bio-samtools 0.4.2 → 0.5.0

data/Gemfile.lock

@@ -10,6 +10,7 @@ GEM
       git (>= 1.2.5)
       rake
     json (1.6.1)
+    json (1.6.1-java)
     rake (0.9.2.2)
     rcov (0.9.9)
     rcov (0.9.9-java)

data/README.rdoc

@@ -42,6 +42,7 @@ I´m getting a segmentation Fault, what did I do wrong?
 I keep seeing this "Invalid gemspec in [some ruby gem path...]", what is wrong?
 - This appears to be a bug in RubyGems that doesn't affect the running of the tools. It will keep happening until someone updates RubyGems. If it really bugs you, downgrade RubyGems.
 
+
 To whom do I complain?
 -about bio-samtools? Try
 Ricardo dot Ramirez-Gonzalez at tgac dot ac dot uk

data/VERSION

@@ -1 +1 @@
-0.4.2
+0.5.0

data/bio-samtools.gemspec

@@ -4,18 +4,15 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-samtools}
-  s.version = "0.4.2"
+  s.name = "bio-samtools"
+  s.version = "0.5.0"
 
   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{2011-11-10}
-  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 
-  the gee_fu genome browser (http://github.com/danmaclean/gee_fu).}
-  s.email = %q{ilpuccio.febo@gmail.com}
-  s.extensions = [%q{ext/mkrf_conf.rb}]
+  s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
+  s.date = "2012-01-13"
+  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"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -32,6 +29,7 @@ Gem::Specification.new do |s|
     "doc/Bio.html",
     "doc/Bio/DB.html",
     "doc/Bio/DB/Alignment.html",
+    "doc/Bio/DB/Pileup.html",
     "doc/Bio/DB/SAM.html",
     "doc/Bio/DB/SAM/Library.html",
     "doc/Bio/DB/SAM/Tools.html",
@@ -43,6 +41,7 @@ Gem::Specification.new do |s|
     "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",
@@ -139,6 +138,7 @@ Gem::Specification.new do |s|
     "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",
@@ -146,6 +146,7 @@ Gem::Specification.new do |s|
     "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",
@@ -156,20 +157,19 @@ Gem::Specification.new do |s|
     "ext/mkrf_conf.rb",
     "lib/bio-samtools.rb",
     "lib/bio/.DS_Store",
+    "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/library.rb",
-    "lib/bio/db/sam/pileup.rb",
     "lib/bio/db/sam/sam.rb",
-    "lib/bio/db/sam/vcf.rb",
-    "test/basictest.rb",
+    "lib/bio/db/vcf.rb",
     "test/helper.rb",
-    "test/pileup.rb",
     "test/samples/small/ids2.txt",
     "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",
@@ -191,11 +191,11 @@ Gem::Specification.new do |s|
     "test/test_bio-samtools.rb",
     "test/test_vcf.rb"
   ]
-  s.homepage = %q{http://github.com/helios/bioruby-samtools}
-  s.licenses = [%q{MIT}]
-  s.require_paths = [%q{lib}]
-  s.rubygems_version = %q{1.8.6}
-  s.summary = %q{Binder of samtools for ruby, on the top of FFI.}
+  s.homepage = "http://github.com/helios/bioruby-samtools"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Binder of samtools for ruby, on the top of FFI."
 
   if s.respond_to? :specification_version then
     s.specification_version = 3

data/doc/Bio.html

@@ -47,11 +47,13 @@
     <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>
 </nav>
 
@@ -87,6 +89,8 @@
   
     <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>
@@ -111,11 +115,9 @@
   
     <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="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="./Vcf.html">Vcf</a>
+    <li><a href="./LibC.html">LibC</a>
   
   </ul>
 </nav>
@@ -128,6 +130,62 @@
 
   <div id="description" class="description">
     
+<h1 id="label-Bio%3A%3ADB%3A%3APileup+"><a href="Bio/DB/Pileup.html">Bio::DB::Pileup</a> </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>
+</dd></dl>
+
+<p>Pileup is described at <a
+href="http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output">sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#I_do_not_understand_the_columns_in_the_pileup_output</a>.
+Briefly (when you invoke pileup with the -c option):</p>
+<ul><li>
+<p>1 reference sequence name</p>
+</li><li>
+<p>2 reference coordinate</p>
+</li><li>
+<p>(3) reference base, or `*‘ 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>
+</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
+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>
+</li><li>
+<p>(7) root mean square (RMS) mapping quality</p>
+</li><li>
+<p>8 # reads covering the position</p>
+</li><li>
+<p>9 read bases at a SNP line (check the manual page for more information);
+the 1st indel allele otherwise</p>
+</li><li>
+<p>10 base quality at a SNP line; the 2nd indel allele otherwise</p>
+</li><li>
+<p>(11) indel line only: # reads directly supporting the 1st indel allele</p>
+</li><li>
+<p>(12) indel line only: # reads directly supporting the 2nd indel allele</p>
+</li><li>
+<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>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>
+
 <p>require ‘rubygems’ require ‘ffi’</p>
 
 <pre class="ruby"><span class="ruby-identifier">require</span> <span class="ruby-string">'bio/db/sam/faidx'</span>
@@ -142,6 +200,15 @@ 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>
+
+<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
+described at <a
+href="http://www.1000genomes.org/node/101">www.1000genomes.org/node/101</a></p>
+
   </div><!-- description -->
 
   

data/doc/Bio/DB.html

@@ -47,11 +47,13 @@
     <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>
 </nav>
 
@@ -93,6 +95,8 @@
   
     <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>
@@ -117,11 +121,9 @@
   
     <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="../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../Vcf.html">Vcf</a>
+    <li><a href="../LibC.html">LibC</a>
   
   </ul>
 </nav>

data/doc/Bio/DB/Alignment.html

@@ -105,6 +105,8 @@
   
     <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>
@@ -129,11 +131,9 @@
   
     <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="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
   
-    <li><a href="../../Vcf.html">Vcf</a>
+    <li><a href="../../LibC.html">LibC</a>
   
   </ul>
 </nav>
@@ -595,7 +595,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
 
           
           <div class="method-source-code" id="finalize-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 553</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 554</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>
@@ -634,7 +634,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
 
           
           <div class="method-source-code" id="new-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 549</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 550</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>)
@@ -671,7 +671,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
 
           
           <div class="method-source-code" id="sam-3D-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 607</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 608</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>)
@@ -724,7 +724,7 @@ for clarity. primary is the negation of is_negative from the BAM format</p>
 
           
           <div class="method-source-code" id="set-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 575</span>
+            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 576</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>) 

data/doc/Bio/DB/Pileup.html

@@ -0,0 +1,515 @@
+<!DOCTYPE html>
+
+<html>
+<head>
+<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
+
+<title>Class: Bio::DB::Pileup</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/pileup.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-new">::new</a>
+    
+    <li><a href="#method-i-non_ref_count">#non_ref_count</a>
+    
+    <li><a href="#method-i-non_refs">#non_refs</a>
+    
+    <li><a href="#method-i-ref_count">#ref_count</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/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="class">class Bio::DB::Pileup</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-ar1" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ar1</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-ar2" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ar2</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-ar3" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ar3</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-consensus" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">consensus</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-consensus_quality" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">consensus_quality</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-coverage" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">coverage</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </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">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-read_bases" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">read_bases</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-read_quals" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">read_quals</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-ref_base" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ref_base</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-ref_name" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">ref_name</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-rms_mapq" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">rms_mapq</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </div>
+      </div>
+      
+      <div id="attribute-i-snp_quality" class="method-detail">
+        <div class="method-heading attribute-method-heading">
+          <span class="method-name">snp_quality</span><span
+            class="attribute-access-type">[RW]</span>
+        </div>
+
+        <div class="method-description">
+        
+        
+        
+        </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-new" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">new</span><span
+            class="method-args">(pile_up_line)</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>creates the <a href="Pileup.html">Pileup</a> object</p>
+
+<pre>pile_up_line = &quot;seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;&quot;
+pile = Bio::DB::Pileup.new(pile_up_line)</pre>
+          
+
+          
+          <div class="method-source-code" id="new-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 35</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">pile_up_line</span>)
+  <span class="ruby-identifier">cols</span> = <span class="ruby-identifier">pile_up_line</span>.<span class="ruby-identifier">split</span>(<span class="ruby-regexp">/\t/</span>)
+  <span class="ruby-keyword">if</span> <span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">6</span> <span class="ruby-comment">##should only be able to get 6 lines from mpileup</span>
+    <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span> = <span class="ruby-identifier">cols</span>
+  <span class="ruby-keyword">elsif</span> (<span class="ruby-value">10</span><span class="ruby-operator">..</span><span class="ruby-value">13</span>).<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">cols</span>.<span class="ruby-identifier">length</span>) <span class="ruby-comment">##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...</span>
+    <span class="ruby-ivar">@ref_name</span>, <span class="ruby-ivar">@pos</span>, <span class="ruby-ivar">@ref_base</span>, <span class="ruby-ivar">@consensus</span>, <span class="ruby-ivar">@consensus_quality</span>, <span class="ruby-ivar">@snp_quality</span>, <span class="ruby-ivar">@rms_mapq</span>, <span class="ruby-ivar">@coverage</span>, <span class="ruby-ivar">@read_bases</span>, <span class="ruby-ivar">@read_quals</span>, <span class="ruby-ivar">@ar1</span>, <span class="ruby-ivar">@ar2</span>, <span class="ruby-ivar">@ar3</span> = <span class="ruby-identifier">cols</span>
+    <span class="ruby-ivar">@consensus_quality</span> = <span class="ruby-ivar">@consensus_quality</span>.<span class="ruby-identifier">to_f</span>
+    <span class="ruby-ivar">@snp_quality</span> = <span class="ruby-ivar">@snp_quality</span>.<span class="ruby-identifier">to_f</span>
+    <span class="ruby-ivar">@rms_mapq</span> = <span class="ruby-ivar">@rms_mapq</span>.<span class="ruby-identifier">to_f</span>
+  <span class="ruby-keyword">else</span>
+    <span class="ruby-comment">#raise RuntimeError, &quot;parsing line '#{pile_up_line.chomp}' failed&quot;</span>
+  <span class="ruby-keyword">end</span>
+    
+  <span class="ruby-ivar">@pos</span> = <span class="ruby-ivar">@pos</span>.<span class="ruby-identifier">to_i</span>
+  <span class="ruby-ivar">@coverage</span> = <span class="ruby-ivar">@coverage</span>.<span class="ruby-identifier">to_f</span>
+  <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword">nil</span>
+  <span class="ruby-ivar">@non_ref_count_hash</span> = <span class="ruby-keyword">nil</span> 
+  <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-keyword">nil</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-non_ref_count" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">non_ref_count</span><span
+            class="method-args">()</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>returns the total non-reference bases in the reads at this position</p>
+          
+
+          
+          <div class="method-source-code" id="non_ref_count-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 65</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_count</span>
+  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count</span>.<span class="ruby-identifier">nil?</span>
+    <span class="ruby-ivar">@non_ref_count</span> = <span class="ruby-ivar">@read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;ATGCatgc&quot;</span>).<span class="ruby-identifier">to_f</span>
+  <span class="ruby-keyword">end</span>
+  <span class="ruby-ivar">@non_ref_count</span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- non_ref_count-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- non_ref_count-method -->
+
+    
+      <div id="method-i-non_refs" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">non_refs</span><span
+            class="method-args">()</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>Calculate the total count of each non-reference nucleotide and return a
+hash of all 4 nt counts, returns a hash</p>
+
+<pre class="ruby"><span class="ruby-identifier">pile</span>.<span class="ruby-identifier">non_refs</span> <span class="ruby-comment">#{:A =&gt; 1, :C =&gt; 0, :T =&gt; 0, :G =&gt; 0}</span>
+</pre>
+          
+
+          
+          <div class="method-source-code" id="non_refs-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 57</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">non_refs</span>
+  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@non_ref_count_hash</span>.<span class="ruby-identifier">nil?</span>
+     <span class="ruby-ivar">@non_ref_count_hash</span> = {<span class="ruby-value">:A</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Aa&quot;</span>), <span class="ruby-value">:C</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Cc&quot;</span>), <span class="ruby-value">:G</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Gg&quot;</span>), <span class="ruby-value">:T</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;Tt&quot;</span>)}
+  <span class="ruby-keyword">end</span>
+    <span class="ruby-ivar">@non_ref_count_hash</span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- non_refs-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- non_refs-method -->
+
+    
+      <div id="method-i-ref_count" class="method-detail ">
+        
+        <div class="method-heading">
+          <span class="method-name">ref_count</span><span
+            class="method-args">()</span>
+          <span class="method-click-advice">click to toggle source</span>
+        </div>
+        
+
+        <div class="method-description">
+          
+          <p>returns the count of reference-bases in the reads at this position</p>
+          
+
+          
+          <div class="method-source-code" id="ref_count-source">
+            <pre><span class="ruby-comment"># File lib/bio/db/pileup.rb, line 73</span>
+<span class="ruby-keyword">def</span> <span class="ruby-identifier">ref_count</span>
+  <span class="ruby-keyword">if</span> <span class="ruby-ivar">@ref_count</span>.<span class="ruby-identifier">nil?</span>
+    <span class="ruby-ivar">@ref_count</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">read_bases</span>.<span class="ruby-identifier">count</span>(<span class="ruby-string">&quot;.,&quot;</span>)
+  <span class="ruby-keyword">end</span>
+  <span class="ruby-ivar">@ref_count</span>
+<span class="ruby-keyword">end</span></pre>
+          </div><!-- ref_count-source -->
+          
+        </div>
+
+        
+
+        
+      </div><!-- ref_count-method -->
+
+    
+    </section><!-- public-instance-method-details -->
+  
+  </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>
+