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/Tag.html CHANGED
@@ -2,145 +2,96 @@
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  <html>
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  <head>
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- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <meta charset="UTF-8">
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  <title>class Bio::DB::Tag - Pileup</title>
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- <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+ <link href="../../fonts.css" rel="stylesheet">
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- <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
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- <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
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+ <script src="../../js/jquery.js"></script>
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+ <script src="../../js/navigation.js"></script>
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+ <script src="../../js/search_index.js"></script>
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+ <script src="../../js/search.js"></script>
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+ <script src="../../js/searcher.js"></script>
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+ <script src="../../js/darkfish.js"></script>
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- <body id="top" class="class">
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- <nav id="metadata">
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- <nav id="home-section" class="section">
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- <h3 class="section-header">
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- <a href="../../index.html">Home</a>
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+ <body id="top" role="document" class="class">
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+ <nav role="navigation">
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+ <div id="project-navigation">
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <h2>
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+ <a href="../../index.html" rel="home">Home</a>
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+ </h2>
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+
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+ <div id="table-of-contents-navigation">
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+ <a href="../../table_of_contents.html#pages">Pages</a>
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  <a href="../../table_of_contents.html#classes">Classes</a>
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  <a href="../../table_of_contents.html#methods">Methods</a>
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- </h3>
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- </nav>
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-
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+ </div>
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+ </div>
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- <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <div id="search-section" role="search" class="project-section initially-hidden">
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  <form action="#" method="get" accept-charset="utf-8">
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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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-
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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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-
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-
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  </div>
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  <div id="class-metadata">
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- <nav id="parent-class-section" class="section">
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Parent</h3>
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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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- <ul class="link-list">
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+ <ul class="link-list" role="directory">
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- <li><a href="#method-i-set">#set</a>
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+ <li ><a href="#method-i-set">#set</a>
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- <nav id="classindex-section" class="section project-section">
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- <h3 class="section-header">Class and Module Index</h3>
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+ <main role="main" aria-labelledby="class-Bio::DB::Tag">
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+ <h1 id="class-Bio::DB::Tag" class="class">
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+ class Bio::DB::Tag
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+ </h1>
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- <li><a href="../../Bio/DB.html">Bio::DB</a>
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-
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- <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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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/Library.html">Bio::DB::SAM::Library</a>
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- <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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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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- <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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- <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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- <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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- <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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-
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- <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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-
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- <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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- <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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+ <p>a class to represent the SAM OPT values, presented in SAM as
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+ <span class="ruby-ivar">@value</span> = <span class="ruby-identifier">str</span>[<span class="ruby-value">5</span><span class="ruby-operator">..</span><span class="ruby-value">-1</span>]
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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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-
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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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- <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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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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- <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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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">
89
+ <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>
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+ <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
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  <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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  <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>
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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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