bio-samtools 0.4.1 → 0.4.2

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Files changed (74) hide show
  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +60 -6
  3. data/doc/Bio.html +171 -0
  4. data/doc/Bio/DB.html +163 -0
  5. data/doc/Bio/DB/Alignment.html +780 -0
  6. data/doc/Bio/DB/SAM.html +1241 -0
  7. data/doc/Bio/DB/SAM/Library.html +217 -0
  8. data/doc/Bio/DB/SAM/Tools.html +331 -0
  9. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
  10. data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
  11. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
  12. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
  13. data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
  14. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
  15. data/doc/Bio/DB/SAMException.html +205 -0
  16. data/doc/Bio/DB/Tag.html +254 -0
  17. data/doc/LICENSE_txt.html +881 -0
  18. data/doc/LibC.html +153 -0
  19. data/doc/Pileup.html +571 -0
  20. data/doc/Vcf.html +473 -0
  21. data/doc/created.rid +10 -1
  22. data/doc/images/add.png +0 -0
  23. data/doc/images/brick.png +0 -0
  24. data/doc/images/brick_link.png +0 -0
  25. data/doc/images/bug.png +0 -0
  26. data/doc/images/bullet_black.png +0 -0
  27. data/doc/images/bullet_toggle_minus.png +0 -0
  28. data/doc/images/bullet_toggle_plus.png +0 -0
  29. data/doc/images/date.png +0 -0
  30. data/doc/images/delete.png +0 -0
  31. data/doc/images/find.png +0 -0
  32. data/doc/images/loadingAnimation.gif +0 -0
  33. data/doc/images/macFFBgHack.png +0 -0
  34. data/doc/images/package.png +0 -0
  35. data/doc/images/page_green.png +0 -0
  36. data/doc/images/page_white_text.png +0 -0
  37. data/doc/images/page_white_width.png +0 -0
  38. data/doc/images/plugin.png +0 -0
  39. data/doc/images/ruby.png +0 -0
  40. data/doc/images/tag_blue.png +0 -0
  41. data/doc/images/tag_green.png +0 -0
  42. data/doc/images/transparent.png +0 -0
  43. data/doc/images/wrench.png +0 -0
  44. data/doc/images/wrench_orange.png +0 -0
  45. data/doc/images/zoom.png +0 -0
  46. data/doc/index.html +109 -21
  47. data/doc/js/darkfish.js +153 -0
  48. data/doc/js/jquery.js +18 -0
  49. data/doc/js/navigation.js +142 -0
  50. data/doc/js/search.js +94 -0
  51. data/doc/js/search_index.js +1 -0
  52. data/doc/js/searcher.js +228 -0
  53. data/doc/lib/bio-samtools_rb.html +115 -0
  54. data/doc/lib/bio/db/sam/bam_rb.html +121 -0
  55. data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
  56. data/doc/lib/bio/db/sam/library_rb.html +115 -0
  57. data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
  58. data/doc/lib/bio/db/sam/sam_rb.html +121 -0
  59. data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
  60. data/doc/lib/bio/db/sam_rb.html +115 -0
  61. data/doc/rdoc.css +543 -0
  62. data/doc/table_of_contents.html +186 -0
  63. data/ext/Makefile-bioruby.patch +1 -1
  64. data/ext/Rakefile +8 -1
  65. data/ext/mkrf_conf.rb +8 -1
  66. data/lib/bio/db/sam.rb +140 -27
  67. data/lib/bio/db/sam/vcf.rb +0 -1
  68. data/test/basictest.rb +4 -4
  69. data/test/test_basic.rb +50 -34
  70. metadata +79 -25
  71. data/test/coverage.rb +0 -26
  72. data/test/coverage_plot.rb +0 -28
  73. data/test/feature.rb +0 -0
  74. data/test/test_pileup.rb +0 -68
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.4.1
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+ 0.4.2
data/bio-samtools.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = %q{bio-samtools}
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- s.version = "0.4.1"
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+ s.version = "0.4.2"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
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- s.date = %q{2011-11-09}
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+ s.date = %q{2011-11-10}
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  s.description = %q{Binder of samtools for ruby, on the top of FFI.
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  This project was born from the need to add support of BAM files to
@@ -29,6 +29,24 @@ Gem::Specification.new do |s|
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  "Rakefile",
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  "VERSION",
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  "bio-samtools.gemspec",
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+ "doc/Bio.html",
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+ "doc/Bio/DB.html",
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+ "doc/Bio/DB/Alignment.html",
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+ "doc/Bio/DB/SAM.html",
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+ "doc/Bio/DB/SAM/Library.html",
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+ "doc/Bio/DB/SAM/Tools.html",
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+ "doc/Bio/DB/SAM/Tools/Bam1CoreT.html",
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+ "doc/Bio/DB/SAM/Tools/Bam1T.html",
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+ "doc/Bio/DB/SAM/Tools/BamHeaderT.html",
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+ "doc/Bio/DB/SAM/Tools/BamPileup1T.html",
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+ "doc/Bio/DB/SAM/Tools/SamfileT.html",
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+ "doc/Bio/DB/SAM/Tools/SamfileTX.html",
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+ "doc/Bio/DB/SAMException.html",
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+ "doc/Bio/DB/Tag.html",
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+ "doc/LICENSE_txt.html",
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+ "doc/LibC.html",
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+ "doc/Pileup.html",
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+ "doc/Vcf.html",
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  "doc/basic_styles.css",
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  "doc/classes/Bio.html",
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  "doc/classes/Bio/DB.html",
@@ -89,8 +107,48 @@ Gem::Specification.new do |s|
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  "doc/fr_class_index.html",
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  "doc/fr_file_index.html",
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  "doc/fr_method_index.html",
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+ "doc/images/add.png",
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+ "doc/images/brick.png",
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+ "doc/images/brick_link.png",
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+ "doc/images/bug.png",
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+ "doc/images/bullet_black.png",
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+ "doc/images/bullet_toggle_minus.png",
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+ "doc/images/bullet_toggle_plus.png",
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+ "doc/images/date.png",
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+ "doc/images/delete.png",
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+ "doc/images/find.png",
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+ "doc/images/loadingAnimation.gif",
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+ "doc/images/macFFBgHack.png",
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+ "doc/images/package.png",
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+ "doc/images/page_green.png",
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+ "doc/images/page_white_text.png",
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+ "doc/images/page_white_width.png",
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+ "doc/images/plugin.png",
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+ "doc/images/ruby.png",
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+ "doc/images/tag_blue.png",
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+ "doc/images/tag_green.png",
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+ "doc/images/transparent.png",
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+ "doc/images/wrench.png",
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+ "doc/images/wrench_orange.png",
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+ "doc/images/zoom.png",
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  "doc/index.html",
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+ "doc/js/darkfish.js",
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+ "doc/js/jquery.js",
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+ "doc/js/navigation.js",
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+ "doc/js/search.js",
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+ "doc/js/search_index.js",
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+ "doc/js/searcher.js",
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+ "doc/lib/bio-samtools_rb.html",
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+ "doc/lib/bio/db/sam/bam_rb.html",
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+ "doc/lib/bio/db/sam/faidx_rb.html",
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+ "doc/lib/bio/db/sam/library_rb.html",
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+ "doc/lib/bio/db/sam/pileup_rb.html",
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+ "doc/lib/bio/db/sam/sam_rb.html",
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+ "doc/lib/bio/db/sam/vcf_rb.html",
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+ "doc/lib/bio/db/sam_rb.html",
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+ "doc/rdoc.css",
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+ "doc/table_of_contents.html",
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  "doc/tutorial.html",
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  "ext/Makefile-bioruby.patch",
@@ -108,9 +166,6 @@ Gem::Specification.new do |s|
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  "lib/bio/db/sam/sam.rb",
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  "lib/bio/db/sam/vcf.rb",
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  "test/basictest.rb",
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- "test/coverage.rb",
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- "test/coverage_plot.rb",
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- "test/feature.rb",
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  "test/helper.rb",
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  "test/pileup.rb",
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  "test/samples/small/ids2.txt",
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  "test/test_basic.rb",
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  "test/test_bio-samtools.rb",
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- "test/test_pileup.rb",
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  "test/test_vcf.rb"
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  ]
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  s.homepage = %q{http://github.com/helios/bioruby-samtools}
data/doc/Bio.html ADDED
@@ -0,0 +1,171 @@
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>Module: Bio</title>
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+
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+ <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "./";
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
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+ <body id="top" class="module">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="./index.html">Home</a>
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+ <a href="./table_of_contents.html#classes">Classes</a>
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+ <a href="./table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/db/sam/bam.rb
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+ <li>lib/bio/db/sam/faidx.rb
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+ <li>lib/bio/db/sam/library.rb
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+ <li>lib/bio/db/sam/sam.rb
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+ <li>lib/bio/db/sam.rb
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+ <h3 class="section-header">Pages</h3>
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+ <li class="file"><a href="./LICENSE_txt.html">LICENSE</a>
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+ </ul>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+ <li><a href="./Bio.html">Bio</a>
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+
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+ <li><a href="./Bio/DB.html">Bio::DB</a>
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+ <li><a href="./Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="./Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="./Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="./Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="./Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+ <li><a href="./Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+ <li><a href="./Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+ <li><a href="./Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+ <li><a href="./Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+ <li><a href="./Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+ <li><a href="./Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+ <li><a href="./Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <li><a href="./Bio/DB/Tag.html">Bio::DB::Tag</a>
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+ <li><a href="./LibC.html">LibC</a>
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+ <li><a href="./Pileup.html">Pileup</a>
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+ <li><a href="./Vcf.html">Vcf</a>
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+ </ul>
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+ </nav>
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+ <div id="documentation">
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+ <h1 class="module">module Bio</h1>
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+ <div id="description" class="description">
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+ <p>require ‘rubygems’ require ‘ffi’</p>
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+ <pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/faidx'</span>
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+ <span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/sam'</span>
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+ </pre>
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+ <p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
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+ <pre>sam.rb
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+ <p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
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+ </div><!-- description -->
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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data/doc/Bio/DB.html ADDED
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../table_of_contents.html#classes">Classes</a>
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+ <a href="../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/db/sam/bam.rb
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+ <li>lib/bio/db/sam/faidx.rb
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+ <li>lib/bio/db/sam/library.rb
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+ <li>lib/bio/db/sam/sam.rb
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+ <li>lib/bio/db/sam.rb
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+ </ul>
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+ <li><a href="../Bio.html">Bio</a>
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+
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+ <li><a href="../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
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+ <li><a href="../Bio/DB/SAM.html">Bio::DB::SAM</a>
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+ <li><a href="../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
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+ <li><a href="../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
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+ <li><a href="../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
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+ <li><a href="../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
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+ <li><a href="../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
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+ <li><a href="../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
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+ <li><a href="../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
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+ <li><a href="../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
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+ <li><a href="../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
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+ <li><a href="../Bio/DB/Sam.html">Bio::DB::Sam</a>
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+ <li><a href="../Bio/DB/Tag.html">Bio::DB::Tag</a>
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+ <li><a href="../LibC.html">LibC</a>
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+ <li><a href="../Pileup.html">Pileup</a>
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+ <div id="documentation">
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+ </nav>
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::Alignment</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+
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+
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+
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+
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+ <!-- Attributes -->
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+ <section id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+
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+
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+ <div id="attribute-i-al" class="method-detail">
168
+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">al</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>Attributes from the format</p>
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-calend" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">calend</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
186
+ <div class="method-description">
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+
188
+ <p>Attributes pulled with the C library</p>
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+
190
+ </div>
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+ </div>
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+
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+ <div id="attribute-i-cigar" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">cigar</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>Attributes from the format</p>
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+
203
+ </div>
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+ </div>
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+
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+ <div id="attribute-i-failed_quality" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">failed_quality</span><span
209
+ class="attribute-access-type">[RW]</span>
210
+ </div>
211
+
212
+ <div class="method-description">
213
+
214
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
215
+ documentation) <a
216
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
217
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
218
+ they are forward. It is the opposite to the definition in the BAM format
219
+ for clarity. primary is the negation of is_negative from the BAM format</p>
220
+
221
+ </div>
222
+ </div>
223
+
224
+ <div id="attribute-i-first_in_pair" class="method-detail">
225
+ <div class="method-heading attribute-method-heading">
226
+ <span class="method-name">first_in_pair</span><span
227
+ class="attribute-access-type">[RW]</span>
228
+ </div>
229
+
230
+ <div class="method-description">
231
+
232
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
233
+ documentation) <a
234
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
235
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
236
+ they are forward. It is the opposite to the definition in the BAM format
237
+ for clarity. primary is the negation of is_negative from the BAM format</p>
238
+
239
+ </div>
240
+ </div>
241
+
242
+ <div id="attribute-i-flag" class="method-detail">
243
+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">flag</span><span
245
+ class="attribute-access-type">[RW]</span>
246
+ </div>
247
+
248
+ <div class="method-description">
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+
250
+ <p>Attributes from the format</p>
251
+
252
+ </div>
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+ </div>
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+
255
+ <div id="attribute-i-is_duplicate" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">is_duplicate</span><span
258
+ class="attribute-access-type">[RW]</span>
259
+ </div>
260
+
261
+ <div class="method-description">
262
+
263
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
264
+ documentation) <a
265
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
266
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
267
+ they are forward. It is the opposite to the definition in the BAM format
268
+ for clarity. primary is the negation of is_negative from the BAM format</p>
269
+
270
+ </div>
271
+ </div>
272
+
273
+ <div id="attribute-i-is_mapped" class="method-detail">
274
+ <div class="method-heading attribute-method-heading">
275
+ <span class="method-name">is_mapped</span><span
276
+ class="attribute-access-type">[RW]</span>
277
+ </div>
278
+
279
+ <div class="method-description">
280
+
281
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
282
+ documentation) <a
283
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
284
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
285
+ they are forward. It is the opposite to the definition in the BAM format
286
+ for clarity. primary is the negation of is_negative from the BAM format</p>
287
+
288
+ </div>
289
+ </div>
290
+
291
+ <div id="attribute-i-is_paired" class="method-detail">
292
+ <div class="method-heading attribute-method-heading">
293
+ <span class="method-name">is_paired</span><span
294
+ class="attribute-access-type">[RW]</span>
295
+ </div>
296
+
297
+ <div class="method-description">
298
+
299
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
300
+ documentation) <a
301
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
302
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
303
+ they are forward. It is the opposite to the definition in the BAM format
304
+ for clarity. primary is the negation of is_negative from the BAM format</p>
305
+
306
+ </div>
307
+ </div>
308
+
309
+ <div id="attribute-i-isize" class="method-detail">
310
+ <div class="method-heading attribute-method-heading">
311
+ <span class="method-name">isize</span><span
312
+ class="attribute-access-type">[RW]</span>
313
+ </div>
314
+
315
+ <div class="method-description">
316
+
317
+ <p>Attributes from the format</p>
318
+
319
+ </div>
320
+ </div>
321
+
322
+ <div id="attribute-i-mapq" class="method-detail">
323
+ <div class="method-heading attribute-method-heading">
324
+ <span class="method-name">mapq</span><span
325
+ class="attribute-access-type">[RW]</span>
326
+ </div>
327
+
328
+ <div class="method-description">
329
+
330
+ <p>Attributes from the format</p>
331
+
332
+ </div>
333
+ </div>
334
+
335
+ <div id="attribute-i-mate_strand" class="method-detail">
336
+ <div class="method-heading attribute-method-heading">
337
+ <span class="method-name">mate_strand</span><span
338
+ class="attribute-access-type">[RW]</span>
339
+ </div>
340
+
341
+ <div class="method-description">
342
+
343
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
344
+ documentation) <a
345
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
346
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
347
+ they are forward. It is the opposite to the definition in the BAM format
348
+ for clarity. primary is the negation of is_negative from the BAM format</p>
349
+
350
+ </div>
351
+ </div>
352
+
353
+ <div id="attribute-i-mate_unmapped" class="method-detail">
354
+ <div class="method-heading attribute-method-heading">
355
+ <span class="method-name">mate_unmapped</span><span
356
+ class="attribute-access-type">[RW]</span>
357
+ </div>
358
+
359
+ <div class="method-description">
360
+
361
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
362
+ documentation) <a
363
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
364
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
365
+ they are forward. It is the opposite to the definition in the BAM format
366
+ for clarity. primary is the negation of is_negative from the BAM format</p>
367
+
368
+ </div>
369
+ </div>
370
+
371
+ <div id="attribute-i-mpos" class="method-detail">
372
+ <div class="method-heading attribute-method-heading">
373
+ <span class="method-name">mpos</span><span
374
+ class="attribute-access-type">[RW]</span>
375
+ </div>
376
+
377
+ <div class="method-description">
378
+
379
+ <p>Attributes from the format</p>
380
+
381
+ </div>
382
+ </div>
383
+
384
+ <div id="attribute-i-mrnm" class="method-detail">
385
+ <div class="method-heading attribute-method-heading">
386
+ <span class="method-name">mrnm</span><span
387
+ class="attribute-access-type">[RW]</span>
388
+ </div>
389
+
390
+ <div class="method-description">
391
+
392
+ <p>Attributes from the format</p>
393
+
394
+ </div>
395
+ </div>
396
+
397
+ <div id="attribute-i-pos" class="method-detail">
398
+ <div class="method-heading attribute-method-heading">
399
+ <span class="method-name">pos</span><span
400
+ class="attribute-access-type">[RW]</span>
401
+ </div>
402
+
403
+ <div class="method-description">
404
+
405
+ <p>Attributes from the format</p>
406
+
407
+ </div>
408
+ </div>
409
+
410
+ <div id="attribute-i-primary" class="method-detail">
411
+ <div class="method-heading attribute-method-heading">
412
+ <span class="method-name">primary</span><span
413
+ class="attribute-access-type">[RW]</span>
414
+ </div>
415
+
416
+ <div class="method-description">
417
+
418
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
419
+ documentation) <a
420
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
421
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
422
+ they are forward. It is the opposite to the definition in the BAM format
423
+ for clarity. primary is the negation of is_negative from the BAM format</p>
424
+
425
+ </div>
426
+ </div>
427
+
428
+ <div id="attribute-i-qlen" class="method-detail">
429
+ <div class="method-heading attribute-method-heading">
430
+ <span class="method-name">qlen</span><span
431
+ class="attribute-access-type">[RW]</span>
432
+ </div>
433
+
434
+ <div class="method-description">
435
+
436
+ <p>Attributes pulled with the C library</p>
437
+
438
+ </div>
439
+ </div>
440
+
441
+ <div id="attribute-i-qname" class="method-detail">
442
+ <div class="method-heading attribute-method-heading">
443
+ <span class="method-name">qname</span><span
444
+ class="attribute-access-type">[RW]</span>
445
+ </div>
446
+
447
+ <div class="method-description">
448
+
449
+ <p>Attributes from the format</p>
450
+
451
+ </div>
452
+ </div>
453
+
454
+ <div id="attribute-i-qual" class="method-detail">
455
+ <div class="method-heading attribute-method-heading">
456
+ <span class="method-name">qual</span><span
457
+ class="attribute-access-type">[RW]</span>
458
+ </div>
459
+
460
+ <div class="method-description">
461
+
462
+ <p>Attributes from the format</p>
463
+
464
+ </div>
465
+ </div>
466
+
467
+ <div id="attribute-i-query_strand" class="method-detail">
468
+ <div class="method-heading attribute-method-heading">
469
+ <span class="method-name">query_strand</span><span
470
+ class="attribute-access-type">[RW]</span>
471
+ </div>
472
+
473
+ <div class="method-description">
474
+
475
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
476
+ documentation) <a
477
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
478
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
479
+ they are forward. It is the opposite to the definition in the BAM format
480
+ for clarity. primary is the negation of is_negative from the BAM format</p>
481
+
482
+ </div>
483
+ </div>
484
+
485
+ <div id="attribute-i-query_unmapped" class="method-detail">
486
+ <div class="method-heading attribute-method-heading">
487
+ <span class="method-name">query_unmapped</span><span
488
+ class="attribute-access-type">[RW]</span>
489
+ </div>
490
+
491
+ <div class="method-description">
492
+
493
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
494
+ documentation) <a
495
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
496
+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
497
+ they are forward. It is the opposite to the definition in the BAM format
498
+ for clarity. primary is the negation of is_negative from the BAM format</p>
499
+
500
+ </div>
501
+ </div>
502
+
503
+ <div id="attribute-i-rname" class="method-detail">
504
+ <div class="method-heading attribute-method-heading">
505
+ <span class="method-name">rname</span><span
506
+ class="attribute-access-type">[RW]</span>
507
+ </div>
508
+
509
+ <div class="method-description">
510
+
511
+ <p>Attributes from the format</p>
512
+
513
+ </div>
514
+ </div>
515
+
516
+ <div id="attribute-i-samstr" class="method-detail">
517
+ <div class="method-heading attribute-method-heading">
518
+ <span class="method-name">samstr</span><span
519
+ class="attribute-access-type">[RW]</span>
520
+ </div>
521
+
522
+ <div class="method-description">
523
+
524
+ <p>Attributes from the format</p>
525
+
526
+ </div>
527
+ </div>
528
+
529
+ <div id="attribute-i-second_in_pair" class="method-detail">
530
+ <div class="method-heading attribute-method-heading">
531
+ <span class="method-name">second_in_pair</span><span
532
+ class="attribute-access-type">[RW]</span>
533
+ </div>
534
+
535
+ <div class="method-description">
536
+
537
+ <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
538
+ documentation) <a
539
+ href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
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+ href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
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+ they are forward. It is the opposite to the definition in the BAM format
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+ for clarity. primary is the negation of is_negative from the BAM format</p>
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-seq" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">seq</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>Attributes from the format</p>
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+
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+ </div>
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+ </div>
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+
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+ <div id="attribute-i-tags" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">tags</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>Attributes from the format</p>
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+
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+ </div>
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+ </div>
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+
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+ </section><!-- attribute-method-details -->
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="method-c-finalize" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">finalize</span><span
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+ class="method-args">(object_id)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+
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+
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+
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+
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+ <div class="method-source-code" id="finalize-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 553</span>
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+ <span class="ruby-keyword">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"># puts &quot;Object #{object_id} dying at #{Time.new}&quot;</span>
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+ <span class="ruby-comment"># p &quot;?&quot; . object_id.al</span>
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+ <span class="ruby-comment"># 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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+
609
+ <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">end</span></pre>
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+ </div><!-- finalize-source -->
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+
613
+ </div>
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+
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+
616
+
617
+
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+ </div><!-- finalize-method -->
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+
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+
621
+ <div id="method-c-new" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
625
+ class="method-args">()</span>
626
+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
629
+
630
+ <div class="method-description">
631
+
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+
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+
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+
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+
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+ <div class="method-source-code" id="new-source">
637
+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 549</span>
638
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
639
+ <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>,
640
+ <span class="ruby-keyword">self</span>.<span class="ruby-identifier">class</span>.<span class="ruby-identifier">method</span>(<span class="ruby-value">:finalize</span>).<span class="ruby-identifier">to_proc</span>)
641
+ <span class="ruby-keyword">end</span></pre>
642
+ </div><!-- new-source -->
643
+
644
+ </div>
645
+
646
+
647
+
648
+
649
+ </div><!-- new-method -->
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+
651
+
652
+ </section><!-- public-class-method-details -->
653
+
654
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
655
+ <h3 class="section-header">Public Instance Methods</h3>
656
+
657
+
658
+ <div id="method-i-sam-3D" class="method-detail ">
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+
660
+ <div class="method-heading">
661
+ <span class="method-name">sam=</span><span
662
+ class="method-args">(sam)</span>
663
+ <span class="method-click-advice">click to toggle source</span>
664
+ </div>
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+
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+
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+ <div class="method-description">
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+
669
+
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+
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+
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+
673
+ <div class="method-source-code" id="sam-3D-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 607</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">sam=</span>(<span class="ruby-identifier">sam</span>)
676
+ <span class="ruby-comment">#p sam</span>
677
+ <span class="ruby-identifier">s</span> = <span class="ruby-identifier">sam</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;\t&quot;</span>)
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+ <span class="ruby-keyword">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">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">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">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">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">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">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">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">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">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">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">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>])
693
+ <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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+ }
695
+
696
+
697
+ <span class="ruby-comment">#&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; \</span>
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+ <span class="ruby-comment">#[&lt;TAG&gt;:&lt;VTYPE&gt;:&lt;VALUE&gt; [...]] </span>
699
+
700
+ <span class="ruby-keyword">end</span></pre>
701
+ </div><!-- sam-3D-source -->
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+
703
+ </div>
704
+
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+
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+
707
+
708
+ </div><!-- sam-3D-method -->
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+
710
+
711
+ <div id="method-i-set" class="method-detail ">
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+
713
+ <div class="method-heading">
714
+ <span class="method-name">set</span><span
715
+ class="method-args">(bam_alignment, header)</span>
716
+ <span class="method-click-advice">click to toggle source</span>
717
+ </div>
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+
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+
720
+ <div class="method-description">
721
+
722
+
723
+
724
+
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+
726
+ <div class="method-source-code" id="set-source">
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+ <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 575</span>
728
+ <span class="ruby-keyword">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">#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">#set the raw data</span>
733
+ <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>)
734
+ <span class="ruby-comment">#self.sam = tmp_str</span>
735
+ <span class="ruby-comment">#ObjectSpace.define_finalizer(self, proc {|id| puts &quot;Finalizer one on #{id}&quot; })</span>
736
+ <span class="ruby-keyword">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>)
737
+ <span class="ruby-comment">#LibC.free tmp_str</span>
738
+ <span class="ruby-comment">#Set values calculated by libbam</span>
739
+ <span class="ruby-identifier">core</span> = <span class="ruby-identifier">al</span>[<span class="ruby-value">:core</span>]
740
+ <span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">al</span>[<span class="ruby-value">:data</span>][<span class="ruby-identifier">core</span>[<span class="ruby-value">:l_qname</span>]]<span class="ruby-comment">#define bam1_cigar(b) ((uint32_t*)((b)-&gt;data + (b)-&gt;core.l_qname)) </span>
741
+ <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>)
742
+ <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>)
743
+
744
+ <span class="ruby-comment">#process the flags</span>
745
+ <span class="ruby-ivar">@is_paired</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0001</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
746
+ <span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0002</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
747
+ <span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0004</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
748
+ <span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0008</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
749
+ <span class="ruby-ivar">@query_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0010</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
750
+ <span class="ruby-ivar">@mate_strand</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0020</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
751
+ <span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0040</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
752
+ <span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0080</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
753
+ <span class="ruby-ivar">@primary</span> = <span class="ruby-operator">!</span>(<span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0100</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>)
754
+ <span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0200</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
755
+ <span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> &amp; <span class="ruby-value">0x0400</span> <span class="ruby-operator">&gt;</span> <span class="ruby-value">0</span>
756
+
757
+ <span class="ruby-keyword">end</span></pre>
758
+ </div><!-- set-source -->
759
+
760
+ </div>
761
+
762
+
763
+
764
+
765
+ </div><!-- set-method -->
766
+
767
+
768
+ </section><!-- public-instance-method-details -->
769
+
770
+ </section><!-- 5Buntitled-5D -->
771
+
772
+ </div><!-- documentation -->
773
+
774
+
775
+ <footer id="validator-badges">
776
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
777
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
778
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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+