RubyGems - bio-samtools - Versions diffs - 0.4.1 → 0.4.2 - Mend

bio-samtools 0.4.1 → 0.4.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (74) hide show

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 Viewed

	@@ -1 +1 @@
1	- 0.4.1
1	+ 0.4.2

data/bio-samtools.gemspec CHANGED Viewed

@@ -5,11 +5,11 @@
 Gem::Specification.new do |s|
   s.name = %q{bio-samtools}
-  s.version = "0.4.1"
+  s.version = "0.4.2"
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = [%q{Ricardo Ramirez-Gonzalez}, %q{Dan MacLean}, %q{Raoul J.P. Bonnal}]
-  s.date = %q{2011-11-09}
+  s.date = %q{2011-11-10}
   s.description = %q{Binder of samtools for ruby, on the top of FFI.
   This project was born from the need to add support of BAM files to
@@ -29,6 +29,24 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bio-samtools.gemspec",
+    "doc/Bio.html",
+    "doc/Bio/DB.html",
+    "doc/Bio/DB/Alignment.html",
+    "doc/Bio/DB/SAM.html",
+    "doc/Bio/DB/SAM/Library.html",
+    "doc/Bio/DB/SAM/Tools.html",
+    "doc/Bio/DB/SAM/Tools/Bam1CoreT.html",
+    "doc/Bio/DB/SAM/Tools/Bam1T.html",
+    "doc/Bio/DB/SAM/Tools/BamHeaderT.html",
+    "doc/Bio/DB/SAM/Tools/BamPileup1T.html",
+    "doc/Bio/DB/SAM/Tools/SamfileT.html",
+    "doc/Bio/DB/SAM/Tools/SamfileTX.html",
+    "doc/Bio/DB/SAMException.html",
+    "doc/Bio/DB/Tag.html",
+    "doc/LICENSE_txt.html",
+    "doc/LibC.html",
+    "doc/Pileup.html",
+    "doc/Vcf.html",
     "doc/basic_styles.css",
     "doc/classes/Bio.html",
     "doc/classes/Bio/DB.html",
@@ -89,8 +107,48 @@ Gem::Specification.new do |s|
     "doc/fr_class_index.html",
     "doc/fr_file_index.html",
     "doc/fr_method_index.html",
+    "doc/images/add.png",
+    "doc/images/brick.png",
+    "doc/images/brick_link.png",
+    "doc/images/bug.png",
+    "doc/images/bullet_black.png",
+    "doc/images/bullet_toggle_minus.png",
+    "doc/images/bullet_toggle_plus.png",
+    "doc/images/date.png",
+    "doc/images/delete.png",
+    "doc/images/find.png",
+    "doc/images/loadingAnimation.gif",
+    "doc/images/macFFBgHack.png",
+    "doc/images/package.png",
+    "doc/images/page_green.png",
+    "doc/images/page_white_text.png",
+    "doc/images/page_white_width.png",
+    "doc/images/plugin.png",
+    "doc/images/ruby.png",
+    "doc/images/tag_blue.png",
+    "doc/images/tag_green.png",
+    "doc/images/transparent.png",
+    "doc/images/wrench.png",
+    "doc/images/wrench_orange.png",
+    "doc/images/zoom.png",
     "doc/index.html",
+    "doc/js/darkfish.js",
+    "doc/js/jquery.js",
+    "doc/js/navigation.js",
+    "doc/js/search.js",
+    "doc/js/search_index.js",
+    "doc/js/searcher.js",
+    "doc/lib/bio-samtools_rb.html",
+    "doc/lib/bio/db/sam/bam_rb.html",
+    "doc/lib/bio/db/sam/faidx_rb.html",
+    "doc/lib/bio/db/sam/library_rb.html",
+    "doc/lib/bio/db/sam/pileup_rb.html",
+    "doc/lib/bio/db/sam/sam_rb.html",
+    "doc/lib/bio/db/sam/vcf_rb.html",
+    "doc/lib/bio/db/sam_rb.html",
     "doc/rdoc-style.css",
+    "doc/rdoc.css",
+    "doc/table_of_contents.html",
     "doc/tutorial.html",
     "doc/tutorial.pdf",
     "ext/Makefile-bioruby.patch",
@@ -108,9 +166,6 @@ Gem::Specification.new do |s|
     "lib/bio/db/sam/sam.rb",
     "lib/bio/db/sam/vcf.rb",
     "test/basictest.rb",
-    "test/coverage.rb",
-    "test/coverage_plot.rb",
-    "test/feature.rb",
     "test/helper.rb",
     "test/pileup.rb",
     "test/samples/small/ids2.txt",
@@ -134,7 +189,6 @@ Gem::Specification.new do |s|
     "test/samples/small/testu.bam.bai",
     "test/test_basic.rb",
     "test/test_bio-samtools.rb",
-    "test/test_pileup.rb",
     "test/test_vcf.rb"
   ]
   s.homepage = %q{http://github.com/helios/bioruby-samtools}

data/doc/Bio.html ADDED Viewed

@@ -0,0 +1,171 @@
+<!DOCTYPE html>
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+<title>Module: Bio</title>
+<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
+<script type="text/javascript">
+  var rdoc_rel_prefix = "./";
+</script>
+<script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
+<body id="top" class="module">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="./index.html">Home</a>
+    <a href="./table_of_contents.html#classes">Classes</a>
+    <a href="./table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+  <div id="file-metadata">
+    <nav id="file-list-section" class="section">
+  <h3 class="section-header">Defined In</h3>
+  <ul>
+    <li>lib/bio/db/sam/bam.rb
+    <li>lib/bio/db/sam/faidx.rb
+    <li>lib/bio/db/sam/library.rb
+    <li>lib/bio/db/sam/sam.rb
+    <li>lib/bio/db/sam.rb
+  </ul>
+</nav>
+  </div>
+  <div id="class-metadata">
+  </div>
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+  <ul>
+    <li class="file"><a href="./LICENSE_txt.html">LICENSE</a>
+  </ul>
+</nav>
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+  <ul class="link-list">
+    <li><a href="./Bio.html">Bio</a>
+    <li><a href="./Bio/DB.html">Bio::DB</a>
+    <li><a href="./Bio/DB/Alignment.html">Bio::DB::Alignment</a>
+    <li><a href="./Bio/DB/SAM.html">Bio::DB::SAM</a>
+    <li><a href="./Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
+    <li><a href="./Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
+    <li><a href="./Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
+    <li><a href="./Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
+    <li><a href="./Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
+    <li><a href="./Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
+    <li><a href="./Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
+    <li><a href="./Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
+    <li><a href="./Bio/DB/SAMException.html">Bio::DB::SAMException</a>
+    <li><a href="./Bio/DB/Sam.html">Bio::DB::Sam</a>
+    <li><a href="./Bio/DB/Tag.html">Bio::DB::Tag</a>
+    <li><a href="./LibC.html">LibC</a>
+    <li><a href="./Pileup.html">Pileup</a>
+    <li><a href="./Vcf.html">Vcf</a>
+  </ul>
+</nav>
+  </div>
+</nav>
+<div id="documentation">
+  <h1 class="module">module Bio</h1>
+  <div id="description" class="description">
+<p>require ‘rubygems’ require ‘ffi’</p>
+<pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/faidx'</span>
+<span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/sam'</span>
+</pre>
+<p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
+<pre>sam.rb
+Created by Ricardo Ramirez on 3/25/10.</pre>
+<p>require ‘rubygems’ require’ffi’ require ‘bio/db/sam/bam’</p>
+  </div><!-- description -->
+  <section id="5Buntitled-5D" class="documentation-section">
+    <!-- Methods -->
+  </section><!-- 5Buntitled-5D -->
+</div><!-- documentation -->
+<footer id="validator-badges">
+  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
+  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
+</footer>

data/doc/Bio/DB.html ADDED Viewed

@@ -0,0 +1,163 @@
+<!DOCTYPE html>
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+<title>Class: Bio::DB</title>
+<link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
+<script type="text/javascript">
+  var rdoc_rel_prefix = "../";
+</script>
+<script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
+<body id="top" class="class">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="../index.html">Home</a>
+    <a href="../table_of_contents.html#classes">Classes</a>
+    <a href="../table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+  <div id="file-metadata">
+    <nav id="file-list-section" class="section">
+  <h3 class="section-header">Defined In</h3>
+  <ul>
+    <li>lib/bio/db/sam/bam.rb
+    <li>lib/bio/db/sam/faidx.rb
+    <li>lib/bio/db/sam/library.rb
+    <li>lib/bio/db/sam/sam.rb
+    <li>lib/bio/db/sam.rb
+  </ul>
+</nav>
+  </div>
+  <div id="class-metadata">
+    <nav id="parent-class-section" class="section">
+  <h3 class="section-header">Parent</h3>
+  <p class="link">Object
+</nav>
+  </div>
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+  <ul>
+    <li class="file"><a href="../LICENSE_txt.html">LICENSE</a>
+  </ul>
+</nav>
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+  <ul class="link-list">
+    <li><a href="../Bio.html">Bio</a>
+    <li><a href="../Bio/DB.html">Bio::DB</a>
+    <li><a href="../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
+    <li><a href="../Bio/DB/SAM.html">Bio::DB::SAM</a>
+    <li><a href="../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
+    <li><a href="../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
+    <li><a href="../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
+    <li><a href="../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
+    <li><a href="../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
+    <li><a href="../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
+    <li><a href="../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
+    <li><a href="../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
+    <li><a href="../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
+    <li><a href="../Bio/DB/Sam.html">Bio::DB::Sam</a>
+    <li><a href="../Bio/DB/Tag.html">Bio::DB::Tag</a>
+    <li><a href="../LibC.html">LibC</a>
+    <li><a href="../Pileup.html">Pileup</a>
+    <li><a href="../Vcf.html">Vcf</a>
+  </ul>
+</nav>
+  </div>
+</nav>
+<div id="documentation">
+  <h1 class="class">class Bio::DB</h1>
+  <div id="description" class="description">
+  </div><!-- description -->
+  <section id="5Buntitled-5D" class="documentation-section">
+    <!-- Methods -->
+  </section><!-- 5Buntitled-5D -->
+</div><!-- documentation -->
+<footer id="validator-badges">
+  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
+  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
+</footer>

data/doc/Bio/DB/Alignment.html ADDED Viewed

@@ -0,0 +1,780 @@
+<!DOCTYPE html>
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+<title>Class: Bio::DB::Alignment</title>
+<link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
+<script type="text/javascript">
+  var rdoc_rel_prefix = "../../";
+</script>
+<script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
+<script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
+<body id="top" class="class">
+<nav id="metadata">
+  <nav id="home-section" class="section">
+  <h3 class="section-header">
+    <a href="../../index.html">Home</a>
+    <a href="../../table_of_contents.html#classes">Classes</a>
+    <a href="../../table_of_contents.html#methods">Methods</a>
+  </h3>
+</nav>
+  <nav id="search-section" class="section project-section" class="initially-hidden">
+  <form action="#" method="get" accept-charset="utf-8">
+    <h3 class="section-header">
+      <input type="text" name="search" placeholder="Search" id="search-field"
+             title="Type to search, Up and Down to navigate, Enter to load">
+    </h3>
+  </form>
+  <ul id="search-results" class="initially-hidden"></ul>
+</nav>
+  <div id="file-metadata">
+    <nav id="file-list-section" class="section">
+  <h3 class="section-header">Defined In</h3>
+  <ul>
+    <li>lib/bio/db/sam.rb
+  </ul>
+</nav>
+  </div>
+  <div id="class-metadata">
+    <nav id="parent-class-section" class="section">
+  <h3 class="section-header">Parent</h3>
+  <p class="link">Object
+</nav>
+    <!-- Method Quickref -->
+<nav id="method-list-section" class="section">
+  <h3 class="section-header">Methods</h3>
+  <ul class="link-list">
+    <li><a href="#method-c-finalize">::finalize</a>
+    <li><a href="#method-c-new">::new</a>
+    <li><a href="#method-i-sam-3D">#sam=</a>
+    <li><a href="#method-i-set">#set</a>
+  </ul>
+</nav>
+  </div>
+  <div id="project-metadata">
+    <nav id="fileindex-section" class="section project-section">
+  <h3 class="section-header">Pages</h3>
+  <ul>
+    <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
+  </ul>
+</nav>
+    <nav id="classindex-section" class="section project-section">
+  <h3 class="section-header">Class and Module Index</h3>
+  <ul class="link-list">
+    <li><a href="../../Bio.html">Bio</a>
+    <li><a href="../../Bio/DB.html">Bio::DB</a>
+    <li><a href="../../Bio/DB/Alignment.html">Bio::DB::Alignment</a>
+    <li><a href="../../Bio/DB/SAM.html">Bio::DB::SAM</a>
+    <li><a href="../../Bio/DB/SAM/Library.html">Bio::DB::SAM::Library</a>
+    <li><a href="../../Bio/DB/SAM/Tools.html">Bio::DB::SAM::Tools</a>
+    <li><a href="../../Bio/DB/SAM/Tools/Bam1CoreT.html">Bio::DB::SAM::Tools::Bam1CoreT</a>
+    <li><a href="../../Bio/DB/SAM/Tools/Bam1T.html">Bio::DB::SAM::Tools::Bam1T</a>
+    <li><a href="../../Bio/DB/SAM/Tools/BamHeaderT.html">Bio::DB::SAM::Tools::BamHeaderT</a>
+    <li><a href="../../Bio/DB/SAM/Tools/BamPileup1T.html">Bio::DB::SAM::Tools::BamPileup1T</a>
+    <li><a href="../../Bio/DB/SAM/Tools/SamfileT.html">Bio::DB::SAM::Tools::SamfileT</a>
+    <li><a href="../../Bio/DB/SAM/Tools/SamfileTX.html">Bio::DB::SAM::Tools::SamfileTX</a>
+    <li><a href="../../Bio/DB/SAMException.html">Bio::DB::SAMException</a>
+    <li><a href="../../Bio/DB/Sam.html">Bio::DB::Sam</a>
+    <li><a href="../../Bio/DB/Tag.html">Bio::DB::Tag</a>
+    <li><a href="../../LibC.html">LibC</a>
+    <li><a href="../../Pileup.html">Pileup</a>
+    <li><a href="../../Vcf.html">Vcf</a>
+  </ul>
+</nav>
+  </div>
+</nav>
+<div id="documentation">
+  <h1 class="class">class Bio::DB::Alignment</h1>
+  <div id="description" class="description">
+  </div><!-- description -->
+  <section id="5Buntitled-5D" class="documentation-section">
+    <!-- Attributes -->
+    <section id="attribute-method-details" class="method-section section">
+      <h3 class="section-header">Attributes</h3>
+      <div id="attribute-i-al" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">al</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-calend" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">calend</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes pulled with the C library</p>
+        </div>
+      </div>
+      <div id="attribute-i-cigar" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">cigar</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-failed_quality" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">failed_quality</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-first_in_pair" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">first_in_pair</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-flag" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">flag</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-is_duplicate" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">is_duplicate</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-is_mapped" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">is_mapped</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-is_paired" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">is_paired</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-isize" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">isize</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-mapq" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">mapq</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-mate_strand" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">mate_strand</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-mate_unmapped" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">mate_unmapped</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-mpos" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">mpos</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-mrnm" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">mrnm</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-pos" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">pos</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-primary" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">primary</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-qlen" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">qlen</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes pulled with the C library</p>
+        </div>
+      </div>
+      <div id="attribute-i-qname" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">qname</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-qual" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">qual</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-query_strand" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">query_strand</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-query_unmapped" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">query_unmapped</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-rname" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">rname</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-samstr" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">samstr</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-second_in_pair" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">second_in_pair</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attrobites frp, the flag field (see chapter 2.2.2 of the sam file
+documentation) <a
+href="Alignment.html#attribute-i-query_strand">#query_strand</a> and <a
+href="Alignment.html#attribute-i-mate_strand">#mate_strand</a> are true if
+they are forward. It is the opposite to the definition in the BAM format
+for clarity. primary is the negation of is_negative from the BAM format</p>
+        </div>
+      </div>
+      <div id="attribute-i-seq" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">seq</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+      <div id="attribute-i-tags" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">tags</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+        <div class="method-description">
+        <p>Attributes from the format</p>
+        </div>
+      </div>
+    </section><!-- attribute-method-details -->
+    <!-- Methods -->
+     <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
+      <h3 class="section-header">Public Class Methods</h3>
+      <div id="method-c-finalize" class="method-detail ">
+        <div class="method-heading">
+          <span class="method-name">finalize</span><span
+            class="method-args">(object_id)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        <div class="method-description">
+          <div class="method-source-code" id="finalize-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 553</span>
+<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>)
+  <span class="ruby-comment">#           puts &quot;Object #{object_id} dying at #{Time.new}&quot;</span>
+  <span class="ruby-comment">#             p  &quot;?&quot; . object_id.al</span>
+  <span class="ruby-comment">#            p object_id.al</span>
+  <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>
+  <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>
+  <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>
+  <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>
+  <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>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- finalize-source -->
+        </div>
+      </div><!-- finalize-method -->
+      <div id="method-c-new" class="method-detail ">
+        <div class="method-heading">
+          <span class="method-name">new</span><span
+            class="method-args">()</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        <div class="method-description">
+          <div class="method-source-code" id="new-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 549</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>
+  <span class="ruby-constant">ObjectSpace</span>.<span class="ruby-identifier">define_finalizer</span>(<span class="ruby-keyword">self</span>,
+  <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>)
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- new-source -->
+        </div>
+      </div><!-- new-method -->
+    </section><!-- public-class-method-details -->
+     <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
+      <h3 class="section-header">Public Instance Methods</h3>
+      <div id="method-i-sam-3D" class="method-detail ">
+        <div class="method-heading">
+          <span class="method-name">sam=</span><span
+            class="method-args">(sam)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        <div class="method-description">
+          <div class="method-source-code" id="sam-3D-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 607</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">sam=</span>(<span class="ruby-identifier">sam</span>)
+  <span class="ruby-comment">#p sam</span>
+  <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>)
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">0</span>]
+  <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>
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">rname</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">2</span>]
+  <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>
+  <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>
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">cigar</span> = <span class="ruby-identifier">s</span>[<span class="ruby-value">5</span>]
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mrnm</span>  = <span class="ruby-identifier">s</span>[<span class="ruby-value">6</span>]
+  <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>
+  <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>
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">seq</span>   = <span class="ruby-identifier">s</span>[<span class="ruby-value">9</span>]
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qual</span> =  <span class="ruby-identifier">s</span>[<span class="ruby-value">10</span>]
+  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">tags</span> = {}
+  <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>
+    <span class="ruby-identifier">t</span> = <span class="ruby-constant">Tag</span>.<span class="ruby-identifier">new</span>
+    <span class="ruby-identifier">t</span>.<span class="ruby-identifier">set</span>(<span class="ruby-identifier">s</span>[<span class="ruby-identifier">n</span>])
+    <span class="ruby-identifier">tags</span>[<span class="ruby-identifier">t</span>.<span class="ruby-identifier">tag</span>] = <span class="ruby-identifier">t</span>
+  }
+  <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>
+  <span class="ruby-comment">#[&lt;TAG&gt;:&lt;VTYPE&gt;:&lt;VALUE&gt; [...]] </span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- sam-3D-source -->
+        </div>
+      </div><!-- sam-3D-method -->
+      <div id="method-i-set" class="method-detail ">
+        <div class="method-heading">
+          <span class="method-name">set</span><span
+            class="method-args">(bam_alignment, header)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        <div class="method-description">
+          <div class="method-source-code" id="set-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 575</span>
+<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>)
+  <span class="ruby-comment">#Create the FFI object</span>
+  <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>)
+  <span class="ruby-comment">#set the raw data</span>
+  <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>)
+  <span class="ruby-comment">#self.sam =  tmp_str</span>
+  <span class="ruby-comment">#ObjectSpace.define_finalizer(self, proc {|id| puts &quot;Finalizer one on #{id}&quot; })</span>
+  <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>)
+  <span class="ruby-comment">#LibC.free tmp_str</span>
+  <span class="ruby-comment">#Set values calculated by libbam</span>
+  <span class="ruby-identifier">core</span> = <span class="ruby-identifier">al</span>[<span class="ruby-value">:core</span>]
+  <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>
+  <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>)
+  <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>)
+  <span class="ruby-comment">#process the flags</span>
+  <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>
+  <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>
+  <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>
+  <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>
+  <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>)
+  <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>)
+  <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>
+  <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>
+  <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>)
+  <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>
+  <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>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- set-source -->
+        </div>
+      </div><!-- set-method -->
+    </section><!-- public-instance-method-details -->
+  </section><!-- 5Buntitled-5D -->
+</div><!-- documentation -->
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