RubyGems - bio-samtools - Versions diffs - 0.6.2 → 2.0.3 - Mend

bio-samtools 0.6.2 → 2.0.3

Files changed (160) hide show

checksums.yaml +4 -4
data/Gemfile +3 -2
data/README.md +4 -7
data/VERSION +1 -1
data/bio-samtools.gemspec +47 -105
data/doc/Bio.html +68 -131
data/doc/Bio/DB.html +51 -111
data/doc/Bio/DB/Alignment.html +135 -363
data/doc/Bio/DB/Pileup.html +183 -170
data/doc/Bio/DB/SAM.html +1396 -820
data/doc/Bio/DB/SAM/Library.html +73 -123
data/doc/Bio/DB/SAM/Tools.html +51 -273
data/doc/Bio/DB/Tag.html +78 -124
data/doc/Bio/DB/Vcf.html +111 -147
data/doc/LICENSE_txt.html +113 -148
data/doc/created.rid +9 -10
data/doc/fonts.css +167 -0
data/doc/fonts/Lato-Light.ttf +0 -0
data/doc/fonts/Lato-LightItalic.ttf +0 -0
data/doc/fonts/Lato-Regular.ttf +0 -0
data/doc/fonts/Lato-RegularItalic.ttf +0 -0
data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
data/doc/images/add.png +0 -0
data/doc/images/arrow_up.png +0 -0
data/doc/images/delete.png +0 -0
data/doc/images/tag_blue.png +0 -0
data/doc/index.html +48 -54
data/doc/js/darkfish.js +9 -22
data/doc/js/search.js +20 -5
data/doc/js/search_index.js +1 -1
data/doc/rdoc.css +255 -218
data/doc/table_of_contents.html +256 -137
data/ext/Rakefile +57 -0
data/lib/bio-samtools.rb +7 -2
data/lib/bio/BIOExtensions.rb +89 -0
data/lib/bio/db/alignment.rb +59 -0
data/lib/bio/db/fastadb.rb +255 -0
data/lib/bio/db/pileup.rb +221 -172
data/lib/bio/db/sam.rb +639 -589
data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
data/lib/bio/db/vcf.rb +69 -68
data/test/.gitignore +1 -0
data/test/{test_basic.rb → old_test_basic.rb} +33 -1
data/test/samples/small/dupes.bam +0 -0
data/test/samples/small/dupes.sam +274 -0
data/test/samples/small/map_for_reheader.sam +8 -0
data/test/samples/small/map_to_merge1.bam +0 -0
data/test/samples/small/map_to_merge1.bam.bai +0 -0
data/test/samples/small/map_to_merge1.sam +8 -0
data/test/samples/small/map_to_merge2.bam +0 -0
data/test/samples/small/map_to_merge2.bam.bai +0 -0
data/test/samples/small/map_to_merge2.sam +8 -0
data/test/samples/small/no_md.sam +8 -0
data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
data/test/samples/small/test_cov.svg +273 -0
data/test/samples/small/testu.bam.bai +0 -0
data/test/svg +133 -0
data/test/test_pileup.rb +84 -0
data/test/test_sam.rb +331 -0
data/test/test_vcf.rb +11 -0
data/{doc → tutorial}/tutorial.html +0 -0
data/{doc → tutorial}/tutorial.pdf +0 -0
metadata +56 -114
data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
data/doc/Bio/DB/SAMException.html +0 -205
data/doc/LibC.html +0 -155
data/doc/Pileup.html +0 -571
data/doc/Vcf.html +0 -473
data/doc/basic_styles.css +0 -31
data/doc/classes/Bio.html +0 -139
data/doc/classes/Bio/DB.html +0 -137
data/doc/classes/Bio/DB/Alignment.html +0 -441
data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
data/doc/classes/Bio/DB/SAM.html +0 -510
data/doc/classes/Bio/DB/SAM/Library.html +0 -135
data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
data/doc/classes/Bio/DB/SAMException.html +0 -140
data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
data/doc/classes/Bio/DB/Tag.html +0 -160
data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
data/doc/classes/LibC.html +0 -105
data/doc/classes/Pileup.html +0 -374
data/doc/classes/Pileup.src/M000001.html +0 -34
data/doc/classes/Pileup.src/M000002.html +0 -21
data/doc/classes/Pileup.src/M000003.html +0 -21
data/doc/classes/Pileup.src/M000004.html +0 -21
data/doc/classes/Pileup.src/M000005.html +0 -31
data/doc/files/lib/bio-samtools_rb.html +0 -109
data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
data/doc/files/lib/bio/db/sam_rb.html +0 -111
data/doc/fr_class_index.html +0 -43
data/doc/fr_file_index.html +0 -33
data/doc/fr_method_index.html +0 -58
data/doc/lib/bio-samtools_rb.html +0 -115
data/doc/lib/bio/db/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/bam_rb.html +0 -121
data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
data/doc/lib/bio/db/sam/library_rb.html +0 -115
data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
data/doc/lib/bio/db/sam/sam_rb.html +0 -121
data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
data/doc/lib/bio/db/sam_rb.html +0 -115
data/doc/lib/bio/db/vcf_rb.html +0 -124
data/doc/rdoc-style.css +0 -208
data/lib/bio/db/sam/bam.rb +0 -210
data/lib/bio/db/sam/sam.rb +0 -86
data/test/samples/pipe_char/test.bam +0 -0
data/test/samples/pipe_char/test.bam.bai +0 -0
data/test/samples/pipe_char/test.tam +0 -10
data/test/samples/pipe_char/test_chr.fasta +0 -1000
data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
data/test/samples/small/test +0 -0
data/test/samples/small/test.bam +0 -0
data/test/samples/small/test.fa +0 -20
data/test/samples/small/test.fai +0 -0

data/doc/Bio/DB/SAMException.html DELETED

@@ -1,205 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
-<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
-<title>class Bio::DB::SAMException - 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">
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-             title="Type to search, Up and Down to navigate, Enter to load">
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-</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">RuntimeError
-</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>
-  </ul>
-</nav>
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-    <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::SAMException</h1>
-  <div id="description" class="description">
-  </div><!-- description -->
-  <section id="5Buntitled-5D" class="documentation-section">
-    <!-- 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">()</span>
-          <span class="method-click-advice">click to toggle source</span>
-        </div>
-        <div class="method-description">
-          <p>we can add further variables to give information of the excpetion</p>
-          <div class="method-source-code" id="new-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam.rb, line 645</span>
-<span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>()
-<span class="ruby-keyword">end</span></pre>
-          </div><!-- new-source -->
-        </div>
-      </div><!-- new-method -->
-    </section><!-- public-class-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> 3.12.
-  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
-</footer>

data/doc/LibC.html DELETED

@@ -1,155 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
-<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
-<title>module LibC - 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>
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-</nav>
-  <nav id="search-section" class="section project-section" class="initially-hidden">
-  <form action="#" method="get" accept-charset="utf-8">
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-             title="Type to search, Up and Down to navigate, Enter to load">
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-  <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">
-  </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 LibC</h1>
-  <div id="description" class="description">
-<p>require ‘bio/db/pileup’ require ‘bio/db/vcf’</p>
-  </div><!-- description -->
-  <section id="5Buntitled-5D" class="documentation-section">
-    <!-- Methods -->
-  </section><!-- 5Buntitled-5D -->
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data/doc/Pileup.html DELETED

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-<!DOCTYPE html>
-<html>
-<head>
-<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
-<title>Class: 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">
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-    <a href="./index.html">Home</a>
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-  <nav id="search-section" class="section project-section" class="initially-hidden">
-  <form action="#" method="get" accept-charset="utf-8">
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-             title="Type to search, Up and Down to navigate, Enter to load">
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-</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/pileup.rb
-  </ul>
-</nav>
-  </div>
-  <div id="class-metadata">
-    <nav id="parent-class-section" class="section">
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-    <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>
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-    <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 Pileup</h1>
-  <div id="description" class="description">
-<h1 id="label-Pileup+"><a href="Pileup.html">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><a href="Pileup.html">Pileup</a> 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;”
-<a href="Pileup.html">Pileup</a> provides accessors for all columns (6 or
-10 column format) and a few other useful methods</p>
-  </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 = Pileup.new(pile_up_line)</pre>
-          <div class="method-source-code" id="new-source">
-            <pre><span class="ruby-comment"># File lib/bio/db/sam/pileup.rb, line 34</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/sam/pileup.rb, line 64</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/sam/pileup.rb, line 56</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/sam/pileup.rb, line 72</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">
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