bio-samtools 0.6.2 → 2.0.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: cfc0474c9c8270a014b34e0125b36df2fc85ab02
+  metadata.gz: f0608dfce24db2fd3c26be69e04123961209e855
+  data.tar.gz: b79cd69ebe66928a53ca9d45f122b1e9538e8c51
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+  data.tar.gz: 716ff9d093fc0ad485ae2dc687dca44aeaa30da77c3e38b32856c194306f5b6f01e8bffe1d5a3da81506d50633cb014bd68b814dd8b518f6559bf0f9c617b7ba

data/Gemfile

@@ -2,9 +2,8 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
-gem "ffi"
+gem "bio-svgenes", ">= 0.4.1"
 gem "bio", ">= 1.4.2"
-gem "systemu", ">=2.5.2"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -16,5 +15,7 @@ group :development do
   gem "jeweler"
   gem "rcov", ">=0", :platforms => :ruby_18
   gem "simplecov", ">= 0",   :platforms => :ruby_19
+
   gem 'rdoc'
+  gem 'test-unit'
 end

data/README.md

@@ -55,17 +55,14 @@ Alignments can be obtained one at a time by looping over a specified region usin
 See more detail on doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutorial. 
 
 ## Dependencies
-* FFI [http://github.com/ffi/ffi](http://github.com/ffi/ffi)
-* BioRuby >= 1.4.1 [https://github.com/bioruby/bioruby](https://github.com/bioruby/bioruby)
 
+* BioRuby >= 1.4.3 [https://github.com/bioruby/bioruby](https://github.com/bioruby/bioruby)
+* Ruby 1.9 and above. 
 	
 ## FAQ
 * I´m getting a **segmentation Fault**, what did I do wrong?
 
-	[Answer] There are two known segmentation faults at the moment
-
-	* When you try to load a text file as binary file
-	* When you try to lad a binary file as a text file
+	[Answer] You are using an old version of bio-samtools, the current version doesn't link directly to the library. 
 
 * I keep seeing this **Invalid gemspec in [some ruby gem path…]**, what is wrong?
 	
@@ -85,7 +82,7 @@ See more detail on doc/tutorial.html or doc/tutorial.pdf for a walkthrough tutor
 1. Filter to the fetching algorithm (give a condition that has to be satisfied to add the alignment to the list)
 
 ### To whom do I complain?
-Try Ricardo dot Ramirez-Gonzalez at tgac dot ac dot uk
+Try [Ricardo.Ramirez-Gonzalez@tgac.ac.uk](Ricardo.Ramirez-Gonzalez@tgac.ac.uk)
  and [dan.maclean@tsl.ac.uk](dan.maclean@tsl.ac.uk)
 
 ### Important Notes

data/VERSION

@@ -1 +1 @@
-0.6.2
+2.0.3

data/bio-samtools.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 0.6.2 ruby lib
+# stub: bio-samtools 2.0.3 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "0.6.2"
+  s.version = "2.0.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2014-02-25"
+  s.date = "2014-04-18"
   s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
   s.email = "ilpuccio.febo@gmail.com"
   s.extensions = ["ext/mkrf_conf.rb"]
@@ -36,80 +36,19 @@ Gem::Specification.new do |s|
     "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/Bio/DB/Vcf.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",
-    "doc/classes/Bio/DB/Alignment.html",
-    "doc/classes/Bio/DB/Alignment.src/M000012.html",
-    "doc/classes/Bio/DB/Alignment.src/M000013.html",
-    "doc/classes/Bio/DB/Alignment.src/M000014.html",
-    "doc/classes/Bio/DB/Alignment.src/M000015.html",
-    "doc/classes/Bio/DB/SAM.html",
-    "doc/classes/Bio/DB/SAM/Library.html",
-    "doc/classes/Bio/DB/SAM/Library.src/M000006.html",
-    "doc/classes/Bio/DB/SAM/Tools.html",
-    "doc/classes/Bio/DB/SAM/Tools.src/M000007.html",
-    "doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html",
-    "doc/classes/Bio/DB/SAM/Tools/Bam1T.html",
-    "doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html",
-    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html",
-    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html",
-    "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html",
-    "doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html",
-    "doc/classes/Bio/DB/SAM/Tools/SamfileT.html",
-    "doc/classes/Bio/DB/SAM/Tools/SamfileTX.html",
-    "doc/classes/Bio/DB/SAMException.html",
-    "doc/classes/Bio/DB/SAMException.src/M000016.html",
-    "doc/classes/Bio/DB/Sam.src/M000017.html",
-    "doc/classes/Bio/DB/Sam.src/M000018.html",
-    "doc/classes/Bio/DB/Sam.src/M000019.html",
-    "doc/classes/Bio/DB/Sam.src/M000020.html",
-    "doc/classes/Bio/DB/Sam.src/M000021.html",
-    "doc/classes/Bio/DB/Sam.src/M000022.html",
-    "doc/classes/Bio/DB/Sam.src/M000023.html",
-    "doc/classes/Bio/DB/Sam.src/M000024.html",
-    "doc/classes/Bio/DB/Sam.src/M000025.html",
-    "doc/classes/Bio/DB/Sam.src/M000026.html",
-    "doc/classes/Bio/DB/Sam.src/M000027.html",
-    "doc/classes/Bio/DB/Sam.src/M000028.html",
-    "doc/classes/Bio/DB/Sam.src/M000029.html",
-    "doc/classes/Bio/DB/Sam.src/M000030.html",
-    "doc/classes/Bio/DB/Sam.src/M000031.html",
-    "doc/classes/Bio/DB/Sam.src/M000032.html",
-    "doc/classes/Bio/DB/Tag.html",
-    "doc/classes/Bio/DB/Tag.src/M000011.html",
-    "doc/classes/LibC.html",
-    "doc/classes/Pileup.html",
-    "doc/classes/Pileup.src/M000001.html",
-    "doc/classes/Pileup.src/M000002.html",
-    "doc/classes/Pileup.src/M000003.html",
-    "doc/classes/Pileup.src/M000004.html",
-    "doc/classes/Pileup.src/M000005.html",
     "doc/created.rid",
-    "doc/files/lib/bio-samtools_rb.html",
-    "doc/files/lib/bio/db/sam/bam_rb.html",
-    "doc/files/lib/bio/db/sam/faidx_rb.html",
-    "doc/files/lib/bio/db/sam/library_rb.html",
-    "doc/files/lib/bio/db/sam/pileup_rb.html",
-    "doc/files/lib/bio/db/sam/sam_rb.html",
-    "doc/files/lib/bio/db/sam_rb.html",
-    "doc/fr_class_index.html",
-    "doc/fr_file_index.html",
-    "doc/fr_method_index.html",
+    "doc/fonts.css",
+    "doc/fonts/Lato-Light.ttf",
+    "doc/fonts/Lato-LightItalic.ttf",
+    "doc/fonts/Lato-Regular.ttf",
+    "doc/fonts/Lato-RegularItalic.ttf",
+    "doc/fonts/SourceCodePro-Bold.ttf",
+    "doc/fonts/SourceCodePro-Regular.ttf",
     "doc/images/add.png",
+    "doc/images/arrow_up.png",
     "doc/images/brick.png",
     "doc/images/brick_link.png",
     "doc/images/bug.png",
@@ -140,64 +79,67 @@ Gem::Specification.new do |s|
     "doc/js/search.js",
     "doc/js/search_index.js",
     "doc/js/searcher.js",
-    "doc/lib/bio-samtools_rb.html",
-    "doc/lib/bio/db/pileup_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/lib/bio/db/vcf_rb.html",
-    "doc/rdoc-style.css",
     "doc/rdoc.css",
     "doc/table_of_contents.html",
-    "doc/tutorial.html",
-    "doc/tutorial.pdf",
     "ext/Makefile-bioruby.patch",
     "ext/Makefile-suse.patch",
+    "ext/Rakefile",
     "ext/mkrf_conf.rb",
     "lib/bio-samtools.rb",
     "lib/bio/.DS_Store",
+    "lib/bio/BIOExtensions.rb",
+    "lib/bio/db/alignment.rb",
+    "lib/bio/db/fastadb.rb",
     "lib/bio/db/pileup.rb",
     "lib/bio/db/sam.rb",
-    "lib/bio/db/sam/bam.rb",
     "lib/bio/db/sam/external/COPYING",
     "lib/bio/db/sam/external/VERSION",
-    "lib/bio/db/sam/faidx.rb",
+    "lib/bio/db/sam/faidx_old.rb",
     "lib/bio/db/sam/library.rb",
-    "lib/bio/db/sam/sam.rb",
     "lib/bio/db/vcf.rb",
+    "test/.gitignore",
     "test/helper.rb",
-    "test/samples/pipe_char/test.bam",
-    "test/samples/pipe_char/test.bam.bai",
-    "test/samples/pipe_char/test.tam",
-    "test/samples/pipe_char/test_chr.fasta",
-    "test/samples/pipe_char/test_chr.fasta.fai",
+    "test/old_test_basic.rb",
+    "test/samples/small/dupes.bam",
+    "test/samples/small/dupes.sam",
     "test/samples/small/ids2.txt",
+    "test/samples/small/map_for_reheader.sam",
+    "test/samples/small/map_to_merge1.bam",
+    "test/samples/small/map_to_merge1.bam.bai",
+    "test/samples/small/map_to_merge1.sam",
+    "test/samples/small/map_to_merge2.bam",
+    "test/samples/small/map_to_merge2.bam.bai",
+    "test/samples/small/map_to_merge2.sam",
+    "test/samples/small/no_md.sam",
     "test/samples/small/sorted.bam",
     "test/samples/small/sorted.bam.bai",
-    "test/samples/small/test",
-    "test/samples/small/test.bam",
-    "test/samples/small/test.fa",
-    "test/samples/small/test.fai",
     "test/samples/small/test.sai",
     "test/samples/small/test.tam",
     "test/samples/small/test_chr.fasta",
+    "test/samples/small/test_chr.fasta.1.bt2",
+    "test/samples/small/test_chr.fasta.2.bt2",
+    "test/samples/small/test_chr.fasta.3.bt2",
+    "test/samples/small/test_chr.fasta.4.bt2",
     "test/samples/small/test_chr.fasta.amb",
     "test/samples/small/test_chr.fasta.ann",
     "test/samples/small/test_chr.fasta.bwt",
     "test/samples/small/test_chr.fasta.pac",
     "test/samples/small/test_chr.fasta.rbwt",
+    "test/samples/small/test_chr.fasta.rev.1.bt2",
+    "test/samples/small/test_chr.fasta.rev.2.bt2",
     "test/samples/small/test_chr.fasta.rpac",
     "test/samples/small/test_chr.fasta.rsa",
     "test/samples/small/test_chr.fasta.sa",
+    "test/samples/small/test_cov.svg",
     "test/samples/small/testu.bam",
     "test/samples/small/testu.bam.bai",
-    "test/test_basic.rb",
+    "test/svg",
     "test/test_bio-samtools.rb",
-    "test/test_vcf.rb"
+    "test/test_pileup.rb",
+    "test/test_sam.rb",
+    "test/test_vcf.rb",
+    "tutorial/tutorial.html",
+    "tutorial/tutorial.pdf"
   ]
   s.homepage = "http://github.com/helios/bioruby-samtools"
   s.licenses = ["MIT"]
@@ -208,9 +150,8 @@ Gem::Specification.new do |s|
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<ffi>, [">= 0"])
+      s.add_runtime_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_runtime_dependency(%q<systemu>, [">= 2.5.2"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<shoulda-context>, [">= 0"])
       s.add_development_dependency(%q<shoulda-matchers>, [">= 0"])
@@ -219,10 +160,10 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<rcov>, [">= 0"])
       s.add_development_dependency(%q<simplecov>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, [">= 0"])
+      s.add_development_dependency(%q<test-unit>, [">= 0"])
     else
-      s.add_dependency(%q<ffi>, [">= 0"])
+      s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_dependency(%q<systemu>, [">= 2.5.2"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<shoulda-context>, [">= 0"])
       s.add_dependency(%q<shoulda-matchers>, [">= 0"])
@@ -231,11 +172,11 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<rcov>, [">= 0"])
       s.add_dependency(%q<simplecov>, [">= 0"])
       s.add_dependency(%q<rdoc>, [">= 0"])
+      s.add_dependency(%q<test-unit>, [">= 0"])
     end
   else
-    s.add_dependency(%q<ffi>, [">= 0"])
+    s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
-    s.add_dependency(%q<systemu>, [">= 2.5.2"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<shoulda-context>, [">= 0"])
     s.add_dependency(%q<shoulda-matchers>, [">= 0"])
@@ -244,6 +185,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<rcov>, [">= 0"])
     s.add_dependency(%q<simplecov>, [">= 0"])
     s.add_dependency(%q<rdoc>, [">= 0"])
+    s.add_dependency(%q<test-unit>, [">= 0"])
   end
 end
 

data/doc/Bio.html

@@ -2,140 +2,90 @@
 
 <html>
 <head>
-<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+<meta charset="UTF-8">
 
 <title>module Bio - Pileup</title>
 
-<link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
+<link href="./fonts.css" rel="stylesheet">
+<link 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>
+<script src="./js/jquery.js"></script>
+<script src="./js/navigation.js"></script>
+<script src="./js/search_index.js"></script>
+<script src="./js/search.js"></script>
+<script src="./js/searcher.js"></script>
+<script 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>
+<body id="top" role="document" class="module">
+<nav role="navigation">
+  <div id="project-navigation">
+    <div id="home-section" role="region" title="Quick navigation" class="nav-section">
+  <h2>
+    <a href="./index.html" rel="home">Home</a>
+  </h2>
+
+  <div id="table-of-contents-navigation">
+    <a href="./table_of_contents.html#pages">Pages</a>
     <a href="./table_of_contents.html#classes">Classes</a>
     <a href="./table_of_contents.html#methods">Methods</a>
-  </h3>
-</nav>
-
+  </div>
+</div>
 
-  <nav id="search-section" class="section project-section" class="initially-hidden">
+    <div id="search-section" role="search" class="project-section initially-hidden">
   <form action="#" method="get" accept-charset="utf-8">
-    <h3 class="section-header">
-      <input type="text" name="search" placeholder="Search" id="search-field"
+    <div id="search-field-wrapper">
+      <input id="search-field" role="combobox" aria-label="Search"
+             aria-autocomplete="list" aria-controls="search-results"
+             type="text" name="search" placeholder="Search" spellcheck="false"
              title="Type to search, Up and Down to navigate, Enter to load">
-    </h3>
+    </div>
+
+    <ul id="search-results" aria-label="Search Results"
+        aria-busy="false" aria-expanded="false"
+        aria-atomic="false" class="initially-hidden"></ul>
   </form>
+</div>
 
-  <ul id="search-results" class="initially-hidden"></ul>
-</nav>
+  </div>
 
+  
+<div class="nav-section">
+  <h3>Table of Contents</h3>
 
-  <div id="file-metadata">
-    <nav id="file-list-section" class="section">
-  <h3 class="section-header">Defined In</h3>
-  <ul>
-    <li>lib/bio/db/pileup.rb
-    <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
-    <li>lib/bio/db/vcf.rb
+  <ul class="link-list" role="directory">
+    <li><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">Bio::DB::Pileup </a>
+    <li><a href="#module-Bio-label-Vcf+">Vcf </a>
   </ul>
-</nav>
+</div>
 
-    
-  </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/Pileup.html">Bio::DB::Pileup</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="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
-  
-    <li><a href="./LibC.html">LibC</a>
-  
-  </ul>
-</nav>
-
+    
   </div>
 </nav>
 
-<div id="documentation">
-  <h1 class="module">module Bio</h1>
+<main role="main" aria-labelledby="module-Bio">
+  <h1 id="module-Bio" class="module">
+    module Bio
+  </h1>
 
-  <div id="description" class="description">
+  <section class="description">
     
-<h1 id="label-Bio%3A%3ADB%3A%3APileup+"><a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a> </h1>
+<h1 id="module-Bio-label-Bio%3A%3ADB%3A%3APileup+"><a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a> <span><a href="#module-Bio-label-Bio%3A%3ADB%3A%3APileup+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
 
 <p>A class representing information in SAMTools pileup format</p>
 <dl class="rdoc-list note-list"><dt>Author
 <dd>
-<p>Dan MacLean (tsl at dan.maclean.ac.uk)</p>
+<p>Dan MacLean (dan.maclean@tsl.ac.uk)</p>
 </dd></dl>
 
 <p>Pileup is described at <a
@@ -146,18 +96,18 @@ Briefly (when you invoke pileup with the -c option):</p>
 </li><li>
 <p>2 reference coordinate</p>
 </li><li>
-<p>(3) reference base, or `*‘ for an indel line</p>
+<p>(3) reference base, or `*&#39; for an indel line</p>
 </li><li>
 <p>(4) genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G,
 W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example,   +A,
 -A   or +CC/-C. There is no difference between */+A or +A/*.</p>
 </li><li>
 <p>(5) Phred-scaled likelihood that the genotype is wrong, which is also
-called `consensus quality’.</p>
+called `consensus quality&#39;.</p>
 </li><li>
 <p>(6) Phred-scaled likelihood that the genotype is identical to the
-reference, which is also called `SNP quality’. Suppose the reference base
-is A and in alignment we see 17 G and 3 A. We will get a low consensus
+reference, which is also called `SNP quality&#39;. Suppose the reference
+base is A and in alignment we see 17 G and 3 A. We will get a low consensus
 quality because it is difficult to distinguish an A/G heterozygote from a
 G/G homozygote. We will get a high SNP quality, though, because the
 evidence of a SNP is very strong.</p>
@@ -178,38 +128,27 @@ the 1st indel allele otherwise</p>
 <p>(13) indel line only: # reads supporting a third indel allele</p>
 </li></ul>
 
-<p>If pileup is invoked without `-c’, indel lines and columns between 3 and
-7 inclusive will not be outputted.</p>
+<p>If pileup is invoked without `-c&#39;, indel lines and columns between 3
+and 7 inclusive will not be outputted.</p>
 
 <p>NB mpileup uses the 6 column output format eg
-“seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;”
-Pileup provides accessors for all columns (6 or 10 column format) and a few
-other useful methods</p>
+“seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
+provides accessors for all columns (6 or 10 column format) and a few other
+useful methods</p>
 
-<p>require ‘rubygems’ require ‘ffi’</p>
+<p>require &#39;rubygems&#39; require&#39;ffi&#39; require
+&#39;bio/db/sam/bam&#39;</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>
-
-<h1 id="label-Vcf+">Vcf </h1>
+<h1 id="module-Bio-label-Vcf+">Vcf <span><a href="#module-Bio-label-Vcf+">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
 
 <p>A class representing information in Variant Call Format Forked from vcfruby
 at <a
 href="https://github.com/jesserod/vcfruby">github.com/jesserod/vcfruby</a> 
-Modified and tests written by Dan MacLean (tsl at dan.maclean.ac.uk) VCF is
+Modified and tests written by Dan MacLean (dan.maclean@tsl.ac.uk) VCF is
 described at <a
 href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
 
-  </div><!-- description -->
+  </section>
 
   
   
@@ -223,16 +162,14 @@ href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
 
     
 
-    <!-- Methods -->
     
-  </section><!-- 5Buntitled-5D -->
-
-</div><!-- documentation -->
+  </section>
+</main>
 
 
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