bio-samtools 0.6.2 → 2.0.3

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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/SAMException.src/M000016.html DELETED
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- <title>new (Bio::DB::SAMException)</title>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 480</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>()
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data/doc/classes/Bio/DB/Sam.src/M000017.html DELETED
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- <title>new (Bio::DB::Sam)</title>
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- <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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- <body class="standalone-code">
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 27</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">optsa</span>={})
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- <span class="ruby-identifier">opts</span> = { <span class="ruby-identifier">:fasta</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">:bam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>,<span class="ruby-identifier">:tam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">:compressed</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>, <span class="ruby-identifier">:write</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">optsa</span>)
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-
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-
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- <span class="ruby-ivar">@fasta_path</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:fasta</span>]
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- <span class="ruby-ivar">@compressed</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:compressed</span>]
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- <span class="ruby-ivar">@write</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:write</span>]
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- <span class="ruby-identifier">bam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:bam</span>]
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- <span class="ruby-identifier">tam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:tam</span>]
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-
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- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword kw">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 kw">nil</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No alignment or reference file&quot;</span>
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Alignment has to be in either text or binary format, not both&quot;</span>
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword kw">true</span>
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- <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">bam</span>
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- <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">tam</span>
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- <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword kw">false</span>
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-
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-ivar">@fasta_file</span> = <span class="ruby-keyword kw">nil</span>
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- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
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- <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-identifier">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
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- <span class="ruby-keyword kw">end</span></pre>
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data/doc/classes/Bio/DB/Sam.src/M000018.html DELETED
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 58</span>
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">open</span>()
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-
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Writing not supported yet&quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@write</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No SAM file specified&quot;</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam</span>
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- <span class="ruby-identifier">opts</span> = <span class="ruby-ivar">@write</span> <span class="ruby-operator">?</span> <span class="ruby-value str">&quot;w&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-value str">&quot;r&quot;</span>
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- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@binary</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">&quot;b&quot;</span>
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- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@write</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">&quot;u&quot;</span>
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- <span class="ruby-keyword kw">end</span>
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- <span class="ruby-identifier">valid</span> = [<span class="ruby-value str">&quot;r&quot;</span>, <span class="ruby-value str">&quot;w&quot;</span>, <span class="ruby-value str">&quot;wh&quot;</span>, <span class="ruby-value str">&quot;rb&quot;</span>, <span class="ruby-value str">&quot;wb&quot;</span> , <span class="ruby-value str">&quot;wbu&quot;</span>]
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- <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">valid</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-keyword kw">then</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Invalid options for samopen: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">opts</span>
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- <span class="ruby-keyword kw">end</span>
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-
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- <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 kw">nil</span>)
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- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">samFile</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
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- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;File not opened: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
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- <span class="ruby-keyword kw">end</span>
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- <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>)
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data/doc/classes/Bio/DB/Sam.src/M000019.html DELETED
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- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>()
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- (<span class="ruby-ivar">@binary</span> <span class="ruby-operator">?</span> <span class="ruby-value str">&quot;Binary&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-value str">&quot;Text&quot;</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">&quot; file: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot; with fasta: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
16
- <span class="ruby-keyword kw">end</span></pre>
17
- </body>
18
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data/doc/classes/Bio/DB/Sam.src/M000020.html DELETED
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 93</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>()
15
- <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 kw">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>
16
- <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 kw">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>
17
- <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 kw">unless</span> <span class="ruby-ivar">@sam_file</span>.<span class="ruby-identifier">nil?</span>
18
- <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
19
- <span class="ruby-ivar">@fasta_index</span> = <span class="ruby-keyword kw">nil</span>
20
- <span class="ruby-keyword kw">end</span></pre>
21
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22
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data/doc/classes/Bio/DB/Sam.src/M000021.html DELETED
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12
- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 102</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-constant">Sam</span>.<span class="ruby-identifier">finalize</span>(<span class="ruby-identifier">id</span>)
15
- <span class="ruby-identifier">id</span>.<span class="ruby-identifier">close</span>()
16
- <span class="ruby-identifier">puts</span> <span class="ruby-node">&quot;Finalizing #{id} at #{Time.new}&quot;</span>
17
- <span class="ruby-keyword kw">end</span></pre>
18
- </body>
19
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data/doc/classes/Bio/DB/Sam.src/M000022.html DELETED
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- <body class="standalone-code">
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 112</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">load_index</span>()
15
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Indexes are only supported by BAM files, please use samtools to convert your SAM file&quot;</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@binary</span>
16
- <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>)
17
- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
18
- <span class="ruby-identifier">p</span> <span class="ruby-value str">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
19
- <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>)
20
- <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>)
21
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Unable to generate bam index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword kw">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>
22
- <span class="ruby-keyword kw">end</span>
23
- <span class="ruby-keyword kw">end</span></pre>
24
- </body>
25
- </html>
data/doc/classes/Bio/DB/Sam.src/M000023.html DELETED
@@ -1,28 +0,0 @@
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- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 126</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">load_reference</span>()
15
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No path for the refernce fasta file. &quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_path</span>.<span class="ruby-identifier">nil?</span>
16
-
17
- <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>)
18
-
19
- <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
20
- <span class="ruby-identifier">p</span> <span class="ruby-value str">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
21
- <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>)
22
- <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>)
23
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&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 kw">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>
24
- <span class="ruby-keyword kw">end</span>
25
-
26
- <span class="ruby-keyword kw">end</span></pre>
27
- </body>
28
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data/doc/classes/Bio/DB/Sam.src/M000024.html DELETED
@@ -1,28 +0,0 @@
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- <title>average_coverage (Bio::DB::Sam)</title>
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- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 141</span>
14
- <span class="ruby-keyword kw">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>)
15
-
16
- <span class="ruby-comment cmt">#reference = fetch_reference(chromosome, qstart,len)</span>
17
- <span class="ruby-comment cmt"># len = reference.length if len &gt; reference.length</span>
18
-
19
-
20
- <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>)
21
- <span class="ruby-identifier">total</span> = <span class="ruby-value">0</span>
22
- <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>] }
23
- <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>
24
- <span class="ruby-comment cmt">#LibC.free reference</span>
25
- <span class="ruby-identifier">avg_cov</span>
26
- <span class="ruby-keyword kw">end</span></pre>
27
- </body>
28
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data/doc/classes/Bio/DB/Sam.src/M000025.html DELETED
@@ -1,46 +0,0 @@
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- <head>
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- <title>chromosome_coverage (Bio::DB::Sam)</title>
9
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10
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11
- </head>
12
- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 158</span>
14
- <span class="ruby-keyword kw">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>)
15
- <span class="ruby-comment cmt"># reference = fetch_reference(chromosome, qstart,len)</span>
16
- <span class="ruby-comment cmt"># len = reference.length if len &gt; reference.length</span>
17
- <span class="ruby-comment cmt">#p qend.to_s + &quot;-&quot; + qstart.to_s + &quot;framesize &quot; + (qend - qstart).to_s</span>
18
- <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>)
19
-
20
- <span class="ruby-identifier">chr_cov_proc</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
21
- <span class="ruby-comment cmt">#last = qstart + len</span>
22
- <span class="ruby-comment cmt">#first = qstart</span>
23
- <span class="ruby-comment cmt">#last = alignment.calend if last &gt; alignment.calend</span>
24
- <span class="ruby-comment cmt">#first = alignment.pos if first &lt; alignment.pos</span>
25
- <span class="ruby-comment cmt"># p first</span>
26
- <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>
27
- <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>
28
- <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">last</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">first</span>
29
- <span class="ruby-identifier">tmp</span> = <span class="ruby-identifier">last</span>
30
- <span class="ruby-identifier">last</span> = <span class="ruby-identifier">first</span>
31
- <span class="ruby-identifier">first</span> = <span class="ruby-identifier">last</span>
32
- <span class="ruby-keyword kw">end</span>
33
-
34
- <span class="ruby-comment cmt"># STDERR.puts &quot;#{first} #{last}\n&quot;</span>
35
- <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>
36
-
37
- <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 kw">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>
38
- }
39
- <span class="ruby-keyword kw">end</span>
40
-
41
- <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>)
42
- <span class="ruby-comment cmt">#p coverages</span>
43
- <span class="ruby-identifier">coverages</span>
44
- <span class="ruby-keyword kw">end</span></pre>
45
- </body>
46
- </html>
data/doc/classes/Bio/DB/Sam.src/M000026.html DELETED
@@ -1,24 +0,0 @@
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- <title>fetch_reference (Bio::DB::Sam)</title>
9
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10
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11
- </head>
12
- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 191</span>
14
- <span class="ruby-keyword kw">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>)
15
- <span class="ruby-identifier">load_reference</span> <span class="ruby-keyword kw">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>
16
- <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>)
17
- <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-identifier">:int</span>
18
- <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>)
19
- <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Unable to get sequence for reference: &quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">query</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">reference</span>.<span class="ruby-identifier">nil?</span>
20
-
21
- <span class="ruby-identifier">reference</span>
22
- <span class="ruby-keyword kw">end</span></pre>
23
- </body>
24
- </html>
data/doc/classes/Bio/DB/Sam.src/M000027.html DELETED
@@ -1,19 +0,0 @@
1
- <?xml version="1.0" encoding="iso-8859-1"?>
2
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- <head>
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- <title>query_string (Bio::DB::Sam)</title>
9
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10
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11
- </head>
12
- <body class="standalone-code">
13
- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 203</span>
14
- <span class="ruby-keyword kw">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>)
15
- <span class="ruby-identifier">query</span> = <span class="ruby-identifier">chromosome</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&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-value str">&quot;-&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qend</span>.<span class="ruby-identifier">to_s</span>
16
- <span class="ruby-identifier">query</span>
17
- <span class="ruby-keyword kw">end</span></pre>
18
- </body>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 209</span>
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- <span class="ruby-keyword kw">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>)
15
- <span class="ruby-identifier">als</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
- <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
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- <span class="ruby-identifier">als</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">clone</span>)
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- <span class="ruby-value">0</span>
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- <span class="ruby-keyword kw">end</span>
20
- <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>)
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 224</span>
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- <span class="ruby-keyword kw">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>)
15
- <span class="ruby-identifier">load_index</span> <span class="ruby-keyword kw">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>
16
- <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-identifier">:int</span>
17
- <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-identifier">:int</span>
18
- <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-identifier">:int</span>
19
- <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>)
20
- <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>)
21
- <span class="ruby-identifier">header</span> = <span class="ruby-ivar">@sam_file</span>[<span class="ruby-identifier">:header</span>]
22
- <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>)
23
- <span class="ruby-comment cmt">#raise SAMException.new(), &quot;invalid query: &quot; + query if(chr.read_int &lt; 0)</span>
24
- <span class="ruby-identifier">count</span> = <span class="ruby-value">0</span>;
25
-
26
- <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">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>
27
- <span class="ruby-identifier">alignment</span> = <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">new</span>
28
- <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>)
29
- <span class="ruby-identifier">function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">alignment</span>)
30
- <span class="ruby-identifier">count</span> = <span class="ruby-identifier">count</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
31
- <span class="ruby-value">0</span>
32
- <span class="ruby-keyword kw">end</span>
33
- <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-identifier">:x</span>][<span class="ruby-identifier">: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 kw">nil</span>, <span class="ruby-identifier">fetchAlignment</span>)
34
- <span class="ruby-comment cmt">#LibC.free chr</span>
35
- <span class="ruby-comment cmt">#LibC.free beg</span>
36
- <span class="ruby-comment cmt">#LibC.free last</span>
37
- <span class="ruby-comment cmt">#LibC.free qpointer</span>
38
- <span class="ruby-identifier">count</span>
39
- <span class="ruby-keyword kw">end</span></pre>
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- <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 257</span>
14
- <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">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>)
15
- <span class="ruby-identifier">strptrs</span> = []
16
- <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-value str">&quot;merge&quot;</span>)
17
- <span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
18
- <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>)
19
- <span class="ruby-keyword kw">end</span>
20
- <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword kw">nil</span>
21
-
22
- <span class="ruby-comment cmt"># Now load all the pointers into a native memory block</span>
23
- <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-identifier">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
24
- <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
25
- <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>)
26
- <span class="ruby-keyword kw">end</span>
27
- <span class="ruby-comment cmt">#void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)</span>
28
- <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>)
29
- <span class="ruby-keyword kw">end</span></pre>
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