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
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  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/SAM/Library.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>module Bio::DB::SAM::Library - 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="module">
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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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+
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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-filename">::filename</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="module-Bio::DB::SAM::Library">
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+ <h1 id="module-Bio::DB::SAM::Library" class="module">
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+ module Bio::DB::SAM::Library
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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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+
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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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+ <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-filename" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">filename</span><span
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+ class="method-args">()</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>Return the path with the file name of the library for the specific
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+ operating system</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="filename-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam/library.rb, line 8</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">filename</span>
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+ <span class="ruby-comment">#TODO refactor this piece of code in all the files</span>
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+ <span class="ruby-identifier">lib_os</span> = <span class="ruby-keyword">case</span> <span class="ruby-constant">RUBY_PLATFORM</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/linux/</span>
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+ <span class="ruby-string">&#39;so.1&#39;</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/darwin/</span>
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+ <span class="ruby-string">&#39;1.dylib&#39;</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/windows/</span>
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+ <span class="ruby-string">&#39;dll&#39;</span>
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+ <span class="ruby-keyword">else</span>
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+ <span class="ruby-keyword">case</span> <span class="ruby-constant">RUBY_DESCRIPTION</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/jruby.*darwin/</span>
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+ <span class="ruby-string">&#39;1.dylib&#39;</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/jruby.*linux/</span>
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+ <span class="ruby-string">&#39;so.1&#39;</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-constant">File</span>.<span class="ruby-identifier">join</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">expand_path</span>(<span class="ruby-constant">File</span>.<span class="ruby-identifier">dirname</span>(<span class="ruby-keyword">__FILE__</span>)),<span class="ruby-string">&#39;external&#39;</span>,<span class="ruby-node">&quot;libbam.#{lib_os}&quot;</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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+
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+ </section>
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+
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+ </section>
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+ </main>
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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/SAM/Tools.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>module Bio::DB::SAM::Tools - 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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+ <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="module">
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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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+ <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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+ <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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+ <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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+ <div id="class-metadata">
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+
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+
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+
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+ <div id="extends-section" class="nav-section">
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+ <h3>Extended With Modules</h3>
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+
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+ <ul class="link-list">
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+
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+
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+ <li><span class="extend">FFI::Library</span>
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+
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+
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+ </ul>
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+ </div>
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+
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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="module-Bio::DB::SAM::Tools">
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+ <h1 id="module-Bio::DB::SAM::Tools" class="module">
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+ module Bio::DB::SAM::Tools
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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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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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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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+