bio-samtools 0.4.1 → 0.4.2

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  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
  24. data/doc/images/brick_link.png +0 -0
  25. data/doc/images/bug.png +0 -0
  26. data/doc/images/bullet_black.png +0 -0
  27. data/doc/images/bullet_toggle_minus.png +0 -0
  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
  43. data/doc/images/wrench.png +0 -0
  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/Tools/Bam1CoreT.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>Class: Bio::DB::SAM::Tools::Bam1CoreT</title>
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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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+ <body id="top" class="class">
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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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+ </ul>
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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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+ <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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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+
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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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+ </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="class">class Bio::DB::SAM::Tools::Bam1CoreT</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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+ <section id="5Buntitled-5D" class="documentation-section">
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+ <!-- Methods -->
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+ </section><!-- 5Buntitled-5D -->
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+ </div><!-- documentation -->
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ </footer>
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data/doc/Bio/DB/SAM/Tools/Bam1T.html ADDED
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+ <!DOCTYPE html>
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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>Class: Bio::DB::SAM::Tools::Bam1T</title>
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+
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+ <link type="text/css" media="screen" 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 type="text/javascript" charset="utf-8" src="../../../../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../../../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../../../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../../../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../../../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../../../js/darkfish.js"></script>
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../../../../index.html">Home</a>
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+ <a href="../../../../table_of_contents.html#classes">Classes</a>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <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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+ </ul>
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+ </nav>
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+ </div>
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+ <div id="class-metadata">
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+ <nav id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+ <p class="link">FFI::Struct
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+ </nav>
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <li><a href="../../../../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../../../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../../../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+
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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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+ <li><a href="../../../../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ </nav>
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::SAM::Tools::Bam1T</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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+ <section id="5Buntitled-5D" class="documentation-section">
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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_NT16_Rev_Table">Bam_NT16_Rev_Table
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+
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+ <dd class="description">
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+ </dl>
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+ </section>
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+
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+ <!-- Methods -->
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+ <div id="method-i-qname" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">qname</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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+ <div class="method-description">
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+ <div class="method-source-code" id="qname-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam/bam.rb, line 63</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">qname</span>
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+ <span class="ruby-comment">#bam1_qname(b) ((char*)((b)-&gt;data))</span>
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+ <span class="ruby-identifier">data</span> = <span class="ruby-keyword">self</span>[<span class="ruby-value">:data</span>]
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+ <span class="ruby-identifier">data</span>.<span class="ruby-identifier">read_string</span>()
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- qname-source -->
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+ </div>
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+ </div><!-- qname-method -->
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+ </section><!-- public-instance-method-details -->
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data/doc/Bio/DB/SAM/Tools/BamHeaderT.html ADDED
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+ <!DOCTYPE html>
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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>Class: Bio::DB::SAM::Tools::BamHeaderT</title>
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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/sam.rb
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+ </ul>
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+ </nav>
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+ <li><a href="#method-i-text">#text</a>
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+ <li><a href="#method-i-text-3D">#text=</a>
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+ <li><a href="../../../../Bio.html">Bio</a>
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::SAM::Tools::BamHeaderT</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>typedef struct {</p>
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+
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+ <pre>int32_t n_targets;
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+ char **target_name;
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+ uint32_t *target_len;
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+ void *dict, *hash, *rg2lib;
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+ int l_text;
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+ char *text;</pre>
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+
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+ <p>} bam_header_t;</p>
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+
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+ </div><!-- description -->
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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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+ <!-- Methods -->
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+
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+
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+ <div class="method-source-code" id="text-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam/sam.rb, line 42</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">text</span>
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+ <span class="ruby-ivar">@text</span>.<span class="ruby-identifier">get_string</span>(<span class="ruby-value">0</span>)
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- text-source -->
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+
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+ </div>
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+
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+ </div><!-- text-method -->
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+ <div id="method-i-text-3D" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">text=</span><span
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+ class="method-args">(str)</span>
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+ <div class="method-description">
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+ <div class="method-source-code" id="text-3D-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam/sam.rb, line 38</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">text=</span>(<span class="ruby-identifier">str</span>)
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+ <span class="ruby-ivar">@text</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">str</span>)
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+ <span class="ruby-keyword">self</span>[<span class="ruby-value">:text</span>] = <span class="ruby-ivar">@text</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- text-3D-source -->
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+
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+ </div>
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+ </div><!-- text-3D-method -->
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+
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+
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+ </section><!-- public-instance-method-details -->
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+ </section><!-- 5Buntitled-5D -->
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+
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