RubyGems - bio-samtools - Versions diffs - 0.5.3 → 0.6.0 - Mend

bio-samtools 0.5.3 → 0.6.0

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Files changed (29) hide show

data/VERSION +1 -1
data/bio-samtools.gemspec +12 -15
data/doc/Bio.html +7 -7
data/doc/Bio/DB.html +2 -2
data/doc/Bio/DB/Alignment.html +6 -6
data/doc/Bio/DB/Pileup.html +190 -7
data/doc/Bio/DB/SAM.html +58 -22
data/doc/Bio/DB/SAM/Library.html +7 -7
data/doc/Bio/DB/SAM/Tools.html +2 -2
data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +2 -2
data/doc/Bio/DB/SAM/Tools/Bam1T.html +2 -2
data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +2 -2
data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +2 -2
data/doc/Bio/DB/SAM/Tools/SamfileT.html +2 -2
data/doc/Bio/DB/SAM/Tools/SamfileTX.html +2 -2
data/doc/Bio/DB/SAMException.html +3 -3
data/doc/Bio/DB/Tag.html +3 -3
data/doc/Bio/DB/Vcf.html +5 -5
data/doc/LICENSE_txt.html +58 -55
data/doc/LibC.html +2 -2
data/doc/created.rid +7 -7
data/doc/index.html +1 -1
data/doc/js/search_index.js +1 -1
data/doc/lib/bio/db/pileup_rb.html +5 -5
data/doc/table_of_contents.html +19 -9
data/lib/bio/db/pileup.rb +113 -3
data/lib/bio/db/sam.rb +8 -2
data/test/test_basic.rb +9 -0
metadata +67 -22

data/doc/LibC.html CHANGED Viewed

@@ -4,7 +4,7 @@
 <head>
 <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
-<title>Module: LibC</title>
+<title>module LibC - Pileup</title>
 <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
@@ -149,7 +149,7 @@
 <footer id="validator-badges">
   <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
-  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
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data/doc/created.rid CHANGED Viewed

@@ -1,10 +1,10 @@
-Fri, 13 Jan 2012 10:07:15 +0000
-./lib/bio/db/pileup.rb	Thu, 12 Jan 2012 15:37:18 +0000
+Mon, 26 Nov 2012 21:26:40 +0000
+./LICENSE.txt	Wed, 02 Nov 2011 11:50:27 +0000
+./lib/bio/db/sam.rb	Mon, 26 Nov 2012 12:30:26 +0000
 ./lib/bio/db/sam/bam.rb	Thu, 12 Jan 2012 15:31:33 +0000
-./lib/bio/db/sam/faidx.rb	Wed, 02 Nov 2011 11:50:27 +0000
-./lib/bio/db/sam/library.rb	Wed, 02 Nov 2011 13:28:41 +0000
-./lib/bio/db/sam/sam.rb	Mon, 07 Nov 2011 10:04:59 +0000
-./lib/bio/db/sam.rb	Thu, 12 Jan 2012 15:38:07 +0000
 ./lib/bio/db/vcf.rb	Thu, 12 Jan 2012 15:52:37 +0000
+./lib/bio/db/sam/sam.rb	Mon, 07 Nov 2011 10:04:59 +0000
+./lib/bio/db/sam/faidx.rb	Wed, 02 Nov 2011 11:50:27 +0000
+./lib/bio/db/pileup.rb	Mon, 26 Nov 2012 21:21:33 +0000
 ./lib/bio-samtools.rb	Wed, 02 Nov 2011 16:15:52 +0000
-./LICENSE.txt	Wed, 02 Nov 2011 11:50:27 +0000
+./lib/bio/db/sam/library.rb	Wed, 02 Nov 2011 13:28:41 +0000

data/doc/index.html CHANGED Viewed

@@ -106,7 +106,7 @@
 <footer id="validator-badges">
   <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
-  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated 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/js/search_index.js CHANGED Viewed

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Initialize expects a hash optsa with the\nfollowing elemets:\n<p>fasta — The fasta …\n"],["new","Bio::DB::Vcf","Bio/DB/Vcf.html#method-c-new","(line=nil, sample_names=nil)","<p>create the vcf object, use the ordered list of sample names to label\nsamples if provided [‘A’, ‘B’, ‘C’], …\n"],["non_ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-non_ref_count","()","<p>returns the total non-reference bases in the reads at this position\n"],["non_refs","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-non_refs","()","<p>Calculate the total count of each non-reference nucleotide and return a\nhash of all 4 nt counts, returns …\n"],["open","Bio::DB::Sam","Bio/DB/Sam.html#method-i-open","()","<p>Function that actually opens the sam file Throws a SAMException if the file\ncan’t be open.\n"],["parse_line","Bio::DB::Vcf","Bio/DB/Vcf.html#method-i-parse_line","(line, sample_names=nil)","<p>gets the info in the Vcf lines and parses it, setting the attributes\n"],["qname","Bio::DB::SAM::Tools::Bam1T","Bio/DB/SAM/Tools/Bam1T.html#method-i-qname","()",""],["query_string","Bio::DB::Sam","Bio/DB/Sam.html#method-i-query_string","(chromosome, qstart,qend)","<p>Generates a query sting to be used by the region parser in samtools. In\nprinciple, you shouldn’t need …\n"],["ref_count","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-ref_count","()","<p>returns the count of reference-bases in the reads at this position\n"],["sam=","Bio::DB::Alignment","Bio/DB/Alignment.html#method-i-sam-3D","(sam)",""],["set","Bio::DB::Alignment","Bio/DB/Alignment.html#method-i-set","(bam_alignment, header)",""],["set","Bio::DB::Tag","Bio/DB/Tag.html#method-i-set","(str)",""],["text","Bio::DB::SAM::Tools::BamHeaderT","Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text","()",""],["text=","Bio::DB::SAM::Tools::BamHeaderT","Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text-3D","(str)",""],["to_s","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_s","()","<p>returns pileup format line as\n"],["to_s","Bio::DB::Sam","Bio/DB/Sam.html#method-i-to_s","()","<p>Prints a description of the sam file in a text format containg if it is\nbinary or text, the path and …\n"],["to_vcf","Bio::DB::Pileup","Bio/DB/Pileup.html#method-i-to_vcf","()","<p>returns basic VCF string as per samtools/misc sam2vcf.pl except that it\nscrimps on the ref for indels, …\n"],["LICENSE","","LICENSE_txt.html","","<p>Copyright © 2011 Raoul J.P. Bonnal\n<p>Permission is hereby granted, free of charge, to any person obtaining …\n"]]}}

data/doc/lib/bio/db/pileup_rb.html CHANGED Viewed

@@ -151,13 +151,13 @@ the 1st indel allele otherwise</p>
 <p>(13) indel line only: # reads supporting a third indel allele</p>
 </li></ul>
-<p>If pileup is invoked without `-c’, indel lines and columns between 3 and 7
-inclusive will not be outputted.</p>
+<p>If pileup is invoked without `-c’, indel lines and columns between 3 and
+7 inclusive will not be outputted.</p>
 <p>NB mpileup uses the 6 column output format eg
-“seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
-provides accessors for all columns (6 or 10 column format) and a few other
-useful methods</p>
+“seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;”
+Pileup provides accessors for all columns (6 or 10 column format) and a few
+other useful methods</p>
 </div>

data/doc/table_of_contents.html CHANGED Viewed

@@ -4,7 +4,7 @@
 <head>
 <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
-<title>Table of Contents</title>
+<title>Table of Contents - Pileup</title>
 <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
@@ -21,7 +21,7 @@
 <body class="indexpage">
-<h1>Table of Contents</h1>
+<h1>Table of Contents - Pileup</h1>
 <h2>Pages</h2>
 <ul>
@@ -101,17 +101,19 @@
     <li class="method"><a href="Bio/DB/Sam.html#method-c-finalize">::finalize &mdash; Bio::DB::Sam</a>
-    <li class="method"><a href="Bio/DB/Sam.html#method-c-merge">::merge &mdash; Bio::DB::Sam</a>
+    <li class="method"><a href="Bio/DB/Pileup.html#method-c-iupac_to_base">::iupac_to_base &mdash; Bio::DB::Pileup</a>
-    <li class="method"><a href="Bio/DB/Alignment.html#method-c-new">::new &mdash; Bio::DB::Alignment</a>
+    <li class="method"><a href="Bio/DB/Sam.html#method-c-merge">::merge &mdash; Bio::DB::Sam</a>
-    <li class="method"><a href="Bio/DB/Vcf.html#method-c-new">::new &mdash; Bio::DB::Vcf</a>
+    <li class="method"><a href="Bio/DB/Pileup.html#method-c-new">::new &mdash; Bio::DB::Pileup</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-c-new">::new &mdash; Bio::DB::Sam</a>
+    <li class="method"><a href="Bio/DB/Alignment.html#method-c-new">::new &mdash; Bio::DB::Alignment</a>
     <li class="method"><a href="Bio/DB/SAMException.html#method-c-new">::new &mdash; Bio::DB::SAMException</a>
-    <li class="method"><a href="Bio/DB/Pileup.html#method-c-new">::new &mdash; Bio::DB::Pileup</a>
+    <li class="method"><a href="Bio/DB/Vcf.html#method-c-new">::new &mdash; Bio::DB::Vcf</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-average_coverage">#average_coverage &mdash; Bio::DB::Sam</a>
@@ -121,12 +123,16 @@
     <li class="method"><a href="Bio/DB/Sam.html#method-i-deprecated_pileup">#deprecated_pileup &mdash; Bio::DB::Sam</a>
+    <li class="method"><a href="Bio/DB/Sam.html#method-i-each_reference">#each_reference &mdash; Bio::DB::Sam</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch">#fetch &mdash; Bio::DB::Sam</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch_reference">#fetch_reference &mdash; Bio::DB::Sam</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch_with_function">#fetch_with_function &mdash; Bio::DB::Sam</a>
+    <li class="method"><a href="Bio/DB/Pileup.html#method-i-genotype_list">#genotype_list &mdash; Bio::DB::Pileup</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-index_stats">#index_stats &mdash; Bio::DB::Sam</a>
     <li class="method"><a href="Bio/DB/Vcf.html#method-i-int_or_raw">#int_or_raw &mdash; Bio::DB::Vcf</a>
@@ -155,22 +161,26 @@
     <li class="method"><a href="Bio/DB/Alignment.html#method-i-sam-3D">#sam= &mdash; Bio::DB::Alignment</a>
-    <li class="method"><a href="Bio/DB/Alignment.html#method-i-set">#set &mdash; Bio::DB::Alignment</a>
     <li class="method"><a href="Bio/DB/Tag.html#method-i-set">#set &mdash; Bio::DB::Tag</a>
+    <li class="method"><a href="Bio/DB/Alignment.html#method-i-set">#set &mdash; Bio::DB::Alignment</a>
     <li class="method"><a href="Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text">#text &mdash; Bio::DB::SAM::Tools::BamHeaderT</a>
     <li class="method"><a href="Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text-3D">#text= &mdash; Bio::DB::SAM::Tools::BamHeaderT</a>
+    <li class="method"><a href="Bio/DB/Pileup.html#method-i-to_s">#to_s &mdash; Bio::DB::Pileup</a>
     <li class="method"><a href="Bio/DB/Sam.html#method-i-to_s">#to_s &mdash; Bio::DB::Sam</a>
+    <li class="method"><a href="Bio/DB/Pileup.html#method-i-to_vcf">#to_vcf &mdash; Bio::DB::Pileup</a>
 </ul>
 <footer id="validator-badges">
   <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
-  <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
+  <p>Generated 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/lib/bio/db/pileup.rb CHANGED Viewed

@@ -27,7 +27,7 @@
 module Bio
   class DB
 class Pileup
-  attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3
+  attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3, :indel_1, :indel_2
   #creates the Pileup object
   #    pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
@@ -37,7 +37,11 @@ class Pileup
     if cols.length == 6 ##should only be able to get 6 lines from mpileup
       @ref_name, @pos, @ref_base, @coverage, @read_bases, @read_quals = cols
     elsif (10..13).include?(cols.length) ##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...
-      @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @read_bases, @read_quals, @ar1, @ar2, @ar3 = cols
+      if cols[2] == '*' #indel
+        @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @indel_1, @indel_2, @ar1, @ar2, @ar3 = cols
+      else #snp / identity
+        @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @read_bases, @read_quals = cols
+      end
       @consensus_quality = @consensus_quality.to_f
       @snp_quality = @snp_quality.to_f
       @rms_mapq = @rms_mapq.to_f
@@ -77,7 +81,7 @@ class Pileup
     @ref_count
   end
-  # returns the consensus (most frequent) base from the pileup, if there are equally represented bases returns a string containing all equally represented bases in alphabetical order
+  # returns the consensus (most frequent) base from the pileup, if there are equally represented bases returns a string of all equally represented bases in alphabetical order
   def consensus
       if @consensus.nil?
         max = self.non_refs.values.max
@@ -95,6 +99,112 @@ class Pileup
       @consensus
   end
+  #returns basic VCF string as per samtools/misc sam2vcf.pl except that it scrimps on the ref for indels, returning a '*' instead of the reference allele
+  def to_vcf
+    alt,g = self.genotype_list
+    alt = self.consensus.split(//).join(',') unless self.ref_base == '*'
+    alt = '.' if alt == self.ref_base
+    [self.ref_name, self.pos, '.', self.ref_base, alt, self.snp_quality.to_i, "0", "DP=#{self.coverage.to_i}", "GT:GQ:DP", "#{g}:#{self.consensus_quality.to_i}:#{self.coverage.to_i}" ].join("\t")
+  end
+  private
+  def Pileup.vcf_header
+    %{##fileformat=VCFv3.3
+      ##INFO=DP,1,Integer,"Total Depth"
+      ##FORMAT=GT,1,String,"Genotype"
+      ##FORMAT=GQ,1,Integer,"Genotype Quality"
+      ##FORMAT=DP,1,Integer,"Read Depth"
+      #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tDATA
+    }.join("\n")
+  end
+  def parse_indel(alt)
+    return "D#{$'.length}" if alt =~/^-/
+    if alt=~/^\+/
+      return "I#{$'}"
+    elsif alt == '*'
+      return nil
+     end
+  end
+  def indel_gt
+    return "undef" if self.consensus.instance_of?(Array)
+    al1, al2 = self.consensus.split(/\//)
+    if al1 == al2 && al1 == '*'
+      al1=self.indel_1
+      al2=self.indel_2
+    end
+    alt1 = parse_indel(al1)
+    alt2 = parse_indel(al2)
+    alt,gt = nil,nil
+    return nil if !alt1 and !alt2
+    if !alt1
+      alt = alt2
+      gt = '0/1'
+    elsif !alt2
+      alt = alt1
+      gt - '0/1'
+    elsif alt1 == alt2
+      alt = alt1
+      gt = '1/1'
+    else
+      alt="#{alt1},#{alt2}"
+      gt= '1/2'
+    end
+    return [alt, gt]
+  end
+  def snp_gt
+    return ['.','0/0'] if self.ref_base == self.consensus
+    bases = Pileup.iupac_to_base(self.consensus)
+    if bases[0] == self.ref_base
+       return [bases[1],'0/1']
+    elsif bases[1] == self.ref_base
+       return [bases[0],'0/1']
+    else
+      return ["#{bases[0]},#{bases[1]}",'1/2']
+    end
+  end
+  public
+  def genotype_list
+    if self.ref_base == '*'
+      return indel_gt
+    else
+     return snp_gt
+   end
+  end
+  public
+  #returns
+  def Pileup.iupac_to_base(alt_base)
+      case alt_base
+            when 'K' then ['G','T']
+            when 'M' then ['A','C']
+            when 'S' then ['C','G']
+            when 'R' then ['A','G']
+            when 'W' then ['A','T']
+            when 'Y' then ['C','T']
+            else alt_base.split(//)
+      end
+  end
+  #returns pileup format line
+  def to_s
+    if @read_quals and !@consensus_quality #6col
+      [@ref_name, @pos, @ref_base, @coverage.to_i, @read_bases, @read_quals].join("\t")
+    elsif @indel_1 #13 cols
+      [@ref_name, @pos, @ref_base, @consensus, @consensus_quality.to_i, @snp_quality.to_i, @rms_mapq.to_i, @coverage.to_i, @indel_1, @indel_2, @ar1, @ar2, @ar3].join("\t")
+    else #10 cols
+      [@ref_name, @pos, @ref_base, @consensus, @consensus_quality.to_i, @snp_quality.to_i, @rms_mapq.to_i, @coverage.to_i, @read_bases, @read_quals].join("\t")
+    end
+  end
 end
 end
 end

data/lib/bio/db/sam.rb CHANGED Viewed

@@ -278,7 +278,7 @@ module Bio
       #the command line options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p)
       #call the option as a symbol of the flag, eg -r for region is called :r => "some SAM compatible region"
       #eg bam.mpileup(:r => "chr1:1000-2000", :q => 50) gets the bases with quality > 50 on chr1 between 1000-5000
-      def mpileup( opts )
+      def mpileup( opts={})
               raise SAMException.new(), "No BAMFile provided" unless @sam and @binary
               raise SAMException.new(), "No FastA provided" unless @fasta_path
@@ -531,7 +531,13 @@ module Bio
         index_stats
       end
+      ##yields each reference name and its length
+      def each_reference
+        refs = index_stats
+        refs.each_pair do |k, v|
+          yield k, v[:length]
+        end
+      end
     end

data/test/test_basic.rb CHANGED Viewed

@@ -329,6 +329,15 @@ class TestBioDbSam < Test::Unit::TestCase
                   "*"=>{:length=>0, :mapped_reads=>0, :unmapped_reads=>0}
                  }, sam.index_stats)
   end
+  def test_each_reference
+    sam = Bio::DB::Sam.new(:bam => @testBAMFile, :fasta => @testReference)
+    sam.each_reference do |name, length|
+      next if name == '*'
+      assert_equal name, "chr_1"
+      assert_equal length, 69930
+    end
+  end
 end
 class Feature

metadata CHANGED Viewed

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 0.5.3
+  version: 0.6.0
   prerelease:
 platform: ruby
 authors:
@@ -11,11 +11,11 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2012-04-14 00:00:00.000000000Z
+date: 2012-12-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2155890140 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -23,10 +23,15 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2155890140
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2153046360 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -34,10 +39,15 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2153046360
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2153045200 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -45,10 +55,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153045200
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2153043840 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -56,10 +71,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2153043840
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2153042320 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -67,10 +87,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153042320
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2153039920 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -78,10 +103,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153039920
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2153031660 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -89,10 +119,15 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2153031660
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2153030200 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -100,10 +135,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153030200
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &2153028420 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -111,7 +151,12 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2153028420
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: ! "Binder of samtools for ruby, on the top of FFI. \n\n  This project
   was born from the need to add support of BAM files to \n  the gee_fu genome browser
   (http://github.com/danmaclean/gee_fu)."
@@ -310,7 +355,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2712419178803943908
+      hash: 2827091236033561121
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -319,7 +364,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project:
-rubygems_version: 1.8.6
+rubygems_version: 1.8.24
 signing_key:
 specification_version: 3
 summary: Binder of samtools for ruby, on the top of FFI.