bio-samtools-wrapper 2.7.0

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  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.travis.yml +27 -0
  4. data/Gemfile +20 -0
  5. data/LICENSE.txt +702 -0
  6. data/README.md +501 -0
  7. data/Rakefile +73 -0
  8. data/VERSION +1 -0
  9. data/bin/bam_consensus.rb +85 -0
  10. data/bio-samtools-wrapper.gemspec +181 -0
  11. data/doc/Bio/DB/Alignment.html +552 -0
  12. data/doc/Bio/DB/Pileup.html +711 -0
  13. data/doc/Bio/DB/SAM/Library.html +167 -0
  14. data/doc/Bio/DB/SAM/Tools.html +109 -0
  15. data/doc/Bio/DB/SAM.html +1853 -0
  16. data/doc/Bio/DB/Tag.html +208 -0
  17. data/doc/Bio/DB/Vcf.html +431 -0
  18. data/doc/Bio/DB.html +105 -0
  19. data/doc/Bio.html +175 -0
  20. data/doc/LICENSE_txt.html +846 -0
  21. data/doc/created.rid +9 -0
  22. data/doc/fonts/Lato-Light.ttf +0 -0
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  27. data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
  28. data/doc/fonts.css +167 -0
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  54. data/doc/index.html +106 -0
  55. data/doc/js/darkfish.js +140 -0
  56. data/doc/js/jquery.js +18 -0
  57. data/doc/js/navigation.js +142 -0
  58. data/doc/js/search.js +109 -0
  59. data/doc/js/search_index.js +1 -0
  60. data/doc/js/searcher.js +228 -0
  61. data/doc/rdoc.css +580 -0
  62. data/doc/table_of_contents.html +305 -0
  63. data/ext/Makefile-bioruby.patch +12 -0
  64. data/ext/Makefile-suse.patch +11 -0
  65. data/ext/mkrf_conf.rb +118 -0
  66. data/lib/bio/BIOExtensions.rb +89 -0
  67. data/lib/bio/db/alignment.rb +64 -0
  68. data/lib/bio/db/fastadb.rb +320 -0
  69. data/lib/bio/db/pileup.rb +273 -0
  70. data/lib/bio/db/sam/external/COPYING +21 -0
  71. data/lib/bio/db/sam/external/VERSION +1 -0
  72. data/lib/bio/db/sam/library.rb +32 -0
  73. data/lib/bio/db/sam.rb +778 -0
  74. data/lib/bio/db/vcf.rb +105 -0
  75. data/lib/bio-samtools-wrapper.rb +9 -0
  76. data/test/.gitignore +1 -0
  77. data/test/helper.rb +18 -0
  78. data/test/sample.vcf +24 -0
  79. data/test/samples/.gitignore +1 -0
  80. data/test/samples/LCI/NC_001988.ffn +2 -0
  81. data/test/samples/LCI/test.bam +0 -0
  82. data/test/samples/LCI/test.bam.bai +0 -0
  83. data/test/samples/small/dupes.bam +0 -0
  84. data/test/samples/small/dupes.sam +274 -0
  85. data/test/samples/small/ids2.txt +1 -0
  86. data/test/samples/small/map_for_reheader.sam +8 -0
  87. data/test/samples/small/map_to_merge1.bam +0 -0
  88. data/test/samples/small/map_to_merge1.bam.bai +0 -0
  89. data/test/samples/small/map_to_merge1.sam +8 -0
  90. data/test/samples/small/map_to_merge2.bam +0 -0
  91. data/test/samples/small/map_to_merge2.bam.bai +0 -0
  92. data/test/samples/small/map_to_merge2.sam +8 -0
  93. data/test/samples/small/no_md.sam +8 -0
  94. data/test/samples/small/sorted.bam +0 -0
  95. data/test/samples/small/sorted.bam.bai +0 -0
  96. data/test/samples/small/test.sai +0 -0
  97. data/test/samples/small/test.tam +10 -0
  98. data/test/samples/small/test_chr.fasta +1000 -0
  99. data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
  100. data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
  101. data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
  102. data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
  103. data/test/samples/small/test_chr.fasta.amb +2 -0
  104. data/test/samples/small/test_chr.fasta.ann +3 -0
  105. data/test/samples/small/test_chr.fasta.bwt +0 -0
  106. data/test/samples/small/test_chr.fasta.pac +0 -0
  107. data/test/samples/small/test_chr.fasta.rbwt +0 -0
  108. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
  109. data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
  110. data/test/samples/small/test_chr.fasta.rpac +0 -0
  111. data/test/samples/small/test_chr.fasta.rsa +0 -0
  112. data/test/samples/small/test_chr.fasta.sa +0 -0
  113. data/test/samples/small/test_cov.svg +273 -0
  114. data/test/samples/small/test_fastadb.fasta +34 -0
  115. data/test/samples/small/testu.bam +0 -0
  116. data/test/samples/small/testu.bed +2 -0
  117. data/test/test_bio-samtools-wrapper.rb +1 -0
  118. data/test/test_fastadb.rb +89 -0
  119. data/test/test_pileup.rb +90 -0
  120. data/test/test_sam.rb +421 -0
  121. data/test/test_vcf.rb +79 -0
  122. data/tutorial/tutorial.html +474 -0
  123. data/tutorial/tutorial.md +424 -0
  124. data/tutorial/tutorial.pdf +0 -0
  125. metadata +254 -0
data/doc/Bio/DB/Tag.html ADDED
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <meta charset="UTF-8">
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+
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+ <title>class Bio::DB::Tag - Pileup</title>
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+
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+ <link href="../../fonts.css" rel="stylesheet">
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+ <link href="../../rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ </script>
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+
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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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+
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+
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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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+ </div>
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+ </div>
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+
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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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+ <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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+ </div>
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+
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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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+
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+ </div>
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+
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+
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+
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+ <div id="class-metadata">
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+
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Parent</h3>
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+
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+
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+ <p class="link">Object
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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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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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+
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+ <ul class="link-list" role="directory">
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+
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+ <li ><a href="#method-i-set">#set</a>
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+
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+ </ul>
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+ </div>
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+
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+ </div>
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+ </nav>
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+
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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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+
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+ <section class="description">
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+
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+ <p>a class to represent the SAM OPT values, presented in SAM as
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+ TAG:VTYPE:VALUE</p>
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+
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+ </section>
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+
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+
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+ <section class="attribute-method-details" class="method-section">
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+ <header>
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+ <h3>Attributes</h3>
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+ </header>
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+
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+
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+ <div id="attribute-i-tag" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">tag</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-type" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">type</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-value" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">value</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ </section>
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+
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+
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Instance Methods</h3>
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+ </header>
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+
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+
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+ <div id="method-i-set" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">set</span><span
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+ class="method-args">(str)</span>
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+
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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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+
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+
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+ <div class="method-description">
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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/alignment.rb, line 7</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">str</span>)
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+ <span class="ruby-ivar">@tag</span> = <span class="ruby-identifier">str</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">1</span>]
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+ <span class="ruby-ivar">@type</span> = <span class="ruby-identifier">str</span>[<span class="ruby-value">3</span>]
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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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+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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+
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+ </div>
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+ </div>
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+
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+ </section>
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+ </section>
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+ </main>
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+
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+
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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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+
data/doc/Bio/DB/Vcf.html ADDED
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <meta charset="UTF-8">
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+
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+ <title>class Bio::DB::Vcf - Pileup</title>
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+
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+ <link href="../../fonts.css" rel="stylesheet">
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+ <link href="../../rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ </script>
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+
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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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+
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+
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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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+ </div>
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+ </div>
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+
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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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+ <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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+ </div>
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+
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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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+
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+ </div>
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+
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+
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+
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+ <div id="class-metadata">
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+
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Parent</h3>
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+
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+
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+ <p class="link">Object
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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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+ <!-- Method Quickref -->
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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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+
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+ <ul class="link-list" role="directory">
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+
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+ <li ><a href="#method-c-new">::new</a>
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+
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+ <li ><a href="#method-i-int_or_raw">#int_or_raw</a>
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+
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+ <li ><a href="#method-i-parse_line">#parse_line</a>
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+
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+ </ul>
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+ </div>
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+
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+ </div>
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+ </nav>
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+
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+ <main role="main" aria-labelledby="class-Bio::DB::Vcf">
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+ <h1 id="class-Bio::DB::Vcf" class="class">
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+ class Bio::DB::Vcf
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+ </h1>
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+
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+ <section class="description">
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+
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+ </section>
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+
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+
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+ <section class="attribute-method-details" class="method-section">
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+ <header>
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+ <h3>Attributes</h3>
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+ </header>
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+
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+
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+ <div id="attribute-i-alt" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">alt</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-chrom" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">chrom</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-filter" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">filter</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-format" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">format</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-id" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">id</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ </div>
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+ </div>
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+ <div id="attribute-i-info" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">info</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+
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+ </div>
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+ </div>
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+ <div id="attribute-i-pos" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">pos</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ </div>
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+ </div>
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+ <div id="attribute-i-qual" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">qual</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-ref" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">ref</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+
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+ <div id="attribute-i-samples" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">samples</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+
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+
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+ </div>
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+ </div>
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+
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+ </section>
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+
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+
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+
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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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+
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+
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+ <div id="method-c-new" class="method-detail ">
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+
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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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+ <span class="method-click-advice">click to toggle source</span>
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+
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+ </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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+ <p>create the vcf object, use the ordered list of sample names to label
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+ samples if provided [&#39;A&#39;, &#39;B&#39;, &#39;C&#39;], otherwise
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+ uses, 1,2,3 etc</p>
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+
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+ <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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+
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+
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+
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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/vcf.rb, line 15</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">line</span>=<span class="ruby-keyword">nil</span>, <span class="ruby-identifier">sample_names</span>=<span class="ruby-keyword">nil</span>)
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+ <span class="ruby-ivar">@info</span> = {}
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+ <span class="ruby-ivar">@samples</span> = {}
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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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+ <span class="ruby-keyword">end</span></pre>
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+ </div>
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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>
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+
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+
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+ </section>
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Instance Methods</h3>
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+ </header>
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+
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+
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+ <div id="method-i-int_or_raw" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">int_or_raw</span><span
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+ class="method-args">(x)</span>
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+
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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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+
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+
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+ <div class="method-description">
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+
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+ <p>tests if the current variable is an Integer</p>
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+ <ul><li>
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+ <p>x - any variable</p>
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+ </li></ul>
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+
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+
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+
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+
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+ <div class="method-source-code" id="int_or_raw-source">
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+ <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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+ </div>
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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>
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+
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+
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+ <div id="method-i-parse_line" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">parse_line</span><span
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+ class="method-args">(line, sample_names=nil)</span>
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+
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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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+
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+
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+ <div class="method-description">
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+
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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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+
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+
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+
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+
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+ <div class="method-source-code" id="parse_line-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/vcf.rb, line 28</span>
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+ <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>)
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+ <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>
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+
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+ <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>)
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+ <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>]
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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>
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+ <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>]
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+ <span class="ruby-ivar">@ref</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">3</span>]
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+ <span class="ruby-ivar">@alt</span> = <span class="ruby-identifier">f</span>[<span class="ruby-value">4</span>]
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+ <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>
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+ <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>]
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+
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+ <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> {}
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+ <span class="ruby-keyword">if</span> <span class="ruby-ivar">@info</span>
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+ <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>)
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+ <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>
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+ <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>)
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+ <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>
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+ <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>]
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+ <span class="ruby-keyword">else</span> <span class="ruby-comment"># Otherwise, it&#39;s just a flag</span>
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+ <span class="ruby-ivar">@info</span>[<span class="ruby-identifier">x</span>] = <span class="ruby-keyword">nil</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span>
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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&#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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+
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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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+ <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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+ <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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+ <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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+ <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>)
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+ <span class="ruby-identifier">raise</span> <span class="ruby-node">&quot;Expected number of sample values to be &lt;= number of sample keys in FORMAT column Format=#{@format} but sample=#{f[i]}&quot;</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">sample_values</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">size</span>
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+ <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>] = {}
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+ <span class="ruby-identifier">sample_keys</span>.<span class="ruby-identifier">each_with_index</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">key</span>, <span class="ruby-identifier">value_index</span><span class="ruby-operator">|</span> <span class="ruby-ivar">@samples</span>[<span class="ruby-identifier">sample_name</span>][<span class="ruby-identifier">key</span>] = <span class="ruby-identifier">sample_values</span>[<span class="ruby-identifier">value_index</span>] <span class="ruby-operator">||</span> <span class="ruby-string">&quot;&quot;</span>}
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+ <span class="ruby-keyword">end</span>
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+
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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>
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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>
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+
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+
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+ </section>
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+
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+ </section>
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+ </main>
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+
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+
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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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+