bio-gngm 0.2.0 → 0.2.1

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 (25) hide show
  1. data/VERSION +1 -1
  2. data/bio-gngm.gemspec +7 -3
  3. data/doc/Bio.html +4 -2
  4. data/doc/Bio/DB.html +4 -2
  5. data/doc/Bio/DB/FastaLengthDB.html +238 -0
  6. data/doc/Bio/DB/Pileup.html +10 -9
  7. data/doc/Bio/DB/Vcf.html +52 -102
  8. data/doc/Bio/Util.html +4 -2
  9. data/doc/Bio/Util/Gngm.html +318 -72
  10. data/doc/LICENSE_txt.html +12 -9
  11. data/doc/created.rid +3 -3
  12. data/doc/index.html +3 -1
  13. data/doc/js/search_index.js +1 -1
  14. data/doc/lib/bio-gngm_rb.html +2 -0
  15. data/doc/lib/bio/util/bio-gngm_rb.html +2 -0
  16. data/doc/table_of_contents.html +20 -7
  17. data/examples/Chr1.html +1483 -0
  18. data/examples/gngm_qtl_mapping_HTML_maker_set_options.rb +243 -0
  19. data/examples/pileup.txt +22 -0
  20. data/examples/snps.vcf +22 -0
  21. data/lib/bio-gngm.rb +0 -1
  22. data/lib/bio/util/bio-gngm.rb +100 -38
  23. data/test/test_bio-gngm.rb +1 -1
  24. metadata +30 -26
  25. data/lib/bio/util/mutation_effects.rb +0 -39
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.0
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+ 0.2.1
data/bio-gngm.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "bio-gngm"
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- s.version = "0.2.0"
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+ s.version = "0.2.1"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Dan MacLean"]
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- s.date = "2012-11-15"
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+ s.date = "2012-12-06"
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  s.description = "Identify causative mutations in a model genome from NGS reads using the NGM method."
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  s.email = "maclean.daniel@gmail.com"
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  s.extra_rdoc_files = [
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
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  "bio-gngm.gemspec",
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  "doc/Bio.html",
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  "doc/Bio/DB.html",
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+ "doc/Bio/DB/FastaLengthDB.html",
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  "doc/Bio/DB/Pileup.html",
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  "doc/Bio/DB/Vcf.html",
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  "doc/Bio/Util.html",
@@ -83,13 +84,16 @@ Gem::Specification.new do |s|
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  "doc/rdoc.css",
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  "doc/table_of_contents.html",
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  "examples/.DS_Store",
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+ "examples/Chr1.html",
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+ "examples/gngm_qtl_mapping_HTML_maker_set_options.rb",
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  "examples/make_histograms.rb",
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  "examples/make_threads.rb",
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  "examples/make_threads_isize.rb",
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+ "examples/pileup.txt",
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+ "examples/snps.vcf",
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  "examples/use_indels.rb",
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  "lib/bio-gngm.rb",
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  "lib/bio/util/bio-gngm.rb",
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- "lib/bio/util/mutation_effects.rb",
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  "scripts/get_subseq.rb",
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  "scripts/make_histograms_laerfyve.rb",
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  "scripts/make_histograms_laerfyve_stitched.rb",
data/doc/Bio.html CHANGED
@@ -4,7 +4,7 @@
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  <head>
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  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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- <title>Module: Bio</title>
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+ <title>module Bio - RDoc Documentation</title>
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  <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
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@@ -81,6 +81,8 @@
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  <li><a href="./Bio/DB.html">Bio::DB</a>
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+ <li><a href="./Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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  <li><a href="./Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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  <li><a href="./Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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  <footer id="validator-badges">
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  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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data/doc/Bio/DB.html CHANGED
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  <head>
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  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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- <title>Module: Bio::DB</title>
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+ <title>module Bio::DB - RDoc Documentation</title>
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  <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
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@@ -80,6 +80,8 @@
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  <li><a href="../Bio/DB.html">Bio::DB</a>
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+ <li><a href="../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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  <li><a href="../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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  <li><a href="../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
@@ -122,7 +124,7 @@
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  <footer id="validator-badges">
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  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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data/doc/Bio/DB/FastaLengthDB.html ADDED
@@ -0,0 +1,238 @@
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+ <!DOCTYPE html>
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+
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>class Bio::DB::FastaLengthDB - RDoc Documentation</title>
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+
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+ <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
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+
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../../";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/darkfish.js"></script>
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+
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+
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../../index.html">Home</a>
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+ <a href="../../table_of_contents.html#classes">Classes</a>
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+ <a href="../../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+
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+
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/bio/util/bio-gngm.rb
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+ </ul>
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+ </nav>
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+
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+ <nav id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object
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+
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+ </nav>
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+
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="#method-c-new">::new</a>
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+
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+ <li><a href="#method-i-each">#each</a>
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+
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+ </ul>
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+ </nav>
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+
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+ </div>
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+
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+
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+ <ul>
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+
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+ <li class="file"><a href="../../LICENSE_txt.html">LICENSE</a>
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+
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+ </ul>
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+ </nav>
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+
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../../Bio.html">Bio</a>
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+
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+ <li><a href="../../Bio/DB.html">Bio::DB</a>
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+
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+ <li><a href="../../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
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+
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+ <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
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+
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+ <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
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+
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+ <li><a href="../../Bio/Util.html">Bio::Util</a>
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+
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+ <li><a href="../../Bio/Util/Gngm.html">Bio::Util::Gngm</a>
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+
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+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="class">class Bio::DB::FastaLengthDB</h1>
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+
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+ <div id="description" class="description">
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+
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+ <p>Simple class representing a file of Fasta format sequences and each ones
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+ length</p>
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+
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+ </div><!-- description -->
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="method-c-new" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(args)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+
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+
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+ <div class="method-description">
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+
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+
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+
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+
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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 20</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">args</span>)
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+ <span class="ruby-ivar">@file</span> = <span class="ruby-identifier">args</span>[<span class="ruby-value">:file</span>]
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+ <span class="ruby-ivar">@seqs</span> = {}
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+ <span class="ruby-identifier">file</span> = <span class="ruby-constant">Bio</span><span class="ruby-operator">::</span><span class="ruby-constant">FastaFormat</span>.<span class="ruby-identifier">open</span>(<span class="ruby-ivar">@file</span>)
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+ <span class="ruby-identifier">file</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">entry</span><span class="ruby-operator">|</span>
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+ <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">entry</span>.<span class="ruby-identifier">entry_id</span>] = <span class="ruby-identifier">entry</span>.<span class="ruby-identifier">length</span>
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each</span>
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+ <span class="ruby-ivar">@seqs</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">k</span>]
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span>
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+
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- new-source -->
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+ </div>
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+ </div><!-- new-method -->
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+ </section><!-- public-class-method-details -->
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+ <div id="method-i-each" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">each</span><span
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+ class="method-args">() { |k, seqs| ... }</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <div class="method-description">
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 28</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each</span>
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+ <span class="ruby-ivar">@seqs</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">sort</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span>
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+ <span class="ruby-keyword">yield</span> <span class="ruby-identifier">k</span>, <span class="ruby-ivar">@seqs</span>[<span class="ruby-identifier">k</span>]
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- each-source -->
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+ </div>
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+ </div><!-- each-method -->
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+ </section><!-- public-instance-method-details -->
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+
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+ </section><!-- 5Buntitled-5D -->
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+
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+ </div><!-- documentation -->
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+
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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data/doc/Bio/DB/Pileup.html CHANGED
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@@ -99,6 +99,8 @@
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@@ -227,7 +229,7 @@ is compared to the next most common base after it.
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">discordant_chastity</span>
232
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  <span class="ruby-identifier">arr</span> = <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_refs</span>.<span class="ruby-identifier">to_a</span>.<span class="ruby-identifier">sort</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">a</span>,<span class="ruby-identifier">b</span><span class="ruby-operator">|</span> <span class="ruby-identifier">b</span>.<span class="ruby-identifier">last</span> <span class="ruby-operator">&lt;=&gt;</span> <span class="ruby-identifier">a</span>.<span class="ruby-identifier">last</span> }
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@@ -282,13 +284,12 @@ reference base is N or n if <code>:ignore_reference_n</code> is set to true</p>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_snp?</span>(<span class="ruby-identifier">opts</span>)
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- <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:ignore_reference_n</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;N&quot;</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;n&quot;</span>
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- <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span>
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- <span class="ruby-keyword">elsif</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">coverage</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_non_ref_count</span>]
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- <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span>
291
- <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">'*'</span>
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+ <span class="ruby-comment">#return false unless is_ct</span>
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+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">false</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:ignore_reference_n</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;N&quot;</span> <span class="ruby-keyword">or</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref_base</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;n&quot;</span>
292
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">coverage</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">opts</span>[<span class="ruby-value">:min_non_ref_count</span>]
292
293
  <span class="ruby-keyword">false</span>
293
294
  <span class="ruby-keyword">end</span></pre>
294
295
  </div><!-- is_snp-3F-source -->
@@ -310,7 +311,7 @@ reference base is N or n if <code>:ignore_reference_n</code> is set to true</p>
310
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311
312
  <footer id="validator-badges">
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313
  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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data/doc/Bio/DB/Vcf.html CHANGED
@@ -4,7 +4,7 @@
4
4
  <head>
5
5
  <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
6
 
7
- <title>Class: Bio::DB::Vcf</title>
7
+ <title>class Bio::DB::Vcf - RDoc Documentation</title>
8
8
 
9
9
  <link type="text/css" media="screen" href="../../rdoc.css" rel="stylesheet">
10
10
 
@@ -74,13 +74,11 @@
74
74
 
75
75
  <li><a href="#method-i-gq">#gq</a>
76
76
 
77
- <li><a href="#method-i-has_just_one_variant-3F">#has_just_one_variant?</a>
78
-
79
- <li><a href="#method-i-is_deletion-3F">#is_deletion?</a>
80
-
81
77
  <li><a href="#method-i-is_indel-3F">#is_indel?</a>
82
78
 
83
- <li><a href="#method-i-is_insertion-3F">#is_insertion?</a>
79
+ <li><a href="#method-i-is_mnp-3F">#is_mnp?</a>
80
+
81
+ <li><a href="#method-i-is_snp-3F">#is_snp?</a>
84
82
 
85
83
  <li><a href="#method-i-mq">#mq</a>
86
84
 
@@ -123,6 +121,8 @@
123
121
 
124
122
  <li><a href="../../Bio/DB.html">Bio::DB</a>
125
123
 
124
+ <li><a href="../../Bio/DB/FastaLengthDB.html">Bio::DB::FastaLengthDB</a>
125
+
126
126
  <li><a href="../../Bio/DB/Pileup.html">Bio::DB::Pileup</a>
127
127
 
128
128
  <li><a href="../../Bio/DB/Vcf.html">Bio::DB::Vcf</a>
@@ -198,7 +198,7 @@ attribute string on commas</p>
198
198
 
199
199
 
200
200
  <div class="method-source-code" id="alternatives-source">
201
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 101</span>
201
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 123</span>
202
202
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">alternatives</span>
203
203
  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>) <span class="ruby-keyword">rescue</span> []
204
204
  <span class="ruby-keyword">end</span></pre>
@@ -230,7 +230,7 @@ href="Vcf.html">Vcf</a> only.</p>
230
230
 
231
231
 
232
232
  <div class="method-source-code" id="gq-source">
233
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 124</span>
233
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 146</span>
234
234
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">gq</span>
235
235
  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">samples</span>[<span class="ruby-string">&quot;1&quot;</span>][<span class="ruby-string">&quot;GQ&quot;</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
236
236
  <span class="ruby-keyword">end</span></pre>
@@ -244,41 +244,42 @@ href="Vcf.html">Vcf</a> only.</p>
244
244
  </div><!-- gq-method -->
245
245
 
246
246
 
247
- <div id="method-i-has_just_one_variant-3F" class="method-detail ">
247
+ <div id="method-i-is_indel-3F" class="method-detail ">
248
248
 
249
249
  <div class="method-heading">
250
- <span class="method-name">has_just_one_variant?</span><span
251
- class="method-args">()</span>
250
+ <span class="method-name">is_indel?</span><span
251
+ class="method-args">(options)</span>
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252
  <span class="method-click-advice">click to toggle source</span>
253
253
  </div>
254
254
 
255
255
 
256
256
  <div class="method-description">
257
257
 
258
- <p>Returns true if only one variant allele is recorded. Loci with more than
259
- one allele are too complicated for now, so are discarded…</p>
258
+ <p>Returns true if ref col is different in length from any of the entries in
259
+ alt column</p>
260
260
 
261
261
 
262
262
 
263
- <div class="method-source-code" id="has_just_one_variant-3F-source">
264
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 134</span>
265
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">has_just_one_variant?</span>
266
- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">variant?</span>
263
+ <div class="method-source-code" id="is_indel-3F-source">
264
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 186</span>
265
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_indel?</span>(<span class="ruby-identifier">options</span>)
266
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">variant?</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">any?</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">!=</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span>} <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>)
267
+ <span class="ruby-keyword">false</span>
267
268
  <span class="ruby-keyword">end</span></pre>
268
- </div><!-- has_just_one_variant-3F-source -->
269
+ </div><!-- is_indel-3F-source -->
269
270
 
270
271
  </div>
271
272
 
272
273
 
273
274
 
274
275
 
275
- </div><!-- has_just_one_variant-3F-method -->
276
+ </div><!-- is_indel-3F-method -->
276
277
 
277
278
 
278
- <div id="method-i-is_deletion-3F" class="method-detail ">
279
+ <div id="method-i-is_mnp-3F" class="method-detail ">
279
280
 
280
281
  <div class="method-heading">
281
- <span class="method-name">is_deletion?</span><span
282
+ <span class="method-name">is_mnp?</span><span
282
283
  class="method-args">(options)</span>
283
284
  <span class="method-click-advice">click to toggle source</span>
284
285
  </div>
@@ -286,107 +287,56 @@ one allele are too complicated for now, so are discarded…</p>
286
287
 
287
288
  <div class="method-description">
288
289
 
289
- <p>Returns true if the length of the alt column is less than that of the ref
290
- column in the <a href="Vcf.html">Vcf</a> and if <a
291
- href="Vcf.html#method-i-pass_quality-3F">#pass_quality?</a> is true. Looks
292
- only at the positions that are predicted simple deletions, any positions
293
- where the alt alleles includes more than one deletion or a SNP or an
294
- insertion also is ignored.</p>
290
+ <p>returns true if ref col has same length as all alternatives and position
291
+ variant passes quality</p>
295
292
 
296
293
 
297
294
 
298
- <div class="method-source-code" id="is_deletion-3F-source">
299
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 153</span>
300
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_deletion?</span>(<span class="ruby-identifier">options</span>)
301
- <span class="ruby-keyword">case</span>
302
- <span class="ruby-keyword">when</span> (<span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">has_just_one_variant?</span>) <span class="ruby-keyword">then</span> <span class="ruby-keyword">false</span>
303
- <span class="ruby-keyword">when</span> ( <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">&lt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>) ) <span class="ruby-keyword">then</span> <span class="ruby-keyword">true</span>
304
- <span class="ruby-keyword">else</span> <span class="ruby-keyword">false</span>
305
- <span class="ruby-keyword">end</span>
306
- <span class="ruby-keyword">rescue</span> <span class="ruby-comment">## if something goes wrong, skip the postion, </span>
295
+ <div class="method-source-code" id="is_mnp-3F-source">
296
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 174</span>
297
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_mnp?</span>(<span class="ruby-identifier">options</span>)
298
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alternatives</span>.<span class="ruby-identifier">all?</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">x</span><span class="ruby-operator">|</span> <span class="ruby-identifier">x</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span>} <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>)
307
299
  <span class="ruby-keyword">false</span>
308
300
  <span class="ruby-keyword">end</span></pre>
309
- </div><!-- is_deletion-3F-source -->
301
+ </div><!-- is_mnp-3F-source -->
310
302
 
311
303
  </div>
312
304
 
313
305
 
314
306
 
315
307
 
316
- </div><!-- is_deletion-3F-method -->
308
+ </div><!-- is_mnp-3F-method -->
317
309
 
318
310
 
319
- <div id="method-i-is_indel-3F" class="method-detail ">
311
+ <div id="method-i-is_snp-3F" class="method-detail ">
320
312
 
321
313
  <div class="method-heading">
322
- <span class="method-name">is_indel?</span><span
323
- class="method-args">(opts)</span>
314
+ <span class="method-name">is_snp?</span><span
315
+ class="method-args">(options)</span>
324
316
  <span class="method-click-advice">click to toggle source</span>
325
317
  </div>
326
318
 
327
319
 
328
320
  <div class="method-description">
329
321
 
330
- <p>Returns true if either <a
331
- href="Vcf.html#method-i-is_insertion-3F">#is_insertion?</a> or <a
332
- href="Vcf.html#method-i-is_deletion-3F">#is_deletion?</a> is true</p>
322
+ <p>returns true if ref col has length of 1 and is_mnp?</p>
333
323
 
334
324
 
335
325
 
336
- <div class="method-source-code" id="is_indel-3F-source">
337
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 176</span>
338
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_indel?</span>(<span class="ruby-identifier">opts</span>)
339
- <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_insertion?</span>(<span class="ruby-identifier">opts</span>) <span class="ruby-operator">||</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_deletion?</span>(<span class="ruby-identifier">opts</span>)
340
- <span class="ruby-keyword">end</span></pre>
341
- </div><!-- is_indel-3F-source -->
342
-
343
- </div>
344
-
345
-
346
-
347
-
348
- </div><!-- is_indel-3F-method -->
349
-
350
-
351
- <div id="method-i-is_insertion-3F" class="method-detail ">
352
-
353
- <div class="method-heading">
354
- <span class="method-name">is_insertion?</span><span
355
- class="method-args">(options)</span>
356
- <span class="method-click-advice">click to toggle source</span>
357
- </div>
358
-
359
-
360
- <div class="method-description">
361
-
362
- <p>Returns true if the length of the alt column is greater than that of the
363
- ref column in the <a href="Vcf.html">Vcf</a> and if <a
364
- href="Vcf.html#method-i-pass_quality-3F">#pass_quality?</a> is true. Looks
365
- only at the positions that are predicted simple deletions, any positions
366
- where the alt alleles includes more than one deletion or a SNP or an
367
- insertion also is ignored.</p>
368
-
369
-
370
-
371
- <div class="method-source-code" id="is_insertion-3F-source">
372
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 165</span>
373
- <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_insertion?</span>(<span class="ruby-identifier">options</span>)
374
- <span class="ruby-keyword">case</span>
375
- <span class="ruby-keyword">when</span> (<span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">has_just_one_variant?</span>) <span class="ruby-keyword">then</span> <span class="ruby-keyword">false</span>
376
- <span class="ruby-keyword">when</span> ( <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">&gt;</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>) ) <span class="ruby-keyword">then</span> <span class="ruby-keyword">true</span>
377
- <span class="ruby-keyword">else</span> <span class="ruby-keyword">false</span>
378
- <span class="ruby-keyword">end</span>
379
- <span class="ruby-keyword">rescue</span> <span class="ruby-comment">## if something goes wrong, skip the postion, </span>
380
- <span class="ruby-keyword">false</span>
326
+ <div class="method-source-code" id="is_snp-3F-source">
327
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 180</span>
328
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">is_snp?</span>(<span class="ruby-identifier">options</span>)
329
+ <span class="ruby-keyword">return</span> <span class="ruby-keyword">true</span> <span class="ruby-keyword">if</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">is_mnp?</span>(<span class="ruby-identifier">options</span>) <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ref</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">==</span> <span class="ruby-value">1</span>
330
+ <span class="ruby-keyword">false</span>
381
331
  <span class="ruby-keyword">end</span></pre>
382
- </div><!-- is_insertion-3F-source -->
332
+ </div><!-- is_snp-3F-source -->
383
333
 
384
334
  </div>
385
335
 
386
336
 
387
337
 
388
338
 
389
- </div><!-- is_insertion-3F-method -->
339
+ </div><!-- is_snp-3F-method -->
390
340
 
391
341
 
392
342
  <div id="method-i-mq" class="method-detail ">
@@ -406,7 +356,7 @@ defined by the <a href="Vcf.html">Vcf</a> MQ attribute.</p>
406
356
 
407
357
 
408
358
  <div class="method-source-code" id="mq-source">
409
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 119</span>
359
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 141</span>
410
360
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">mq</span>
411
361
  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;MQ&quot;</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
412
362
  <span class="ruby-keyword">end</span></pre>
@@ -437,7 +387,7 @@ of the last two figures in the DP4 attribute.</p>
437
387
 
438
388
 
439
389
  <div class="method-source-code" id="non_ref_allele_count-source">
440
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 106</span>
390
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 128</span>
441
391
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_count</span>
442
392
  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;DP4&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>)[<span class="ruby-value">2</span><span class="ruby-operator">..</span><span class="ruby-value">3</span>].<span class="ruby-identifier">inject</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>,<span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">to_f</span> } <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
443
393
  <span class="ruby-keyword">end</span></pre>
@@ -472,7 +422,7 @@ the genotype call,</p>
472
422
 
473
423
 
474
424
  <div class="method-source-code" id="non_ref_allele_freq-source">
475
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 114</span>
425
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 136</span>
476
426
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">non_ref_allele_freq</span>
477
427
  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_allele_count</span> <span class="ruby-operator">/</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">used_depth</span>
478
428
  <span class="ruby-keyword">end</span></pre>
@@ -510,15 +460,15 @@ the genotype call,</p>
510
460
 
511
461
  <p>Example</p>
512
462
 
513
- <pre class="ruby"><span class="ruby-identifier">vcf</span>.<span class="ruby-identifier">pass_quality?</span>(:<span class="ruby-identifier">min_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span>, :<span class="ruby-identifier">min_non_ref_count</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">2</span>, :<span class="ruby-identifier">mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">25</span>)
463
+ <pre class="ruby"><span class="ruby-identifier">vcf</span>.<span class="ruby-identifier">pass_quality?</span>(:<span class="ruby-identifier">min_depth</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">5</span>, :<span class="ruby-identifier">min_non_ref_count</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">2</span>, :<span class="ruby-identifier">mapping_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">25</span>, :<span class="ruby-identifier">min_snp_quality</span> =<span class="ruby-operator">&gt;</span> <span class="ruby-value">20</span>)
514
464
  </pre>
515
465
 
516
466
 
517
467
 
518
468
  <div class="method-source-code" id="pass_quality-3F-source">
519
- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 147</span>
469
+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 169</span>
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470
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">pass_quality?</span>(<span class="ruby-identifier">options</span>)
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- (<span class="ruby-keyword">self</span>.<span class="ruby-identifier">used_depth</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mq</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:mapping_quality</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_allele_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_non_ref_count</span>])
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+ (<span class="ruby-keyword">self</span>.<span class="ruby-identifier">used_depth</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_depth</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">mq</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:mapping_quality</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">non_ref_allele_count</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_non_ref_count</span>] <span class="ruby-keyword">and</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">qual</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:min_snp_quality</span>])
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  <span class="ruby-keyword">end</span></pre>
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  </div><!-- pass_quality-3F-source -->
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@@ -548,7 +498,7 @@ sample in the <a href="Vcf.html">Vcf</a> only.</p>
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  <div class="method-source-code" id="pl-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 129</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 151</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">pl</span>
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  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">samples</span>[<span class="ruby-string">&quot;1&quot;</span>][<span class="ruby-string">&quot;PL&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>)[<span class="ruby-value">1</span>].<span class="ruby-identifier">to_f</span> <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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  <span class="ruby-keyword">end</span></pre>
@@ -580,7 +530,7 @@ href="Vcf.html">Vcf</a> object.</p>
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  <div class="method-source-code" id="to_s-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 85</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 107</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
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  <span class="ruby-node">&quot;#{self.chrom} #{self.pos} #{self.ref} #{self.alt} #{self.info}&quot;</span>
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  <span class="ruby-keyword">end</span></pre>
@@ -611,7 +561,7 @@ of the DP4 attribute. Returns 0.0 if no value is calculated.</p>
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  <div class="method-source-code" id="used_depth-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 90</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 112</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">used_depth</span>
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  <span class="ruby-keyword">self</span>.<span class="ruby-identifier">info</span>[<span class="ruby-string">&quot;DP4&quot;</span>].<span class="ruby-identifier">split</span>(<span class="ruby-string">&quot;,&quot;</span>).<span class="ruby-identifier">inject</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">sum</span>,<span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">sum</span>.<span class="ruby-identifier">to_f</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">to_f</span>} <span class="ruby-keyword">rescue</span> <span class="ruby-value">0.0</span>
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  <span class="ruby-keyword">end</span></pre>
@@ -654,7 +604,7 @@ href="Vcf.html">Vcf</a> is not <strong>.</strong></p>
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  <div class="method-source-code" id="variant-3F-source">
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- <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 80</span>
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+ <pre><span class="ruby-comment"># File lib/bio/util/bio-gngm.rb, line 102</span>
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  <span class="ruby-keyword">def</span> <span class="ruby-identifier">variant?</span>
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  <span class="ruby-keyword">not</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">alt</span> <span class="ruby-operator">==</span> <span class="ruby-string">&quot;.&quot;</span> <span class="ruby-keyword">rescue</span> <span class="ruby-keyword">false</span>
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  <span class="ruby-keyword">end</span></pre>
@@ -677,7 +627,7 @@ href="Vcf.html">Vcf</a> is not <strong>.</strong></p>
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  <footer id="validator-badges">
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  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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  </footer>
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