bio-samtools 0.2.5 → 0.3.0

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Files changed (73) hide show
  1. data/README.rdoc +7 -20
  2. data/Rakefile +11 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +67 -1
  5. data/doc/basic_styles.css +31 -0
  6. data/doc/classes/Bio.html +139 -0
  7. data/doc/classes/Bio/DB.html +137 -0
  8. data/doc/classes/Bio/DB/Alignment.html +441 -0
  9. data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
  10. data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
  11. data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
  12. data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
  13. data/doc/classes/Bio/DB/SAM.html +510 -0
  14. data/doc/classes/Bio/DB/SAM/Library.html +135 -0
  15. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
  16. data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
  17. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
  18. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
  19. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
  20. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
  21. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
  22. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
  23. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
  24. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
  25. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
  26. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
  27. data/doc/classes/Bio/DB/SAMException.html +140 -0
  28. data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
  29. data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
  30. data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
  31. data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
  32. data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
  33. data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
  34. data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
  35. data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
  36. data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
  37. data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
  38. data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
  39. data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
  40. data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
  41. data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
  42. data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
  43. data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
  44. data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
  45. data/doc/classes/Bio/DB/Tag.html +160 -0
  46. data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
  47. data/doc/classes/LibC.html +105 -0
  48. data/doc/classes/Pileup.html +374 -0
  49. data/doc/classes/Pileup.src/M000001.html +34 -0
  50. data/doc/classes/Pileup.src/M000002.html +21 -0
  51. data/doc/classes/Pileup.src/M000003.html +21 -0
  52. data/doc/classes/Pileup.src/M000004.html +21 -0
  53. data/doc/classes/Pileup.src/M000005.html +31 -0
  54. data/doc/created.rid +1 -0
  55. data/doc/files/lib/bio-samtools_rb.html +109 -0
  56. data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
  57. data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
  58. data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
  59. data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
  60. data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
  61. data/doc/files/lib/bio/db/sam_rb.html +111 -0
  62. data/doc/fr_class_index.html +43 -0
  63. data/doc/fr_file_index.html +33 -0
  64. data/doc/fr_method_index.html +58 -0
  65. data/doc/index.html +24 -0
  66. data/doc/rdoc-style.css +208 -0
  67. data/doc/tutorial.html +165 -0
  68. data/doc/tutorial.pdf +0 -0
  69. data/lib/bio/db/sam.rb +163 -1
  70. data/lib/bio/db/sam/pileup.rb +98 -0
  71. data/test/basictest.rb +14 -0
  72. data/test/pileup.rb +68 -0
  73. metadata +84 -18
data/doc/classes/Bio/DB/SAM/Library.html ADDED
@@ -0,0 +1,135 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: Bio::DB::SAM::Library</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">Bio::DB::SAM::Library</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../../files/lib/bio/db/sam/library_rb.html">
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+ lib/bio/db/sam/library.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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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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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000006">filename</a>&nbsp;&nbsp;
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+ </div>
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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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+ <!-- if includes -->
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+
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+ <div id="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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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000006" class="method-detail">
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+ <a name="M000006"></a>
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+
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+ <div class="method-heading">
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+ <a href="Library.src/M000006.html" target="Code" class="method-signature"
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+ onclick="popupCode('Library.src/M000006.html');return false;">
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+ <span class="method-name">filename</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ Return the path with the file name of the library for the specific
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+ operating system
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+ </p>
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+ </div>
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+ </div>
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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>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/SAM/Library.src/M000006.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>filename (Bio::DB::SAM::Library)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/library.rb, line 8</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">filename</span>
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+ <span class="ruby-comment cmt">#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 kw">case</span> <span class="ruby-constant">RUBY_PLATFORM</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/linux/</span>
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+ <span class="ruby-value str">'so.1'</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/darwin/</span>
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+ <span class="ruby-value str">'1.dylib'</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-regexp re">/windows/</span>
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+ <span class="ruby-value str">'dll'</span>
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+ <span class="ruby-keyword kw">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 kw">__FILE__</span>)),<span class="ruby-value str">'external'</span>,<span class="ruby-node">&quot;libbam.#{lib_os}&quot;</span>)
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/SAM/Tools.html ADDED
@@ -0,0 +1,278 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: Bio::DB::SAM::Tools</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
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+
19
+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">Bio::DB::SAM::Tools</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../../files/lib/bio/db/sam/bam_rb.html">
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+ lib/bio/db/sam/bam.rb
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+ </a>
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+ <br />
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+ <a href="../../../../files/lib/bio/db/sam/faidx_rb.html">
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+ lib/bio/db/sam/faidx.rb
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+ </a>
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+ <br />
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+ <a href="../../../../files/lib/bio/db/sam/sam_rb.html">
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+ lib/bio/db/sam/sam.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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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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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000007">bam_sort</a>&nbsp;&nbsp;
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+ </div>
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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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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+ <div id="class-list">
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+ <h3 class="section-bar">Classes and Modules</h3>
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+
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+ Class <a href="Tools/Bam1CoreT.html" class="link">Bio::DB::SAM::Tools::Bam1CoreT</a><br />
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+ Class <a href="Tools/Bam1T.html" class="link">Bio::DB::SAM::Tools::Bam1T</a><br />
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+ Class <a href="Tools/BamHeaderT.html" class="link">Bio::DB::SAM::Tools::BamHeaderT</a><br />
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+ Class <a href="Tools/BamPileup1T.html" class="link">Bio::DB::SAM::Tools::BamPileup1T</a><br />
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+ Class <a href="Tools/SamfileT.html" class="link">Bio::DB::SAM::Tools::SamfileT</a><br />
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+ Class <a href="Tools/SamfileTX.html" class="link">Bio::DB::SAM::Tools::SamfileTX</a><br />
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+
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+ </div>
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+
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+ <div id="constants-list">
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+ <h3 class="section-bar">Constants</h3>
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+
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+ <div class="name-list">
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+ <table summary="Constants">
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FPAIRED</td>
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+ <td>=</td>
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+ <td class="context-item-value">1</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FPROPER_PAIR</td>
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+ <td>=</td>
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+ <td class="context-item-value">2</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FUNMAP</td>
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+ <td>=</td>
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+ <td class="context-item-value">4</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FMUNMAP</td>
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+ <td>=</td>
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+ <td class="context-item-value">8</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FREVERSE</td>
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+ <td>=</td>
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+ <td class="context-item-value">16</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FMREVERSE</td>
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+ <td>=</td>
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+ <td class="context-item-value">32</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FREAD1</td>
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+ <td>=</td>
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+ <td class="context-item-value">64</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FREAD2</td>
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+ <td>=</td>
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+ <td class="context-item-value">128</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FSECONDARY</td>
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+ <td>=</td>
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+ <td class="context-item-value">256</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FQCFAIL</td>
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+ <td>=</td>
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+ <td class="context-item-value">512</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_FDUP</td>
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+ <td>=</td>
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+ <td class="context-item-value">1024</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_OFDEC</td>
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+ <td>=</td>
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+ <td class="context-item-value">0</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_OFHEX</td>
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+ <td>=</td>
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+ <td class="context-item-value">1</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_OFSTR</td>
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+ <td>=</td>
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+ <td class="context-item-value">2</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_DEF_MASK</td>
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+ <td>=</td>
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+ <td class="context-item-value">(4|256|512|1024)</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CIGAR_SHIFT</td>
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+ <td>=</td>
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+ <td class="context-item-value">4</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CIGAR_MASK</td>
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+ <td>=</td>
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+ <td class="context-item-value">((1 &lt;&lt; 4) -1)</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CMATCH</td>
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+ <td>=</td>
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+ <td class="context-item-value">0</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CINS</td>
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+ <td>=</td>
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+ <td class="context-item-value">1</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CDEL</td>
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+ <td>=</td>
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+ <td class="context-item-value">2</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CREF_SKIP</td>
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+ <td>=</td>
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+ <td class="context-item-value">3</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CSOFT_CLIP</td>
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+ <td>=</td>
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+ <td class="context-item-value">4</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CHARD_CLIP</td>
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+ <td>=</td>
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+ <td class="context-item-value">5</td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">BAM_CPAD</td>
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+ <td>=</td>
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+ <td class="context-item-value">6</td>
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+ </tr>
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+ </table>
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+ </div>
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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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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000007" class="method-detail">
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+ <a name="M000007"></a>
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+
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+ <div class="method-heading">
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+ <a href="Tools.src/M000007.html" target="Code" class="method-signature"
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+ onclick="popupCode('Tools.src/M000007.html');return false;">
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+ <span class="method-name">bam_sort</span><span class="method-args">(bam_filename, bam_output_prefix)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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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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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html>
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+ <head>
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+ <title>bam_sort (Bio::DB::SAM::Tools)</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
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+ </head>
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+ <body class="standalone-code">
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+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam/bam.rb, line 172</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">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 kw">end</span></pre>
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+ </body>
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+ </html>