bio-samtools 0.4.1 → 0.4.2
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- data/VERSION +1 -1
- data/bio-samtools.gemspec +60 -6
- data/doc/Bio.html +171 -0
- data/doc/Bio/DB.html +163 -0
- data/doc/Bio/DB/Alignment.html +780 -0
- data/doc/Bio/DB/SAM.html +1241 -0
- data/doc/Bio/DB/SAM/Library.html +217 -0
- data/doc/Bio/DB/SAM/Tools.html +331 -0
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +159 -0
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +220 -0
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +249 -0
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +159 -0
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +171 -0
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +159 -0
- data/doc/Bio/DB/SAMException.html +205 -0
- data/doc/Bio/DB/Tag.html +254 -0
- data/doc/LICENSE_txt.html +881 -0
- data/doc/LibC.html +153 -0
- data/doc/Pileup.html +571 -0
- data/doc/Vcf.html +473 -0
- data/doc/created.rid +10 -1
- data/doc/images/add.png +0 -0
- data/doc/images/brick.png +0 -0
- data/doc/images/brick_link.png +0 -0
- data/doc/images/bug.png +0 -0
- data/doc/images/bullet_black.png +0 -0
- data/doc/images/bullet_toggle_minus.png +0 -0
- data/doc/images/bullet_toggle_plus.png +0 -0
- data/doc/images/date.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/find.png +0 -0
- data/doc/images/loadingAnimation.gif +0 -0
- data/doc/images/macFFBgHack.png +0 -0
- data/doc/images/package.png +0 -0
- data/doc/images/page_green.png +0 -0
- data/doc/images/page_white_text.png +0 -0
- data/doc/images/page_white_width.png +0 -0
- data/doc/images/plugin.png +0 -0
- data/doc/images/ruby.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +109 -21
- data/doc/js/darkfish.js +153 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/lib/bio-samtools_rb.html +115 -0
- data/doc/lib/bio/db/sam/bam_rb.html +121 -0
- data/doc/lib/bio/db/sam/faidx_rb.html +117 -0
- data/doc/lib/bio/db/sam/library_rb.html +115 -0
- data/doc/lib/bio/db/sam/pileup_rb.html +171 -0
- data/doc/lib/bio/db/sam/sam_rb.html +121 -0
- data/doc/lib/bio/db/sam/vcf_rb.html +124 -0
- data/doc/lib/bio/db/sam_rb.html +115 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +186 -0
- data/ext/Makefile-bioruby.patch +1 -1
- data/ext/Rakefile +8 -1
- data/ext/mkrf_conf.rb +8 -1
- data/lib/bio/db/sam.rb +140 -27
- data/lib/bio/db/sam/vcf.rb +0 -1
- data/test/basictest.rb +4 -4
- data/test/test_basic.rb +50 -34
- metadata +79 -25
- data/test/coverage.rb +0 -26
- data/test/coverage_plot.rb +0 -28
- data/test/feature.rb +0 -0
- data/test/test_pileup.rb +0 -68
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.4.
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1
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0.4.2
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data/bio-samtools.gemspec
CHANGED
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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.
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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-
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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
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@@ -29,6 +29,24 @@ Gem::Specification.new do |s|
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"Rakefile",
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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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@@ -89,8 +107,48 @@ Gem::Specification.new do |s|
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"doc/fr_class_index.html",
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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-style.css",
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"doc/table_of_contents.html",
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"doc/tutorial.html",
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"doc/tutorial.pdf",
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"ext/Makefile-bioruby.patch",
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@@ -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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169
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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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@@ -134,7 +189,6 @@ Gem::Specification.new do |s|
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"test/samples/small/testu.bam.bai",
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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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138
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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}
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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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<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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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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<h3 class="section-header">
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title="Type to search, Up and Down to navigate, Enter to load">
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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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</ul>
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<nav id="fileindex-section" class="section project-section">
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<h3 class="section-header">Pages</h3>
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<ul>
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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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<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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<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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|
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Created by Ricardo Ramirez on 3/25/10.</pre>
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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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<!-- Methods -->
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</section><!-- 5Buntitled-5D -->
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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
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<title>Class: Bio::DB</title>
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<div class="method-heading attribute-method-heading">
|
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|
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<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">
|
244
|
+
<span class="method-name">flag</span><span
|
245
|
+
class="attribute-access-type">[RW]</span>
|
246
|
+
</div>
|
247
|
+
|
248
|
+
<div class="method-description">
|
249
|
+
|
250
|
+
<p>Attributes from the format</p>
|
251
|
+
|
252
|
+
</div>
|
253
|
+
</div>
|
254
|
+
|
255
|
+
<div id="attribute-i-is_duplicate" class="method-detail">
|
256
|
+
<div class="method-heading attribute-method-heading">
|
257
|
+
<span class="method-name">is_duplicate</span><span
|
258
|
+
class="attribute-access-type">[RW]</span>
|
259
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+
</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">
|
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|
+
<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
|
540
|
+
href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
|
541
|
+
they are forward. It is the opposite to the definition in the BAM format
|
542
|
+
for clarity. primary is the negation of is_negative from the BAM format</p>
|
543
|
+
|
544
|
+
</div>
|
545
|
+
</div>
|
546
|
+
|
547
|
+
<div id="attribute-i-seq" class="method-detail">
|
548
|
+
<div class="method-heading attribute-method-heading">
|
549
|
+
<span class="method-name">seq</span><span
|
550
|
+
class="attribute-access-type">[RW]</span>
|
551
|
+
</div>
|
552
|
+
|
553
|
+
<div class="method-description">
|
554
|
+
|
555
|
+
<p>Attributes from the format</p>
|
556
|
+
|
557
|
+
</div>
|
558
|
+
</div>
|
559
|
+
|
560
|
+
<div id="attribute-i-tags" class="method-detail">
|
561
|
+
<div class="method-heading attribute-method-heading">
|
562
|
+
<span class="method-name">tags</span><span
|
563
|
+
class="attribute-access-type">[RW]</span>
|
564
|
+
</div>
|
565
|
+
|
566
|
+
<div class="method-description">
|
567
|
+
|
568
|
+
<p>Attributes from the format</p>
|
569
|
+
|
570
|
+
</div>
|
571
|
+
</div>
|
572
|
+
|
573
|
+
</section><!-- attribute-method-details -->
|
574
|
+
|
575
|
+
|
576
|
+
<!-- Methods -->
|
577
|
+
|
578
|
+
<section id="public-class-5Buntitled-5D-method-details" class="method-section section">
|
579
|
+
<h3 class="section-header">Public Class Methods</h3>
|
580
|
+
|
581
|
+
|
582
|
+
<div id="method-c-finalize" class="method-detail ">
|
583
|
+
|
584
|
+
<div class="method-heading">
|
585
|
+
<span class="method-name">finalize</span><span
|
586
|
+
class="method-args">(object_id)</span>
|
587
|
+
<span class="method-click-advice">click to toggle source</span>
|
588
|
+
</div>
|
589
|
+
|
590
|
+
|
591
|
+
<div class="method-description">
|
592
|
+
|
593
|
+
|
594
|
+
|
595
|
+
|
596
|
+
|
597
|
+
<div class="method-source-code" id="finalize-source">
|
598
|
+
<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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<span class="ruby-comment"># puts "Object #{object_id} dying at #{Time.new}"</span>
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<span class="ruby-comment"># p "?" . 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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+
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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">end</span></pre>
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</div><!-- finalize-source -->
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<span class="method-name">new</span><span
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class="method-args">()</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 549</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
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<span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>,
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<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>)
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<span class="ruby-keyword">end</span></pre>
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</div><!-- new-source -->
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</section><!-- public-class-method-details -->
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<section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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<h3 class="section-header">Public Instance Methods</h3>
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<div id="method-i-sam-3D" class="method-detail ">
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<div class="method-heading">
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<span class="method-name">sam=</span><span
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class="method-args">(sam)</span>
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<span class="method-click-advice">click to toggle source</span>
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</div>
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<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>)
|
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+
<span class="ruby-comment">#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-string">"\t"</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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681
|
+
<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>
|
683
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
|
684
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">mrnm</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
|
685
|
+
<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>
|
686
|
+
<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>
|
687
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">seq</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
|
688
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">qual</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
|
689
|
+
<span class="ruby-keyword">self</span>.<span class="ruby-identifier">tags</span> = {}
|
690
|
+
<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>
|
691
|
+
<span class="ruby-identifier">t</span> = <span class="ruby-constant">Tag</span>.<span class="ruby-identifier">new</span>
|
692
|
+
<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>
|
694
|
+
}
|
695
|
+
|
696
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+
|
697
|
+
<span class="ruby-comment">#<QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> \</span>
|
698
|
+
<span class="ruby-comment">#[<TAG>:<VTYPE>:<VALUE> [...]] </span>
|
699
|
+
|
700
|
+
<span class="ruby-keyword">end</span></pre>
|
701
|
+
</div><!-- sam-3D-source -->
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702
|
+
|
703
|
+
</div>
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704
|
+
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705
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+
|
706
|
+
|
707
|
+
|
708
|
+
</div><!-- sam-3D-method -->
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709
|
+
|
710
|
+
|
711
|
+
<div id="method-i-set" class="method-detail ">
|
712
|
+
|
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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<div class="method-description">
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<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>)
|
729
|
+
<span class="ruby-comment">#Create the FFI object</span>
|
730
|
+
<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>)
|
731
|
+
|
732
|
+
<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 "Finalizer one on #{id}" })</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)->data + (b)->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> & <span class="ruby-value">0x0001</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
746
|
+
<span class="ruby-ivar">@is_mapped</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0002</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
747
|
+
<span class="ruby-ivar">@query_unmapped</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0004</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
748
|
+
<span class="ruby-ivar">@mate_unmapped</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0008</span> <span class="ruby-operator">></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> & <span class="ruby-value">0x0010</span> <span class="ruby-operator">></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> & <span class="ruby-value">0x0020</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>)
|
751
|
+
<span class="ruby-ivar">@first_in_pair</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0040</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
752
|
+
<span class="ruby-ivar">@second_in_pair</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0080</span> <span class="ruby-operator">></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> & <span class="ruby-value">0x0100</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>)
|
754
|
+
<span class="ruby-ivar">@failed_quality</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0200</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
755
|
+
<span class="ruby-ivar">@is_duplicate</span> = <span class="ruby-ivar">@flag</span> & <span class="ruby-value">0x0400</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
756
|
+
|
757
|
+
<span class="ruby-keyword">end</span></pre>
|
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|
+
</div><!-- set-source -->
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|
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</div>
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|
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</div><!-- set-method -->
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</section><!-- public-instance-method-details -->
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</section><!-- 5Buntitled-5D -->
|
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</div><!-- documentation -->
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<footer id="validator-badges">
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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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</footer>
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