section>
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- </section><!-- 5Buntitled-5D -->
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-
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- </div><!-- documentation -->
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+ </section>
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+ </main>
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- <footer id="validator-badges">
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- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ <footer id="validator-badges" role="contentinfo">
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+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
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+ <p>Generated by <a href="http://rdoc.rubyforge.org">RDoc</a> 4.1.1.
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+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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  </footer>
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