bio-samtools 0.6.2 → 2.0.3

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  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/Tag.html CHANGED
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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::Tag - Pileup</title>
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- <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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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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+ <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#methods">Methods</a>
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- </h3>
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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/sam.rb
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- </ul>
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- </nav>
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+ <div id="parent-class-section" class="nav-section">
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+ class Bio::DB::Tag
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data/doc/Bio/DB/Vcf.html CHANGED
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- <li>lib/bio/db/vcf.rb
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+ <ul id="search-results" aria-label="Search Results"
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-
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- <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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-
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- <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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- <li><a href="../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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-
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- <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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- <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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-
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-
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- <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
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-
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-
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- <li><a href="../../LibC.html">LibC</a>
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-
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- </nav>
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+ </div>
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- <div id="documentation">
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- <h1 class="class">class Bio::DB::Vcf</h1>
88
+ <main role="main" aria-labelledby="class-Bio::DB::Vcf">
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+ <h1 id="class-Bio::DB::Vcf" class="class">
90
+ class Bio::DB::Vcf
91
+ </h1>
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- <!-- Attributes -->
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+ <h3>Attributes</h3>
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+ </header>
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Class Methods</h3>
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+ </header>
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  <div id="method-c-new" class="method-detail ">
@@ -306,16 +256,20 @@
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  <div class="method-heading">
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  <span class="method-name">new</span><span
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  class="method-args">(line=nil, sample_names=nil)</span>
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+
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  </div>
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  <p>create the vcf object, use the ordered list of sample names to label
316
- samples if provided [‘A’, ‘B’, ‘C’], otherwise uses, 1,2,3 etc
317
- vcf = Bio::DB::Vcf(“19 111 . A C 9.6 . .
318
- GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3”)</p>
268
+ samples if provided [&#39;A&#39;, &#39;B&#39;, &#39;C&#39;], otherwise
269
+ uses, 1,2,3 etc</p>
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+
271
+ <pre>vcf = Bio::DB::Vcf(&quot;19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3&quot;)</pre>
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@@ -326,20 +280,22 @@ GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3”)</p>
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  <span class="ruby-ivar">@samples</span> = {}
327
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  <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>) <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">nil</span>
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@@ -347,29 +303,35 @@ GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3”)</p>
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+ <p>tests if the current variable is an Integer</p>
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+ <p>x - any variable</p>
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- <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 21</span>
323
+ <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 23</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">int_or_raw</span>(<span class="ruby-identifier">x</span>)
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  <span class="ruby-constant">Integer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">x</span>) <span class="ruby-keyword">rescue</span> <span class="ruby-identifier">x</span>
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  <span class="ruby-keyword">end</span></pre>
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@@ -377,7 +339,9 @@ GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3”)</p>
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@@ -386,52 +350,53 @@ GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3”)</p>
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  <p>gets the info in the <a href="Vcf.html">Vcf</a> lines and parses it,
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  setting the attributes</p>
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- <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 26</span>
357
+ <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 28</span>
393
358
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">parse_line</span>(<span class="ruby-identifier">line</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
394
- <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">'#'</span>
395
-
359
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">line</span>[<span class="ruby-value">0</span>,<span class="ruby-value">1</span>] <span class="ruby-operator">==</span> <span class="ruby-string">&#39;#&#39;</span>
360
+
396
361
  <span class="ruby-identifier">f</span> = <span class="ruby-identifier">line</span>.<span class="ruby-identifier">chomp</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>, <span class="ruby-value">-1</span>)
397
362
  <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;VCF lines must have at least 8 fields&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">8</span>
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  <span class="ruby-ivar">@chrom</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">0</span>]
399
364
  <span class="ruby-ivar">@pos</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
400
- <span class="ruby-ivar">@id</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>]
365
+ <span class="ruby-ivar">@id</span> = <span class="ruby-string">&#39;.&#39;</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">2</span>]
401
366
  <span class="ruby-ivar">@ref</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">3</span>]
402
367
  <span class="ruby-ivar">@alt</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">4</span>]
403
368
  <span class="ruby-ivar">@qual</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">5</span>].<span class="ruby-identifier">to_f</span>
404
- <span class="ruby-ivar">@filter</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>]
405
-
406
- <span class="ruby-ivar">@info</span> = <span class="ruby-string">'.'</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> {}
369
+ <span class="ruby-ivar">@filter</span> = <span class="ruby-string">&#39;.&#39;</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">6</span>]
370
+
371
+ <span class="ruby-ivar">@info</span> = <span class="ruby-string">&#39;.&#39;</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>] <span class="ruby-operator">?</span> <span class="ruby-keyword">nil</span> <span class="ruby-operator">:</span> {}
407
372
  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@info</span>
408
373
  <span class="ruby-identifier">info_vec</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;;&quot;</span>)
409
374
  <span class="ruby-identifier">info_vec</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span>
410
375
  <span class="ruby-identifier">keyval</span> = <span class="ruby-identifier">x</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;=&quot;</span>, <span class="ruby-value">-1</span>)
411
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">keyval</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span> <span class="ruby-comment"># If it's key=value</span>
376
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">keyval</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">2</span> <span class="ruby-comment"># If it&#39;s key=value</span>
412
377
  <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">keyval</span>[<span class="ruby-value">0</span>]] = <span class="ruby-identifier">keyval</span>[<span class="ruby-value">1</span>]
413
- <span class="ruby-keyword">else</span> <span class="ruby-comment"># Otherwise, it's just a flag</span>
378
+ <span class="ruby-keyword">else</span> <span class="ruby-comment"># Otherwise, it&#39;s just a flag</span>
414
379
  <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">x</span>] = <span class="ruby-keyword">nil</span>
415
380
  <span class="ruby-keyword">end</span>
416
381
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417
382
  <span class="ruby-keyword">end</span>
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-
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+
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  <span class="ruby-ivar">@samples</span> = {}
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  <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">8</span> <span class="ruby-comment"># Has just upto info</span>
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- <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Can't have format with no samples&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">9</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-string">&quot;Can&#39;t have format with no samples&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">9</span>
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  <span class="ruby-ivar">@format</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">8</span>]
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-
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+
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  <span class="ruby-identifier">sample_keys</span> = <span class="ruby-ivar">@format</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
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-
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+
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  <span class="ruby-identifier">num_samples</span> = <span class="ruby-identifier">f</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">-</span> <span class="ruby-value">9</span> <span class="ruby-comment"># How many fields are past the format</span>
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-
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+
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  <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_names</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">nil</span> <span class="ruby-comment"># Make the sample names just [&quot;1&quot;, &quot;2&quot;, ... , &quot;num_samples}&quot;</span>
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  <span class="ruby-identifier">sample_names</span> = (<span class="ruby-value">1</span><span class="ruby-operator">..</span><span class="ruby-identifier">num_samples</span>).<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">i</span>.<span class="ruby-identifier">to_s</span>}
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  <span class="ruby-keyword">elsif</span> <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">num_samples</span>
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  <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Unexpected number of samples (#{num_samples}) based on the provided sample names (#{sample_names.inspect})&quot;</span>
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  <span class="ruby-keyword">end</span>
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-
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+
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  <span class="ruby-identifier">sample_names</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">sample_name</span>, <span class="ruby-identifier">sample_index</span><span class="ruby-operator">|</span>
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  <span class="ruby-identifier">i</span> = <span class="ruby-identifier">sample_index</span> <span class="ruby-operator">+</span> <span class="ruby-value">9</span> <span class="ruby-comment"># index into columns (f)</span>
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  <span class="ruby-identifier">sample_values</span> = <span class="ruby-identifier">f</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;:&quot;</span>)
@@ -442,26 +407,25 @@ setting the attributes</p>
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  <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span>;
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- parse_line-source -->
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  </div>
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- </div><!-- parse_line-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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