bio-samtools 0.4.1 → 0.4.2

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Files changed (74) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +60 -6
  3. data/doc/Bio.html +171 -0
  4. data/doc/Bio/DB.html +163 -0
  5. data/doc/Bio/DB/Alignment.html +780 -0
  6. data/doc/Bio/DB/SAM.html +1241 -0
  7. data/doc/Bio/DB/SAM/Library.html +217 -0
  8. data/doc/Bio/DB/SAM/Tools.html +331 -0
  9. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
  10. data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
  11. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
  12. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
  13. data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
  14. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
  15. data/doc/Bio/DB/SAMException.html +205 -0
  16. data/doc/Bio/DB/Tag.html +254 -0
  17. data/doc/LICENSE_txt.html +881 -0
  18. data/doc/LibC.html +153 -0
  19. data/doc/Pileup.html +571 -0
  20. data/doc/Vcf.html +473 -0
  21. data/doc/created.rid +10 -1
  22. data/doc/images/add.png +0 -0
  23. data/doc/images/brick.png +0 -0
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  28. data/doc/images/bullet_toggle_plus.png +0 -0
  29. data/doc/images/date.png +0 -0
  30. data/doc/images/delete.png +0 -0
  31. data/doc/images/find.png +0 -0
  32. data/doc/images/loadingAnimation.gif +0 -0
  33. data/doc/images/macFFBgHack.png +0 -0
  34. data/doc/images/package.png +0 -0
  35. data/doc/images/page_green.png +0 -0
  36. data/doc/images/page_white_text.png +0 -0
  37. data/doc/images/page_white_width.png +0 -0
  38. data/doc/images/plugin.png +0 -0
  39. data/doc/images/ruby.png +0 -0
  40. data/doc/images/tag_blue.png +0 -0
  41. data/doc/images/tag_green.png +0 -0
  42. data/doc/images/transparent.png +0 -0
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  44. data/doc/images/wrench_orange.png +0 -0
  45. data/doc/images/zoom.png +0 -0
  46. data/doc/index.html +109 -21
  47. data/doc/js/darkfish.js +153 -0
  48. data/doc/js/jquery.js +18 -0
  49. data/doc/js/navigation.js +142 -0
  50. data/doc/js/search.js +94 -0
  51. data/doc/js/search_index.js +1 -0
  52. data/doc/js/searcher.js +228 -0
  53. data/doc/lib/bio-samtools_rb.html +115 -0
  54. data/doc/lib/bio/db/sam/bam_rb.html +121 -0
  55. data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
  56. data/doc/lib/bio/db/sam/library_rb.html +115 -0
  57. data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
  58. data/doc/lib/bio/db/sam/sam_rb.html +121 -0
  59. data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
  60. data/doc/lib/bio/db/sam_rb.html +115 -0
  61. data/doc/rdoc.css +543 -0
  62. data/doc/table_of_contents.html +186 -0
  63. data/ext/Makefile-bioruby.patch +1 -1
  64. data/ext/Rakefile +8 -1
  65. data/ext/mkrf_conf.rb +8 -1
  66. data/lib/bio/db/sam.rb +140 -27
  67. data/lib/bio/db/sam/vcf.rb +0 -1
  68. data/test/basictest.rb +4 -4
  69. data/test/test_basic.rb +50 -34
  70. metadata +79 -25
  71. data/test/coverage.rb +0 -26
  72. data/test/coverage_plot.rb +0 -28
  73. data/test/feature.rb +0 -0
  74. data/test/test_pileup.rb +0 -68
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 content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+
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+ <title>Module: Bio::DB::SAM::Library</title>
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+
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+ <link type="text/css" media="screen" href="../../../rdoc.css" rel="stylesheet">
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../../";
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+ title="Type to search, Up and Down to navigate, Enter to load">
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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/library.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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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+ <li class="file"><a href="../../../LICENSE_txt.html">LICENSE</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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+ <ul class="link-list">
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+
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+ <li><a href="../../../Bio.html">Bio</a>
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+
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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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+
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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/Library.html">Bio::DB::SAM::Library</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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+
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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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+
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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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+ <li><a href="../../../LibC.html">LibC</a>
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+ <li><a href="../../../Pileup.html">Pileup</a>
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+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="module">module Bio::DB::SAM::Library</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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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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+
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+
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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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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+ <span class="method-click-advice">click to toggle source</span>
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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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+ <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">'so.1'</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">'1.dylib'</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">'dll'</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">/darwin.*java/</span>
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+ <span class="ruby-string">'1.dylib'</span>
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+ <span class="ruby-keyword">when</span> <span class="ruby-regexp">/linux.*java/</span>
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+ <span class="ruby-string">'so.1'</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">'external'</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><!-- filename-source -->
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+ </div>
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+ </div><!-- filename-method -->
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+
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+ </section><!-- public-class-method-details -->
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+
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+ </div><!-- documentation -->
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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 content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>Module: Bio::DB::SAM::Tools</title>
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+ <body id="top" class="module">
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </nav>
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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/bam.rb
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+ <li>lib/bio/db/sam/faidx.rb
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+ <li>lib/bio/db/sam/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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+
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+ <div id="class-metadata">
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+
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+
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-bam_sort">::bam_sort</a>
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+
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+ </ul>
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+ <ul class="link-list">
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+
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+ <li><a href="../../../Bio.html">Bio</a>
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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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+
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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/Library.html">Bio::DB::SAM::Library</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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+
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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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+
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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/Tag.html">Bio::DB::Tag</a>
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+ <li><a href="../../../LibC.html">LibC</a>
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+ </ul>
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+ </nav>
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="module">module Bio::DB::SAM::Tools</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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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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+
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+
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+
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+
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+ <!-- Constants -->
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+ <section id="constants-list" class="section">
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+ <h3 class="section-header">Constants</h3>
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+ <dl>
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+
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+ <dt id="BAM_CDEL">BAM_CDEL
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+
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+ <dd class="description">
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+ <dt id="BAM_CHARD_CLIP">BAM_CHARD_CLIP
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+ <dd class="description">
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+ <dt id="BAM_CIGAR_MASK">BAM_CIGAR_MASK
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+
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+ <dd class="description">
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+ <dt id="BAM_CIGAR_SHIFT">BAM_CIGAR_SHIFT
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+ <dd class="description">
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+ <dt id="BAM_CINS">BAM_CINS
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+ <dd class="description">
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+ <dt id="BAM_CMATCH">BAM_CMATCH
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+ <dd class="description">
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+ <dt id="BAM_CPAD">BAM_CPAD
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+ <dd class="description">
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+ <dt id="BAM_CREF_SKIP">BAM_CREF_SKIP
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+ <dd class="description">
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+ <dt id="BAM_CSOFT_CLIP">BAM_CSOFT_CLIP
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+ <dd class="description">
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+ <dt id="BAM_DEF_MASK">BAM_DEF_MASK
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+ <dd class="description">
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+ <dt id="BAM_FDUP">BAM_FDUP
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+ <dd class="description">
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+ <dt id="BAM_FMREVERSE">BAM_FMREVERSE
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+ <dt id="BAM_FMUNMAP">BAM_FMUNMAP
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+ <dt id="BAM_FPAIRED">BAM_FPAIRED
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+ <dd class="description">
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+ <dt id="BAM_FPROPER_PAIR">BAM_FPROPER_PAIR
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+ <dd class="description">
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+ <dt id="BAM_FQCFAIL">BAM_FQCFAIL
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+ <dd class="description">
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+ <dt id="BAM_FREAD1">BAM_FREAD1
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+ <dd class="description">
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+ <dt id="BAM_FREAD2">BAM_FREAD2
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_FREVERSE">BAM_FREVERSE
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_FSECONDARY">BAM_FSECONDARY
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_FUNMAP">BAM_FUNMAP
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_OFDEC">BAM_OFDEC
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_OFHEX">BAM_OFHEX
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+
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+ <dd class="description">
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+
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+
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+ <dt id="BAM_OFSTR">BAM_OFSTR
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+
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+ <dd class="description">
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+
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+
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+ </dl>
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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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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="method-c-bam_sort" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">bam_sort</span><span
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+ class="method-args">(bam_filename, bam_output_prefix)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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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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+
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+
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+
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+
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+ <div class="method-source-code" id="bam_sort-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam/bam.rb, line 172</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">bam_sort</span>(<span class="ruby-identifier">bam_filename</span>, <span class="ruby-identifier">bam_output_prefix</span>)
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+ <span class="ruby-identifier">is_by_name</span> = <span class="ruby-value">0</span>
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+ <span class="ruby-identifier">max_mem</span> = <span class="ruby-value">500000000</span>
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+ <span class="ruby-identifier">bam_sort_core</span>(<span class="ruby-identifier">is_by_name</span>, <span class="ruby-identifier">bam_filename</span>, <span class="ruby-identifier">bam_output_prefix</span>, <span class="ruby-identifier">max_mem</span>)
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- bam_sort-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- bam_sort-method -->
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+
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+
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+ </section><!-- public-class-method-details -->
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+
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+ </section><!-- 5Buntitled-5D -->
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+
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+ </div><!-- documentation -->
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+
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+
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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> 3.11.
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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>
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+