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/Pileup.src/M000001.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>new (Pileup)</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/pileup.rb, line 34</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
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+ <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp re">/\t/</span>)
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">6</span> <span class="ruby-comment cmt">##should only be able to get 6 lines from mpileup</span>
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+ <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
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+ <span class="ruby-keyword kw">elsif</span> (<span class="ruby-value">10</span><span class="ruby-operator">..</span><span class="ruby-value">13</span>).<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span>) <span class="ruby-comment cmt">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</span>
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+ <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span> = <span class="ruby-identifier">cols</span>
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+ <span class="ruby-ivar">@consensus_quality</span> = <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@snp_quality</span> = <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@rms_mapq</span> = <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-comment cmt">#raise RuntimeError, &quot;parsing line '#{pile_up_line.chomp}' failed&quot;</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-ivar">@pos</span> = <span class="ruby-ivar">@pos</span>.<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-ivar">@coverage</span> = <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword kw">nil</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/Pileup.src/M000002.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>non_refs (Pileup)</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/pileup.rb, line 56</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">non_refs</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@non_ref_count_hash</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</span> = {<span class="ruby-identifier">:A</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Aa&quot;</span>), <span class="ruby-identifier">:C</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Cc&quot;</span>), <span class="ruby-identifier">:G</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Gg&quot;</span>), <span class="ruby-identifier">:T</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;Tt&quot;</span>)}
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@non_ref_count_hash</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/Pileup.src/M000003.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>non_ref_count (Pileup)</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/pileup.rb, line 64</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">non_ref_count</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@non_ref_count</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-ivar">@read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;ATGCatgc&quot;</span>).<span class="ruby-identifier">to_f</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@non_ref_count</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/Pileup.src/M000004.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>ref_count (Pileup)</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/pileup.rb, line 72</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">ref_count</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@ref_count</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-value str">&quot;.,&quot;</span>)
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@ref_count</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/Pileup.src/M000005.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>consensus (Pileup)</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/pileup.rb, line 80</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">consensus</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@consensus</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-identifier">max</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">values</span>.<span class="ruby-identifier">max</span>
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+ <span class="ruby-keyword kw">if</span> (<span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">/</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">coverage</span>) <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span><span class="ruby-value">.5</span>
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+ <span class="ruby-ivar">@consensus</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span>
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+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">max</span>
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+ <span class="ruby-ivar">@consensus</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span>
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+ <span class="ruby-keyword kw">else</span>
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+ <span class="ruby-identifier">arr</span> = <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">select</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span> <span class="ruby-identifier">v</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">max</span> }
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+ <span class="ruby-identifier">bases</span> = <span class="ruby-identifier">arr</span>.<span class="ruby-identifier">collect</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">b</span>[<span class="ruby-value">0</span>].<span class="ruby-identifier">to_s</span> }
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+ <span class="ruby-identifier">bases</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">ref_count</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">max</span>
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+ <span class="ruby-ivar">@consensus</span> = <span class="ruby-identifier">bases</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">join</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@consensus</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/created.rid ADDED
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+ Wed, 26 Oct 2011 22:02:06 +0100
data/doc/files/lib/bio-samtools_rb.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 xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: bio-samtools.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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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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+ 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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+ elemStyle = elem.style;
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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="fileHeader">
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+ <h1>bio-samtools.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio-samtools.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Wed Oct 26 21:06:33 +0100 2011</td>
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+ </tr>
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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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+ <div id="requires-list">
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+ <h3 class="section-bar">Required files</h3>
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+
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+ <div class="name-list">
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+ ffi&nbsp;&nbsp;
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+ bio/db/sam&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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+ </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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+ <!-- if method_list -->
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+ </div>
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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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+ </body>
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+ </html>
data/doc/files/lib/bio/db/sam/bam_rb.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 xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: bam.rb</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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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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+
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+ 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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+ 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="fileHeader">
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+ <h1>bam.rb</h1>
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Path:</strong></td>
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+ <td>lib/bio/db/sam/bam.rb
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+ </td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>Last Update:</strong></td>
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+ <td>Wed Oct 26 21:06:33 +0100 2011</td>
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+ </tr>
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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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+ <div id="description">
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+ <p>
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+ require &#8216;rubygems&#8217; require&#8216;ffi&#8217; require
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+ &#8216;bio/db/sam/faidx&#8217; require &#8216;bio/db/sam/sam&#8216;
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+ </p>
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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>
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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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+ <!-- if method_list -->
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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/files/lib/bio/db/sam/faidx_rb.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 xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>File: faidx.rb</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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+
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+ 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;
36
+ }
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+
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+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
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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="fileHeader">
50
+ <h1>faidx.rb</h1>
51
+ <table class="header-table">
52
+ <tr class="top-aligned-row">
53
+ <td><strong>Path:</strong></td>
54
+ <td>lib/bio/db/sam/faidx.rb
55
+ </td>
56
+ </tr>
57
+ <tr class="top-aligned-row">
58
+ <td><strong>Last Update:</strong></td>
59
+ <td>Wed Oct 26 21:06:33 +0100 2011</td>
60
+ </tr>
61
+ </table>
62
+ </div>
63
+ <!-- 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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+ <div id="description">
72
+ <p>
73
+ require &#8216;rubygems&#8217; require&#8216;ffi&#8217; require
74
+ &#8216;bio/db/sam/bam&#8216;
75
+ </p>
76
+
77
+ </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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+ <!-- 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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+
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+
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+ </div>
101
+
102
+
103
+ <div id="validator-badges">
104
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
105
+ </div>
106
+
107
+ </body>
108
+ </html>