bio-samtools 0.2.5 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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/SAMException.src/M000016.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 (Bio::DB::SAMException)</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.rb, line 480</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>()
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+
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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.src/M000017.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 (Bio::DB::Sam)</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.rb, line 27</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">optsa</span>={})
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+ <span class="ruby-identifier">opts</span> = { <span class="ruby-identifier">:fasta</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">:bam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>,<span class="ruby-identifier">:tam</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">:compressed</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">true</span>, <span class="ruby-identifier">:write</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword kw">false</span> }.<span class="ruby-identifier">merge!</span>(<span class="ruby-identifier">optsa</span>)
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+
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+
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+
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+ <span class="ruby-ivar">@fasta_path</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:fasta</span>]
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+ <span class="ruby-ivar">@compressed</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:compressed</span>]
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+ <span class="ruby-ivar">@write</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:write</span>]
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+ <span class="ruby-identifier">bam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:bam</span>]
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+ <span class="ruby-identifier">tam</span> = <span class="ruby-identifier">opts</span>[<span class="ruby-identifier">:tam</span>]
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+
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">==</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-operator">==</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No alignment or reference file&quot;</span>
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+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Alignment has to be in either text or binary format, not both&quot;</span>
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+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">bam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword kw">true</span>
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+ <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">bam</span>
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+ <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">tam</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword kw">nil</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-ivar">@sam</span> = <span class="ruby-identifier">tam</span>
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+ <span class="ruby-ivar">@binary</span> = <span class="ruby-keyword kw">false</span>
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+
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+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@fasta_file</span> = <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
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+
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+ <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword kw">self</span>, <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-identifier">:finalize</span>).<span class="ruby-identifier">to_proc</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.src/M000018.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>open (Bio::DB::Sam)</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.rb, line 58</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">open</span>()
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+
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Writing not supported yet&quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@write</span>
17
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No SAM file specified&quot;</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam</span>
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+
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+ <span class="ruby-identifier">opts</span> = <span class="ruby-ivar">@write</span> <span class="ruby-operator">?</span> <span class="ruby-value str">&quot;w&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-value str">&quot;r&quot;</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@binary</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">&quot;b&quot;</span>
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+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@write</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@compressed</span> <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-identifier">opts</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">&quot;u&quot;</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-keyword kw">end</span>
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+ <span class="ruby-identifier">valid</span> = [<span class="ruby-value str">&quot;r&quot;</span>, <span class="ruby-value str">&quot;w&quot;</span>, <span class="ruby-value str">&quot;wh&quot;</span>, <span class="ruby-value str">&quot;rb&quot;</span>, <span class="ruby-value str">&quot;wb&quot;</span> , <span class="ruby-value str">&quot;wbu&quot;</span>]
29
+ <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">valid</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-keyword kw">then</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Invalid options for samopen: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">opts</span>
31
+ <span class="ruby-keyword kw">end</span>
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+
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+ <span class="ruby-identifier">samFile</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samopen</span>(<span class="ruby-ivar">@sam</span>, <span class="ruby-identifier">opts</span>, <span class="ruby-keyword kw">nil</span>)
34
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">samFile</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
35
+ <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
36
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;File not opened: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
37
+ <span class="ruby-keyword kw">end</span>
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+ <span class="ruby-ivar">@sam_file</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span><span class="ruby-operator">::</span><span class="ruby-constant">SamfileT</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">samFile</span>)
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+
40
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/Sam.src/M000019.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>to_s (Bio::DB::Sam)</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.rb, line 88</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">to_s</span>()
15
+ (<span class="ruby-ivar">@binary</span> <span class="ruby-operator">?</span> <span class="ruby-value str">&quot;Binary&quot;</span> <span class="ruby-operator">:</span> <span class="ruby-value str">&quot;Text&quot;</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">&quot; file: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot; with fasta: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</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.src/M000020.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>close (Bio::DB::Sam)</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.rb, line 93</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">close</span>()
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+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_destroy</span>(<span class="ruby-ivar">@fasta_index</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
16
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_destroy</span>(<span class="ruby-ivar">@sam_index</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
17
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">samclose</span>(<span class="ruby-ivar">@sam_file</span>) <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@sam_file</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-ivar">@sam_file</span> = <span class="ruby-keyword kw">nil</span>
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+ <span class="ruby-ivar">@fasta_index</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/Bio/DB/Sam.src/M000021.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>finalize (Bio::DB::Sam)</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.rb, line 102</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-constant">Sam</span>.<span class="ruby-identifier">finalize</span>(<span class="ruby-identifier">id</span>)
15
+ <span class="ruby-identifier">id</span>.<span class="ruby-identifier">close</span>()
16
+ <span class="ruby-identifier">puts</span> <span class="ruby-node">&quot;Finalizing #{id} at #{Time.new}&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.src/M000022.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>load_index (Bio::DB::Sam)</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.rb, line 112</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">load_index</span>()
15
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Indexes are only supported by BAM files, please use samtools to convert your SAM file&quot;</span> <span class="ruby-keyword kw">unless</span> <span class="ruby-ivar">@binary</span>
16
+ <span class="ruby-ivar">@sam_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
17
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
18
+ <span class="ruby-identifier">p</span> <span class="ruby-value str">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span>
19
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_build</span>(<span class="ruby-ivar">@sam</span>)
20
+ <span class="ruby-ivar">@sam_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_index_load</span>(<span class="ruby-ivar">@sam</span>)
21
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Unable to generate bam index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@sam</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
22
+ <span class="ruby-keyword kw">end</span>
23
+ <span class="ruby-keyword kw">end</span></pre>
24
+ </body>
25
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000023.html ADDED
@@ -0,0 +1,28 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
3
+ 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>load_reference (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 126</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">load_reference</span>()
15
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;No path for the refernce fasta file. &quot;</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_path</span>.<span class="ruby-identifier">nil?</span>
16
+
17
+ <span class="ruby-ivar">@fasta_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
18
+
19
+ <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span> <span class="ruby-keyword kw">then</span>
20
+ <span class="ruby-identifier">p</span> <span class="ruby-value str">&quot;Generating index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span>
21
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_build</span>(<span class="ruby-ivar">@fasta_path</span>)
22
+ <span class="ruby-ivar">@fasta_index</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_load</span>(<span class="ruby-ivar">@fasta_path</span>)
23
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Unable to generate fasta index for: &quot;</span> <span class="ruby-operator">+</span> <span class="ruby-ivar">@fasta_path</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
24
+ <span class="ruby-keyword kw">end</span>
25
+
26
+ <span class="ruby-keyword kw">end</span></pre>
27
+ </body>
28
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000024.html ADDED
@@ -0,0 +1,28 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>average_coverage (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 141</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">average_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
15
+
16
+ <span class="ruby-comment cmt">#reference = fetch_reference(chromosome, qstart,len)</span>
17
+ <span class="ruby-comment cmt"># len = reference.length if len &gt; reference.length</span>
18
+
19
+
20
+ <span class="ruby-identifier">coverages</span> = <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
21
+ <span class="ruby-identifier">total</span> = <span class="ruby-value">0</span>
22
+ <span class="ruby-identifier">len</span>.<span class="ruby-identifier">times</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">total</span>= <span class="ruby-identifier">total</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span>] }
23
+ <span class="ruby-identifier">avg_cov</span> = <span class="ruby-identifier">total</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">/</span> <span class="ruby-identifier">len</span>
24
+ <span class="ruby-comment cmt">#LibC.free reference</span>
25
+ <span class="ruby-identifier">avg_cov</span>
26
+ <span class="ruby-keyword kw">end</span></pre>
27
+ </body>
28
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000025.html ADDED
@@ -0,0 +1,46 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>chromosome_coverage (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 158</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">chromosome_coverage</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">len</span>)
15
+ <span class="ruby-comment cmt"># reference = fetch_reference(chromosome, qstart,len)</span>
16
+ <span class="ruby-comment cmt"># len = reference.length if len &gt; reference.length</span>
17
+ <span class="ruby-comment cmt">#p qend.to_s + &quot;-&quot; + qstart.to_s + &quot;framesize &quot; + (qend - qstart).to_s</span>
18
+ <span class="ruby-identifier">coverages</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">len</span>, <span class="ruby-value">0</span>)
19
+
20
+ <span class="ruby-identifier">chr_cov_proc</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
21
+ <span class="ruby-comment cmt">#last = qstart + len</span>
22
+ <span class="ruby-comment cmt">#first = qstart</span>
23
+ <span class="ruby-comment cmt">#last = alignment.calend if last &gt; alignment.calend</span>
24
+ <span class="ruby-comment cmt">#first = alignment.pos if first &lt; alignment.pos</span>
25
+ <span class="ruby-comment cmt"># p first</span>
26
+ <span class="ruby-identifier">last</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">calend</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
27
+ <span class="ruby-identifier">first</span> = <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">pos</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">qstart</span>
28
+ <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">last</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">first</span>
29
+ <span class="ruby-identifier">tmp</span> = <span class="ruby-identifier">last</span>
30
+ <span class="ruby-identifier">last</span> = <span class="ruby-identifier">first</span>
31
+ <span class="ruby-identifier">first</span> = <span class="ruby-identifier">last</span>
32
+ <span class="ruby-keyword kw">end</span>
33
+
34
+ <span class="ruby-comment cmt"># STDERR.puts &quot;#{first} #{last}\n&quot;</span>
35
+ <span class="ruby-identifier">first</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">last</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) { <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
36
+
37
+ <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] = <span class="ruby-value">1</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">coverages</span>[<span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>] <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">i</span><span class="ruby-operator">-</span><span class="ruby-value">1</span> <span class="ruby-operator">&lt;</span> <span class="ruby-identifier">len</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">i</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
38
+ }
39
+ <span class="ruby-keyword kw">end</span>
40
+
41
+ <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qstart</span><span class="ruby-operator">+</span><span class="ruby-identifier">len</span>, <span class="ruby-identifier">chr_cov_proc</span>)
42
+ <span class="ruby-comment cmt">#p coverages</span>
43
+ <span class="ruby-identifier">coverages</span>
44
+ <span class="ruby-keyword kw">end</span></pre>
45
+ </body>
46
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000026.html ADDED
@@ -0,0 +1,24 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>fetch_reference (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 191</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">fetch_reference</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
15
+ <span class="ruby-identifier">load_reference</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@fasta_index</span>.<span class="ruby-identifier">null?</span>
16
+ <span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
17
+ <span class="ruby-identifier">len</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:int</span>
18
+ <span class="ruby-identifier">reference</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">fai_fetch</span>(<span class="ruby-ivar">@fasta_index</span>, <span class="ruby-identifier">query</span>, <span class="ruby-identifier">len</span>)
19
+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">SAMException</span>.<span class="ruby-identifier">new</span>(), <span class="ruby-value str">&quot;Unable to get sequence for reference: &quot;</span><span class="ruby-operator">+</span><span class="ruby-identifier">query</span> <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">reference</span>.<span class="ruby-identifier">nil?</span>
20
+
21
+ <span class="ruby-identifier">reference</span>
22
+ <span class="ruby-keyword kw">end</span></pre>
23
+ </body>
24
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000027.html ADDED
@@ -0,0 +1,19 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>query_string (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 203</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
15
+ <span class="ruby-identifier">query</span> = <span class="ruby-identifier">chromosome</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;:&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qstart</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;-&quot;</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">qend</span>.<span class="ruby-identifier">to_s</span>
16
+ <span class="ruby-identifier">query</span>
17
+ <span class="ruby-keyword kw">end</span></pre>
18
+ </body>
19
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000028.html ADDED
@@ -0,0 +1,24 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>fetch (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 209</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">fetch</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>)
15
+ <span class="ruby-identifier">als</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
16
+ <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">alignment</span><span class="ruby-operator">|</span>
17
+ <span class="ruby-identifier">als</span>.<span class="ruby-identifier">push</span>(<span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">clone</span>)
18
+ <span class="ruby-value">0</span>
19
+ <span class="ruby-keyword kw">end</span>
20
+ <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">fetchAlignment</span>)
21
+ <span class="ruby-identifier">als</span>
22
+ <span class="ruby-keyword kw">end</span></pre>
23
+ </body>
24
+ </html>
data/doc/classes/Bio/DB/Sam.src/M000029.html ADDED
@@ -0,0 +1,41 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html>
7
+ <head>
8
+ <title>fetch_with_function (Bio::DB::Sam)</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <link rel="stylesheet" href="../../../.././rdoc-style.css" type="text/css" media="screen" />
11
+ </head>
12
+ <body class="standalone-code">
13
+ <pre><span class="ruby-comment cmt"># File lib/bio/db/sam.rb, line 224</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">fetch_with_function</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>, <span class="ruby-identifier">qend</span>, <span class="ruby-identifier">function</span>)
15
+ <span class="ruby-identifier">load_index</span> <span class="ruby-keyword kw">if</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-ivar">@sam_index</span>.<span class="ruby-identifier">null?</span>
16
+ <span class="ruby-identifier">chr</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:int</span>
17
+ <span class="ruby-identifier">beg</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:int</span>
18
+ <span class="ruby-identifier">last</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:int</span>
19
+ <span class="ruby-identifier">query</span> = <span class="ruby-identifier">query_string</span>(<span class="ruby-identifier">chromosome</span>, <span class="ruby-identifier">qstart</span>,<span class="ruby-identifier">qend</span>)
20
+ <span class="ruby-identifier">qpointer</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">query</span>)
21
+ <span class="ruby-identifier">header</span> = <span class="ruby-ivar">@sam_file</span>[<span class="ruby-identifier">:header</span>]
22
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_parse_region</span>(<span class="ruby-identifier">header</span>,<span class="ruby-identifier">qpointer</span>, <span class="ruby-identifier">chr</span>, <span class="ruby-identifier">beg</span>, <span class="ruby-identifier">last</span>)
23
+ <span class="ruby-comment cmt">#raise SAMException.new(), &quot;invalid query: &quot; + query if(chr.read_int &lt; 0)</span>
24
+ <span class="ruby-identifier">count</span> = <span class="ruby-value">0</span>;
25
+
26
+ <span class="ruby-identifier">fetchAlignment</span> = <span class="ruby-constant">Proc</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">data</span><span class="ruby-operator">|</span>
27
+ <span class="ruby-identifier">alignment</span> = <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">new</span>
28
+ <span class="ruby-identifier">alignment</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
29
+ <span class="ruby-identifier">function</span>.<span class="ruby-identifier">call</span>(<span class="ruby-identifier">alignment</span>)
30
+ <span class="ruby-identifier">count</span> = <span class="ruby-identifier">count</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>
31
+ <span class="ruby-value">0</span>
32
+ <span class="ruby-keyword kw">end</span>
33
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_fetch</span>(<span class="ruby-ivar">@sam_file</span>[<span class="ruby-identifier">:x</span>][<span class="ruby-identifier">:bam</span>], <span class="ruby-ivar">@sam_index</span>,<span class="ruby-identifier">chr</span>.<span class="ruby-identifier">read_int</span>,<span class="ruby-identifier">beg</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-identifier">last</span>.<span class="ruby-identifier">read_int</span>, <span class="ruby-keyword kw">nil</span>, <span class="ruby-identifier">fetchAlignment</span>)
34
+ <span class="ruby-comment cmt">#LibC.free chr</span>
35
+ <span class="ruby-comment cmt">#LibC.free beg</span>
36
+ <span class="ruby-comment cmt">#LibC.free last</span>
37
+ <span class="ruby-comment cmt">#LibC.free qpointer</span>
38
+ <span class="ruby-identifier">count</span>
39
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>
data/doc/classes/Bio/DB/Sam.src/M000030.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+
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+ <html>
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+ <head>
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+ <title>merge (Bio::DB::Sam)</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.rb, line 257</span>
14
+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">merge</span>(<span class="ruby-identifier">files</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">add_RG</span>, <span class="ruby-identifier">by_qname</span>)
15
+ <span class="ruby-identifier">strptrs</span> = []
16
+ <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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-value str">&quot;merge&quot;</span>)
17
+ <span class="ruby-identifier">files</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
18
+ <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</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">file</span>)
19
+ <span class="ruby-keyword kw">end</span>
20
+ <span class="ruby-identifier">strptrs</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-keyword kw">nil</span>
21
+
22
+ <span class="ruby-comment cmt"># Now load all the pointers into a native memory block</span>
23
+ <span class="ruby-identifier">argv</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:pointer</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>)
24
+ <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span>, <span class="ruby-identifier">i</span><span class="ruby-operator">|</span>
25
+ <span class="ruby-identifier">argv</span>[<span class="ruby-identifier">i</span>].<span class="ruby-identifier">put_pointer</span>(<span class="ruby-value">0</span>, <span class="ruby-identifier">p</span>)
26
+ <span class="ruby-keyword kw">end</span>
27
+ <span class="ruby-comment cmt">#void bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int add_RG)</span>
28
+ <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">DB</span><span class="ruby-operator">::</span><span class="ruby-constant">SAM</span><span class="ruby-operator">::</span><span class="ruby-constant">Tools</span>.<span class="ruby-identifier">bam_merge_core</span>(<span class="ruby-identifier">by_qname</span>, <span class="ruby-identifier">merged_file</span>, <span class="ruby-identifier">headers</span>, <span class="ruby-identifier">strptrs</span>.<span class="ruby-identifier">length</span>, <span class="ruby-identifier">argv</span>, <span class="ruby-identifier">add_RG</span>)
29
+ <span class="ruby-keyword kw">end</span></pre>
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+ </body>
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+ </html>