bio-samtools 0.2.5 → 0.3.0

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Files changed (73) hide show
  1. data/README.rdoc +7 -20
  2. data/Rakefile +11 -0
  3. data/VERSION +1 -1
  4. data/bio-samtools.gemspec +67 -1
  5. data/doc/basic_styles.css +31 -0
  6. data/doc/classes/Bio.html +139 -0
  7. data/doc/classes/Bio/DB.html +137 -0
  8. data/doc/classes/Bio/DB/Alignment.html +441 -0
  9. data/doc/classes/Bio/DB/Alignment.src/M000012.html +19 -0
  10. data/doc/classes/Bio/DB/Alignment.src/M000013.html +27 -0
  11. data/doc/classes/Bio/DB/Alignment.src/M000014.html +45 -0
  12. data/doc/classes/Bio/DB/Alignment.src/M000015.html +40 -0
  13. data/doc/classes/Bio/DB/SAM.html +510 -0
  14. data/doc/classes/Bio/DB/SAM/Library.html +135 -0
  15. data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +28 -0
  16. data/doc/classes/Bio/DB/SAM/Tools.html +278 -0
  17. data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +20 -0
  18. data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +111 -0
  19. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +150 -0
  20. data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +20 -0
  21. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +169 -0
  22. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +19 -0
  23. data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +18 -0
  24. data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +111 -0
  25. data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +129 -0
  26. data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +111 -0
  27. data/doc/classes/Bio/DB/SAMException.html +140 -0
  28. data/doc/classes/Bio/DB/SAMException.src/M000016.html +18 -0
  29. data/doc/classes/Bio/DB/Sam.src/M000017.html +43 -0
  30. data/doc/classes/Bio/DB/Sam.src/M000018.html +42 -0
  31. data/doc/classes/Bio/DB/Sam.src/M000019.html +18 -0
  32. data/doc/classes/Bio/DB/Sam.src/M000020.html +22 -0
  33. data/doc/classes/Bio/DB/Sam.src/M000021.html +19 -0
  34. data/doc/classes/Bio/DB/Sam.src/M000022.html +25 -0
  35. data/doc/classes/Bio/DB/Sam.src/M000023.html +28 -0
  36. data/doc/classes/Bio/DB/Sam.src/M000024.html +28 -0
  37. data/doc/classes/Bio/DB/Sam.src/M000025.html +46 -0
  38. data/doc/classes/Bio/DB/Sam.src/M000026.html +24 -0
  39. data/doc/classes/Bio/DB/Sam.src/M000027.html +19 -0
  40. data/doc/classes/Bio/DB/Sam.src/M000028.html +24 -0
  41. data/doc/classes/Bio/DB/Sam.src/M000029.html +41 -0
  42. data/doc/classes/Bio/DB/Sam.src/M000030.html +31 -0
  43. data/doc/classes/Bio/DB/Sam.src/M000031.html +86 -0
  44. data/doc/classes/Bio/DB/Sam.src/M000032.html +34 -0
  45. data/doc/classes/Bio/DB/Tag.html +160 -0
  46. data/doc/classes/Bio/DB/Tag.src/M000011.html +21 -0
  47. data/doc/classes/LibC.html +105 -0
  48. data/doc/classes/Pileup.html +374 -0
  49. data/doc/classes/Pileup.src/M000001.html +34 -0
  50. data/doc/classes/Pileup.src/M000002.html +21 -0
  51. data/doc/classes/Pileup.src/M000003.html +21 -0
  52. data/doc/classes/Pileup.src/M000004.html +21 -0
  53. data/doc/classes/Pileup.src/M000005.html +31 -0
  54. data/doc/created.rid +1 -0
  55. data/doc/files/lib/bio-samtools_rb.html +109 -0
  56. data/doc/files/lib/bio/db/sam/bam_rb.html +108 -0
  57. data/doc/files/lib/bio/db/sam/faidx_rb.html +108 -0
  58. data/doc/files/lib/bio/db/sam/library_rb.html +101 -0
  59. data/doc/files/lib/bio/db/sam/pileup_rb.html +178 -0
  60. data/doc/files/lib/bio/db/sam/sam_rb.html +113 -0
  61. data/doc/files/lib/bio/db/sam_rb.html +111 -0
  62. data/doc/fr_class_index.html +43 -0
  63. data/doc/fr_file_index.html +33 -0
  64. data/doc/fr_method_index.html +58 -0
  65. data/doc/index.html +24 -0
  66. data/doc/rdoc-style.css +208 -0
  67. data/doc/tutorial.html +165 -0
  68. data/doc/tutorial.pdf +0 -0
  69. data/lib/bio/db/sam.rb +163 -1
  70. data/lib/bio/db/sam/pileup.rb +98 -0
  71. data/test/basictest.rb +14 -0
  72. data/test/pileup.rb +68 -0
  73. metadata +84 -18
data/doc/classes/Bio/DB/Alignment.src/M000013.html ADDED
@@ -0,0 +1,27 @@
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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::Alignment)</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 395</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-constant">Alignment</span>.<span class="ruby-identifier">finalize</span>(<span class="ruby-identifier">object_id</span>)
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+
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+ <span class="ruby-comment cmt"># puts &quot;Object #{object_id} dying at #{Time.new}&quot;</span>
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+ <span class="ruby-comment cmt"># p &quot;?&quot; . object_id.al</span>
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+ <span class="ruby-comment cmt"># p object_id.al</span>
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+ <span class="ruby-constant">LibC</span>.<span class="ruby-identifier">free</span> <span class="ruby-identifier">object_id</span>.<span class="ruby-identifier">al</span>
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+ <span class="ruby-constant">LibC</span>.<span class="ruby-identifier">free</span> <span class="ruby-identifier">object_id</span>.<span class="ruby-identifier">sam</span>
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+ <span class="ruby-constant">LibC</span>.<span class="ruby-identifier">free</span> <span class="ruby-identifier">object_id</span>.<span class="ruby-identifier">calend</span>
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+ <span class="ruby-constant">LibC</span>.<span class="ruby-identifier">free</span> <span class="ruby-identifier">object_id</span>.<span class="ruby-identifier">qlen</span>
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+
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+ <span class="ruby-constant">LibC</span>.<span class="ruby-identifier">free</span> <span class="ruby-identifier">object_id</span>.<span class="ruby-identifier">samstr</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/Alignment.src/M000014.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>set (Bio::DB::Alignment)</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 417</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">set</span>(<span class="ruby-identifier">bam_alignment</span>, <span class="ruby-identifier">header</span>)
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+ <span class="ruby-comment cmt">#Create the FFI object</span>
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+ <span class="ruby-ivar">@al</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">Bam1T</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">bam_alignment</span>)
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+
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+ <span class="ruby-comment cmt">#set the raw data</span>
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+ <span class="ruby-identifier">tmp_str</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_format1</span>(<span class="ruby-identifier">header</span>,<span class="ruby-identifier">al</span>)
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+ <span class="ruby-comment cmt">#self.sam = tmp_str</span>
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+ <span class="ruby-comment cmt">#ObjectSpace.define_finalizer(self, proc {|id| puts &quot;Finalizer one on #{id}&quot; })</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">sam</span> = <span class="ruby-constant">String</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">tmp_str</span>)
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+ <span class="ruby-comment cmt">#LibC.free tmp_str</span>
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+ <span class="ruby-comment cmt">#Set values calculated by libbam</span>
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+ <span class="ruby-identifier">core</span> = <span class="ruby-identifier">al</span>[<span class="ruby-identifier">:core</span>]
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+ <span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">al</span>[<span class="ruby-identifier">:data</span>][<span class="ruby-identifier">core</span>[<span class="ruby-identifier">:l_qname</span>]]<span class="ruby-comment cmt">#define bam1_cigar(b) ((uint32_t*)((b)-&gt;data + (b)-&gt;core.l_qname)) </span>
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+ <span class="ruby-ivar">@calend</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_calend</span>(<span class="ruby-identifier">core</span>,<span class="ruby-identifier">cigar</span>)
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+ <span class="ruby-ivar">@qlen</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_cigar2qlen</span>(<span class="ruby-identifier">core</span>,<span class="ruby-identifier">cigar</span>)
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+
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+ <span class="ruby-comment cmt">#process the flags</span>
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+ <span class="ruby-ivar">@is_paired</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0001</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0002</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0004</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0008</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0010</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0020</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0040</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0080</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0100</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0200</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
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+ <span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> <span class="ruby-operator">&amp;</span> <span class="ruby-value">0x0400</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</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/Alignment.src/M000015.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>sam= (Bio::DB::Alignment)</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 449</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">sam=</span>(<span class="ruby-identifier">sam</span>)
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+ <span class="ruby-comment cmt">#p sam</span>
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+ <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam</span>.<span class="ruby-identifier">split</span>(<span class="ruby-value str">&quot;\t&quot;</span>)
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">flag</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">pos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">3</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">mapq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">4</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">mpos</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">7</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">isize</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">8</span>].<span class="ruby-identifier">to_i</span>
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
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+ <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">tags</span> = {}
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+ <span class="ruby-value">11</span>.<span class="ruby-identifier">upto</span>(<span class="ruby-identifier">s</span>.<span class="ruby-identifier">size</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>) {<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
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+ <span class="ruby-identifier">t</span> = <span class="ruby-constant">Tag</span>.<span class="ruby-identifier">new</span>
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+ <span class="ruby-identifier">t</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">s</span>[<span class="ruby-identifier">n</span>])
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+ <span class="ruby-identifier">tags</span>[<span class="ruby-identifier">t</span>.<span class="ruby-identifier">tag</span>] = <span class="ruby-identifier">t</span>
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+ }
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+
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+
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+ <span class="ruby-comment cmt">#&lt;QNAME&gt; &lt;FLAG&gt; &lt;RNAME&gt; &lt;POS&gt; &lt;MAPQ&gt; &lt;CIGAR&gt; &lt;MRNM&gt; &lt;MPOS&gt; &lt;ISIZE&gt; &lt;SEQ&gt; &lt;QUAL&gt; #[&lt;TAG&gt;:&lt;VTYPE&gt;:&lt;VALUE&gt; [...]] </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.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>Class: Bio::DB::Sam</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;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Bio::DB::Sam</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../files/lib/bio/db/sam_rb.html">
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+ lib/bio/db/sam.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </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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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000024">average_coverage</a>&nbsp;&nbsp;
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+ <a href="#M000025">chromosome_coverage</a>&nbsp;&nbsp;
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+ <a href="#M000020">close</a>&nbsp;&nbsp;
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+ <a href="#M000032">deprecated_pileup</a>&nbsp;&nbsp;
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+ <a href="#M000028">fetch</a>&nbsp;&nbsp;
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+ <a href="#M000026">fetch_reference</a>&nbsp;&nbsp;
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+ <a href="#M000029">fetch_with_function</a>&nbsp;&nbsp;
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+ <a href="#M000021">finalize</a>&nbsp;&nbsp;
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+ <a href="#M000022">load_index</a>&nbsp;&nbsp;
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+ <a href="#M000023">load_reference</a>&nbsp;&nbsp;
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+ <a href="#M000030">merge</a>&nbsp;&nbsp;
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+ <a href="#M000031">mpileup</a>&nbsp;&nbsp;
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+ <a href="#M000017">new</a>&nbsp;&nbsp;
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+ <a href="#M000018">open</a>&nbsp;&nbsp;
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+ <a href="#M000027">query_string</a>&nbsp;&nbsp;
104
+ <a href="#M000019">to_s</a>&nbsp;&nbsp;
105
+ </div>
106
+ </div>
107
+
108
+ </div>
109
+
110
+
111
+ <!-- if includes -->
112
+
113
+ <div id="section">
114
+
115
+
116
+
117
+
118
+
119
+ <div id="attribute-list">
120
+ <h3 class="section-bar">Attributes</h3>
121
+
122
+ <div class="name-list">
123
+ <table>
124
+ <tr class="top-aligned-row context-row">
125
+ <td class="context-item-name">sam_file</td>
126
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
127
+ <td class="context-item-desc"></td>
128
+ </tr>
129
+ </table>
130
+ </div>
131
+ </div>
132
+
133
+
134
+
135
+ <!-- if method_list -->
136
+ <div id="methods">
137
+ <h3 class="section-bar">Public Class methods</h3>
138
+
139
+ <div id="method-M000021" class="method-detail">
140
+ <a name="M000021"></a>
141
+
142
+ <div class="method-heading">
143
+ <a href="Sam.src/M000021.html" target="Code" class="method-signature"
144
+ onclick="popupCode('Sam.src/M000021.html');return false;">
145
+ <span class="method-name">finalize</span><span class="method-args">(id)</span>
146
+ </a>
147
+ </div>
148
+
149
+ <div class="method-description">
150
+ <p>
151
+ Destructor method that closes the file before letting the object be garbage
152
+ collected.
153
+ </p>
154
+ </div>
155
+ </div>
156
+
157
+ <div id="method-M000030" class="method-detail">
158
+ <a name="M000030"></a>
159
+
160
+ <div class="method-heading">
161
+ <a href="Sam.src/M000030.html" target="Code" class="method-signature"
162
+ onclick="popupCode('Sam.src/M000030.html');return false;">
163
+ <span class="method-name">merge</span><span class="method-args">(files, merged_file, headers, add_RG, by_qname)</span>
164
+ </a>
165
+ </div>
166
+
167
+ <div class="method-description">
168
+ <p>
169
+ Merges n BAM files. This doesn&#8216;t require to create a <a
170
+ href="SAM.html">SAM</a> object
171
+ </p>
172
+ <table>
173
+ <tr><td valign="top">files:</td><td>An array with the paths to the files.
174
+
175
+ </td></tr>
176
+ <tr><td valign="top">merged_file:</td><td>The path to the merged file
177
+
178
+ </td></tr>
179
+ <tr><td valign="top">headers:</td><td>The BAM file containing the header
180
+
181
+ </td></tr>
182
+ <tr><td valign="top">add_RG:</td><td>If true, the RG tag is added (infered from the filenames)
183
+
184
+ </td></tr>
185
+ <tr><td valign="top">by_qname:</td><td>If true, the bamfiles should by ordered by query name, if false, by
186
+ coordinates.
187
+
188
+ </td></tr>
189
+ </table>
190
+ </div>
191
+ </div>
192
+
193
+ <div id="method-M000017" class="method-detail">
194
+ <a name="M000017"></a>
195
+
196
+ <div class="method-heading">
197
+ <a href="Sam.src/M000017.html" target="Code" class="method-signature"
198
+ onclick="popupCode('Sam.src/M000017.html');return false;">
199
+ <span class="method-name">new</span><span class="method-args">(optsa={})</span>
200
+ </a>
201
+ </div>
202
+
203
+ <div class="method-description">
204
+ <p>
205
+ To make a <a href="Sam.html#M000017">new</a> sam object. Initialize expects
206
+ a hash optsa with the following elemets:
207
+ </p>
208
+ <table>
209
+ <tr><td valign="top">fasta:</td><td>The fasta file with the reference. (nil)
210
+
211
+ </td></tr>
212
+ <tr><td valign="top">bam:</td><td>path to a binary <a href="SAM.html">SAM</a> file (nil)
213
+
214
+ </td></tr>
215
+ <tr><td valign="top">tam:</td><td>path to a text <a href="SAM.html">SAM</a> file (nil)
216
+
217
+ </td></tr>
218
+ <tr><td valign="top">compressed:</td><td>If the binary file is compressed (true)
219
+
220
+ </td></tr>
221
+ <tr><td valign="top">write:</td><td>If the file is to be writen (false). Not supported yet.
222
+
223
+ </td></tr>
224
+ </table>
225
+ <p>
226
+ *NOTE:* you can&#8216;t use binary and text formats simultaneusly. To make
227
+ queries, the file has to be a sorted binary. This function doesn&#8216;t
228
+ actually <a href="Sam.html#M000018">open</a> the file, it just prepares the
229
+ object to be opened in a later stage.
230
+ </p>
231
+ </div>
232
+ </div>
233
+
234
+ <h3 class="section-bar">Public Instance methods</h3>
235
+
236
+ <div id="method-M000024" class="method-detail">
237
+ <a name="M000024"></a>
238
+
239
+ <div class="method-heading">
240
+ <a href="Sam.src/M000024.html" target="Code" class="method-signature"
241
+ onclick="popupCode('Sam.src/M000024.html');return false;">
242
+ <span class="method-name">average_coverage</span><span class="method-args">(chromosome, qstart, len)</span>
243
+ </a>
244
+ </div>
245
+
246
+ <div class="method-description">
247
+ <p>
248
+ Returns the average coverage of a region in a bam file.
249
+ </p>
250
+ </div>
251
+ </div>
252
+
253
+ <div id="method-M000025" class="method-detail">
254
+ <a name="M000025"></a>
255
+
256
+ <div class="method-heading">
257
+ <a href="Sam.src/M000025.html" target="Code" class="method-signature"
258
+ onclick="popupCode('Sam.src/M000025.html');return false;">
259
+ <span class="method-name">chromosome_coverage</span><span class="method-args">(chromosome, qstart, len)</span>
260
+ </a>
261
+ </div>
262
+
263
+ <div class="method-description">
264
+ <p>
265
+ Returns an array with the coverage at each possition in the queried region
266
+ This is a simple average coverage just calculated with the first and last
267
+ possition of the alignment, ignoring the gaps.
268
+ </p>
269
+ </div>
270
+ </div>
271
+
272
+ <div id="method-M000020" class="method-detail">
273
+ <a name="M000020"></a>
274
+
275
+ <div class="method-heading">
276
+ <a href="Sam.src/M000020.html" target="Code" class="method-signature"
277
+ onclick="popupCode('Sam.src/M000020.html');return false;">
278
+ <span class="method-name">close</span><span class="method-args">()</span>
279
+ </a>
280
+ </div>
281
+
282
+ <div class="method-description">
283
+ <p>
284
+ Closes the sam file and destroys the C pointers using the functions
285
+ provided by libbam
286
+ </p>
287
+ </div>
288
+ </div>
289
+
290
+ <div id="method-M000032" class="method-detail">
291
+ <a name="M000032"></a>
292
+
293
+ <div class="method-heading">
294
+ <a href="Sam.src/M000032.html" target="Code" class="method-signature"
295
+ onclick="popupCode('Sam.src/M000032.html');return false;">
296
+ <span class="method-name">deprecated_pileup</span><span class="method-args">( cmd ) {|Pileup.new(line)| ...}</span>
297
+ </a>
298
+ </div>
299
+
300
+ <div class="method-description">
301
+ <p>
302
+ utility method that does not use the samtools API, it calls samtools
303
+ directly as if on the command line and catches the output, to use this
304
+ method you must have a version of samtools that supports the pileup command
305
+ (&lt; 0.1.17) otherwise the command will fail. <a
306
+ href="Sam.html#M000031">mpileup</a> is the preferred method for getting
307
+ pileups. With this method the sam object should be created as usual, but
308
+ you need to pass this method a string of options for samtools you
309
+ don&#8216;t need to provide the call to samtools pileup itself or -f
310
+ &lt;fasta file&gt; or the bam file itself, these are taken from the sam
311
+ object
312
+ </p>
313
+ </div>
314
+ </div>
315
+
316
+ <div id="method-M000028" class="method-detail">
317
+ <a name="M000028"></a>
318
+
319
+ <div class="method-heading">
320
+ <a href="Sam.src/M000028.html" target="Code" class="method-signature"
321
+ onclick="popupCode('Sam.src/M000028.html');return false;">
322
+ <span class="method-name">fetch</span><span class="method-args">(chromosome, qstart, qend)</span>
323
+ </a>
324
+ </div>
325
+
326
+ <div class="method-description">
327
+ <p>
328
+ Returns an array of Alignments on a given region.
329
+ </p>
330
+ </div>
331
+ </div>
332
+
333
+ <div id="method-M000026" class="method-detail">
334
+ <a name="M000026"></a>
335
+
336
+ <div class="method-heading">
337
+ <a href="Sam.src/M000026.html" target="Code" class="method-signature"
338
+ onclick="popupCode('Sam.src/M000026.html');return false;">
339
+ <span class="method-name">fetch_reference</span><span class="method-args">(chromosome, qstart,qend)</span>
340
+ </a>
341
+ </div>
342
+
343
+ <div class="method-description">
344
+ <p>
345
+ Returns the sequence for a given region.
346
+ </p>
347
+ </div>
348
+ </div>
349
+
350
+ <div id="method-M000029" class="method-detail">
351
+ <a name="M000029"></a>
352
+
353
+ <div class="method-heading">
354
+ <a href="Sam.src/M000029.html" target="Code" class="method-signature"
355
+ onclick="popupCode('Sam.src/M000029.html');return false;">
356
+ <span class="method-name">fetch_with_function</span><span class="method-args">(chromosome, qstart, qend, function)</span>
357
+ </a>
358
+ </div>
359
+
360
+ <div class="method-description">
361
+ <p>
362
+ Executes a function on each <a href="Alignment.html">Alignment</a> inside
363
+ the queried region of the chromosome. The chromosome can be either the
364
+ textual name or a FixNum with the internal index. However, you need to get
365
+ the internal index with the provided API, otherwise the pointer is outside
366
+ the scope of the C library. Returns the count of alignments in the region.
367
+ WARNING: Accepts an index already parsed by the library. It fails when you
368
+ use your own FixNum (FFI-bug?)
369
+ </p>
370
+ </div>
371
+ </div>
372
+
373
+ <div id="method-M000022" class="method-detail">
374
+ <a name="M000022"></a>
375
+
376
+ <div class="method-heading">
377
+ <a href="Sam.src/M000022.html" target="Code" class="method-signature"
378
+ onclick="popupCode('Sam.src/M000022.html');return false;">
379
+ <span class="method-name">load_index</span><span class="method-args">()</span>
380
+ </a>
381
+ </div>
382
+
383
+ <div class="method-description">
384
+ <p>
385
+ Loads the bam index to be used for fetching. If the index doesn&#8216;t
386
+ exists the index is built provided that the user has writing access to the
387
+ folder where the BAM file is located. If the creation of the file fails a
388
+ <a href="SAMException.html">SAMException</a> is thrown. If the index
389
+ doesn&#8216;t exist, loading it will take more time. It is suggested to
390
+ generate the index separatedly if the bam file sits on a server where the
391
+ executing user may not have writing permissions in the server.
392
+ </p>
393
+ </div>
394
+ </div>
395
+
396
+ <div id="method-M000023" class="method-detail">
397
+ <a name="M000023"></a>
398
+
399
+ <div class="method-heading">
400
+ <a href="Sam.src/M000023.html" target="Code" class="method-signature"
401
+ onclick="popupCode('Sam.src/M000023.html');return false;">
402
+ <span class="method-name">load_reference</span><span class="method-args">()</span>
403
+ </a>
404
+ </div>
405
+
406
+ <div class="method-description">
407
+ <p>
408
+ Loads the reference file to be able to query regions of it. This requires
409
+ the fai index to exist in the same folder than the reference. If it
410
+ doesn&#8216;t exisits, this functions attempts to generate it. If user
411
+ doesn&#8216;t have writing permissions on the folder, or the creation of
412
+ the fai fails for any reason, a <a
413
+ href="SAMException.html">SAMException</a> is thrown.
414
+ </p>
415
+ </div>
416
+ </div>
417
+
418
+ <div id="method-M000031" class="method-detail">
419
+ <a name="M000031"></a>
420
+
421
+ <div class="method-heading">
422
+ <a href="Sam.src/M000031.html" target="Code" class="method-signature"
423
+ onclick="popupCode('Sam.src/M000031.html');return false;">
424
+ <span class="method-name">mpileup</span><span class="method-args">( opts ) {|Pileup.new(line)| ...}</span>
425
+ </a>
426
+ </div>
427
+
428
+ <div class="method-description">
429
+ <p>
430
+ calls the <a href="Sam.html#M000031">mpileup</a> function, opts is a hash
431
+ of options identical to the command line options for <a
432
+ href="Sam.html#M000031">mpileup</a>. is an iterator that yields a <a
433
+ href="../../Pileup.html">Pileup</a> object for each postion the command
434
+ line options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p)
435
+ call the option as a symbol of the flag, eg -r for region is called :r
436
+ =&gt; &quot;some <a href="SAM.html">SAM</a> compatible region&quot; eg
437
+ bam.mpileup(:r =&gt; &quot;chr1:1000-2000&quot;, :q =&gt; 50) gets the
438
+ bases with quality &gt; 50 on chr1 between 1000-5000
439
+ </p>
440
+ </div>
441
+ </div>
442
+
443
+ <div id="method-M000018" class="method-detail">
444
+ <a name="M000018"></a>
445
+
446
+ <div class="method-heading">
447
+ <a href="Sam.src/M000018.html" target="Code" class="method-signature"
448
+ onclick="popupCode('Sam.src/M000018.html');return false;">
449
+ <span class="method-name">open</span><span class="method-args">()</span>
450
+ </a>
451
+ </div>
452
+
453
+ <div class="method-description">
454
+ <p>
455
+ Function that actually opens the sam file Throws a <a
456
+ href="SAMException.html">SAMException</a> if the file can&#8216;t be <a
457
+ href="Sam.html#M000018">open</a>.
458
+ </p>
459
+ </div>
460
+ </div>
461
+
462
+ <div id="method-M000027" class="method-detail">
463
+ <a name="M000027"></a>
464
+
465
+ <div class="method-heading">
466
+ <a href="Sam.src/M000027.html" target="Code" class="method-signature"
467
+ onclick="popupCode('Sam.src/M000027.html');return false;">
468
+ <span class="method-name">query_string</span><span class="method-args">(chromosome, qstart,qend)</span>
469
+ </a>
470
+ </div>
471
+
472
+ <div class="method-description">
473
+ <p>
474
+ Generates a query sting to be used by the region parser in samtools. In
475
+ principle, you shouldn&#8216;t need to use this function.
476
+ </p>
477
+ </div>
478
+ </div>
479
+
480
+ <div id="method-M000019" class="method-detail">
481
+ <a name="M000019"></a>
482
+
483
+ <div class="method-heading">
484
+ <a href="Sam.src/M000019.html" target="Code" class="method-signature"
485
+ onclick="popupCode('Sam.src/M000019.html');return false;">
486
+ <span class="method-name">to_s</span><span class="method-args">()</span>
487
+ </a>
488
+ </div>
489
+
490
+ <div class="method-description">
491
+ <p>
492
+ Prints a description of the sam file in a text format containg if it is
493
+ binary or text, the path and the fasta file of the reference
494
+ </p>
495
+ </div>
496
+ </div>
497
+
498
+
499
+ </div>
500
+
501
+
502
+ </div>
503
+
504
+
505
+ <div id="validator-badges">
506
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
507
+ </div>
508
+
509
+ </body>
510
+ </html>