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.html CHANGED
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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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+ <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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+ <a href="../index.html" rel="home">Home</a>
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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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- <li>lib/bio/db/sam/bam.rb
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- <li>lib/bio/db/sam.rb
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494
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540
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601
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609
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475
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-
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- <div class="method-source-code" id="new-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 556</span>
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- <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
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- <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>,
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-value">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
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- <span class="ruby-keyword">end</span></pre>
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- </div><!-- new-source -->
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-
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- </div>
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-
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-
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-
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-
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- </div><!-- new-method -->
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-
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-
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- </section><!-- public-class-method-details -->
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-
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- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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- <h3 class="section-header">Public Instance Methods</h3>
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-
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-
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- <div id="method-i-sam-3D" class="method-detail ">
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-
660
- <div class="method-heading">
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- <span class="method-name">sam=</span><span
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- class="method-args">(sam)</span>
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  <span class="method-click-advice">click to toggle source</span>
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+
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  </div>
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  <div class="method-description">
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+ <p>parses the SAM string into its constituents and set its attributes</p>
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- <div class="method-source-code" id="sam-3D-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 614</span>
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- <span class="ruby-keyword">def</span> <span class="ruby-identifier">sam=</span>(<span class="ruby-identifier">sam</span>)
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- <span class="ruby-comment">#p sam</span>
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- <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">flag</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mapq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">4</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mpos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">isize</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">8</span>].<span class="ruby-identifier">to_i</span>
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
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- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">tags</span> = {}
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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/alignment.rb, line 24</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">sam_string</span>)
499
+ <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam_string</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>)
500
+ <span class="ruby-ivar">@qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
501
+ <span class="ruby-ivar">@flag</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
502
+ <span class="ruby-ivar">@rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
503
+ <span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span>
504
+ <span class="ruby-ivar">@mapq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">4</span>].<span class="ruby-identifier">to_i</span>
505
+ <span class="ruby-ivar">@cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
506
+ <span class="ruby-ivar">@mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
507
+ <span class="ruby-ivar">@mpos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">to_i</span>
508
+ <span class="ruby-ivar">@isize</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">8</span>].<span class="ruby-identifier">to_i</span>
509
+ <span class="ruby-ivar">@seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
510
+ <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
511
+ <span class="ruby-ivar">@tags</span> = {}
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512
  <span class="ruby-value">11</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">s</span>.<span class="ruby-identifier">size</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
691
- <span class="ruby-identifier">t</span> = <span class="ruby-constant">Tag</span>.<span class="ruby-identifier">new</span>
513
+ <span class="ruby-identifier">t</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">Tag</span>.<span class="ruby-identifier">new</span>
692
514
  <span class="ruby-identifier">t</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">s</span>[<span class="ruby-identifier">n</span>])
693
515
  <span class="ruby-identifier">tags</span>[<span class="ruby-identifier">t</span>.<span class="ruby-identifier">tag</span>] = <span class="ruby-identifier">t</span>
694
- }
695
-
696
-
697
- <span class="ruby-comment">#&lt;QNAME&gt; &lt;FLAG&gt; &lt;RNAME&gt; &lt;POS&gt; &lt;MAPQ&gt; &lt;CIGAR&gt; &lt;MRNM&gt; &lt;MPOS&gt; &lt;ISIZE&gt; &lt;SEQ&gt; &lt;QUAL&gt; \</span>
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- <span class="ruby-comment">#[&lt;TAG&gt;:&lt;VTYPE&gt;:&lt;VALUE&gt; [...]] </span>
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-
700
- <span class="ruby-keyword">end</span></pre>
701
- </div><!-- sam-3D-source -->
702
-
703
- </div>
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-
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-
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-
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-
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- </div><!-- sam-3D-method -->
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-
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-
711
- <div id="method-i-set" class="method-detail ">
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-
713
- <div class="method-heading">
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- <span class="method-name">set</span><span
715
- class="method-args">(bam_alignment, header)</span>
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- <span class="method-click-advice">click to toggle source</span>
717
- </div>
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-
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-
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- <div class="method-description">
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-
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-
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-
724
-
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-
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- <div class="method-source-code" id="set-source">
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- <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 582</span>
728
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
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- <span class="ruby-comment">#Create the FFI object</span>
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- <span class="ruby-ivar">@al</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">Bam1T</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">bam_alignment</span>)
731
-
732
- <span class="ruby-comment">#set the raw data</span>
733
- <span class="ruby-identifier">tmp_str</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_format1</span>(<span class="ruby-identifier">header</span>,<span class="ruby-identifier">al</span>)
734
- <span class="ruby-comment">#self.sam = tmp_str</span>
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- <span class="ruby-comment">#ObjectSpace.define_finalizer(self, proc {|id| puts &quot;Finalizer one on #{id}&quot; })</span>
736
- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">sam</span> = <span class="ruby-constant">String</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">tmp_str</span>)
737
- <span class="ruby-comment">#LibC.free tmp_str</span>
738
- <span class="ruby-comment">#Set values calculated by libbam</span>
739
- <span class="ruby-identifier">core</span> = <span class="ruby-identifier">al</span>[<span class="ruby-value">:core</span>]
740
- <span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">al</span>[<span class="ruby-value">:data</span>][<span class="ruby-identifier">core</span>[<span class="ruby-value">:l_qname</span>]]<span class="ruby-comment">#define bam1_cigar(b) ((uint32_t*)((b)-&gt;data + (b)-&gt;core.l_qname)) </span>
741
- <span class="ruby-ivar">@calend</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_calend</span>(<span class="ruby-identifier">core</span>,<span class="ruby-identifier">cigar</span>)
742
- <span class="ruby-ivar">@qlen</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_cigar2qlen</span>(<span class="ruby-identifier">core</span>,<span class="ruby-identifier">cigar</span>)
743
-
744
- <span class="ruby-comment">#process the flags</span>
745
- <span class="ruby-ivar">@is_paired</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0001</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
746
- <span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0002</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
747
- <span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0004</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
748
- <span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0008</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
749
- <span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0010</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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- <span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0020</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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- <span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0040</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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- <span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0080</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
753
- <span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0100</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
754
- <span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0200</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
755
- <span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0400</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
516
+ }
517
+
518
+ <span class="ruby-ivar">@is_paired</span> = (<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0001</span>) <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
519
+ <span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0002</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
520
+ <span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0004</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0008</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0010</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
523
+ <span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0020</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
524
+ <span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0040</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
525
+ <span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0080</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
526
+ <span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0100</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
527
+ <span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0200</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
528
+ <span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0400</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
756
529
 
757
530
  <span class="ruby-keyword">end</span></pre>
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- </div><!-- set-source -->
531
+ </div>
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532
 
760
533
  </div>
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534
 
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536
 
764
537
 
765
- </div><!-- set-method -->
538
+ </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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775
- <footer id="validator-badges">
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- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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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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