bio-samtools 0.5.3 → 0.6.0

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  1. data/VERSION +1 -1
  2. data/bio-samtools.gemspec +12 -15
  3. data/doc/Bio.html +7 -7
  4. data/doc/Bio/DB.html +2 -2
  5. data/doc/Bio/DB/Alignment.html +6 -6
  6. data/doc/Bio/DB/Pileup.html +190 -7
  7. data/doc/Bio/DB/SAM.html +58 -22
  8. data/doc/Bio/DB/SAM/Library.html +7 -7
  9. data/doc/Bio/DB/SAM/Tools.html +2 -2
  10. data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +2 -2
  11. data/doc/Bio/DB/SAM/Tools/Bam1T.html +2 -2
  12. data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +2 -2
  13. data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +2 -2
  14. data/doc/Bio/DB/SAM/Tools/SamfileT.html +2 -2
  15. data/doc/Bio/DB/SAM/Tools/SamfileTX.html +2 -2
  16. data/doc/Bio/DB/SAMException.html +3 -3
  17. data/doc/Bio/DB/Tag.html +3 -3
  18. data/doc/Bio/DB/Vcf.html +5 -5
  19. data/doc/LICENSE_txt.html +58 -55
  20. data/doc/LibC.html +2 -2
  21. data/doc/created.rid +7 -7
  22. data/doc/index.html +1 -1
  23. data/doc/js/search_index.js +1 -1
  24. data/doc/lib/bio/db/pileup_rb.html +5 -5
  25. data/doc/table_of_contents.html +19 -9
  26. data/lib/bio/db/pileup.rb +113 -3
  27. data/lib/bio/db/sam.rb +8 -2
  28. data/test/test_basic.rb +9 -0
  29. metadata +67 -22
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- Fri, 13 Jan 2012 10:07:15 +0000
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- ./lib/bio/db/pileup.rb Thu, 12 Jan 2012 15:37:18 +0000
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+ Mon, 26 Nov 2012 21:26:40 +0000
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+ ./LICENSE.txt Wed, 02 Nov 2011 11:50:27 +0000
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+ ./lib/bio/db/sam.rb Mon, 26 Nov 2012 12:30:26 +0000
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- ./lib/bio/db/sam/faidx.rb Wed, 02 Nov 2011 11:50:27 +0000
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- ./lib/bio/db/sam/library.rb Wed, 02 Nov 2011 13:28:41 +0000
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- ./lib/bio/db/sam/sam.rb Mon, 07 Nov 2011 10:04:59 +0000
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- ./lib/bio/db/sam.rb Thu, 12 Jan 2012 15:38:07 +0000
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  ./lib/bio/db/vcf.rb Thu, 12 Jan 2012 15:52:37 +0000
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+ ./lib/bio/db/sam/sam.rb Mon, 07 Nov 2011 10:04:59 +0000
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+ ./lib/bio/db/sam/faidx.rb Wed, 02 Nov 2011 11:50:27 +0000
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+ ./lib/bio/db/pileup.rb Mon, 26 Nov 2012 21:21:33 +0000
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- ./LICENSE.txt Wed, 02 Nov 2011 11:50:27 +0000
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+ ./lib/bio/db/sam/library.rb Wed, 02 Nov 2011 13:28:41 +0000
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data/doc/js/search_index.js CHANGED
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Initialize expects a hash optsa with the\nfollowing elemets:\n<p>fasta &mdash; 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
@@ -151,13 +151,13 @@ the 1st indel allele otherwise</p>
151
151
  <p>(13) indel line only: # reads supporting a third indel allele</p>
152
152
  </li></ul>
153
153
 
154
- <p>If pileup is invoked without `-c’, indel lines and columns between 3 and 7
155
- inclusive will not be outputted.</p>
154
+ <p>If pileup is invoked without `-c’, indel lines and columns between 3 and
155
+ 7 inclusive will not be outputted.</p>
156
156
 
157
157
  <p>NB mpileup uses the 6 column output format eg
158
- “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;” Pileup
159
- provides accessors for all columns (6 or 10 column format) and a few other
160
- useful methods</p>
158
+ “seq2t151tGtGt36t0t99t12t.….……At:9&lt;;;7=&lt;&lt;&lt;&lt;&lt;”
159
+ Pileup provides accessors for all columns (6 or 10 column format) and a few
160
+ other useful methods</p>
161
161
 
162
162
  </div>
163
163
 
data/doc/table_of_contents.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>Table of Contents</title>
7
+ <title>Table of Contents - Pileup</title>
8
8
 
9
9
  <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
10
10
 
@@ -21,7 +21,7 @@
21
21
 
22
22
 
23
23
  <body class="indexpage">
24
- <h1>Table of Contents</h1>
24
+ <h1>Table of Contents - Pileup</h1>
25
25
 
26
26
  <h2>Pages</h2>
27
27
  <ul>
@@ -101,17 +101,19 @@
101
101
 
102
102
  <li class="method"><a href="Bio/DB/Sam.html#method-c-finalize">::finalize &mdash; Bio::DB::Sam</a>
103
103
 
104
- <li class="method"><a href="Bio/DB/Sam.html#method-c-merge">::merge &mdash; Bio::DB::Sam</a>
104
+ <li class="method"><a href="Bio/DB/Pileup.html#method-c-iupac_to_base">::iupac_to_base &mdash; Bio::DB::Pileup</a>
105
105
 
106
- <li class="method"><a href="Bio/DB/Alignment.html#method-c-new">::new &mdash; Bio::DB::Alignment</a>
106
+ <li class="method"><a href="Bio/DB/Sam.html#method-c-merge">::merge &mdash; Bio::DB::Sam</a>
107
107
 
108
- <li class="method"><a href="Bio/DB/Vcf.html#method-c-new">::new &mdash; Bio::DB::Vcf</a>
108
+ <li class="method"><a href="Bio/DB/Pileup.html#method-c-new">::new &mdash; Bio::DB::Pileup</a>
109
109
 
110
110
  <li class="method"><a href="Bio/DB/Sam.html#method-c-new">::new &mdash; Bio::DB::Sam</a>
111
111
 
112
+ <li class="method"><a href="Bio/DB/Alignment.html#method-c-new">::new &mdash; Bio::DB::Alignment</a>
113
+
112
114
  <li class="method"><a href="Bio/DB/SAMException.html#method-c-new">::new &mdash; Bio::DB::SAMException</a>
113
115
 
114
- <li class="method"><a href="Bio/DB/Pileup.html#method-c-new">::new &mdash; Bio::DB::Pileup</a>
116
+ <li class="method"><a href="Bio/DB/Vcf.html#method-c-new">::new &mdash; Bio::DB::Vcf</a>
115
117
 
116
118
  <li class="method"><a href="Bio/DB/Sam.html#method-i-average_coverage">#average_coverage &mdash; Bio::DB::Sam</a>
117
119
 
@@ -121,12 +123,16 @@
121
123
 
122
124
  <li class="method"><a href="Bio/DB/Sam.html#method-i-deprecated_pileup">#deprecated_pileup &mdash; Bio::DB::Sam</a>
123
125
 
126
+ <li class="method"><a href="Bio/DB/Sam.html#method-i-each_reference">#each_reference &mdash; Bio::DB::Sam</a>
127
+
124
128
  <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch">#fetch &mdash; Bio::DB::Sam</a>
125
129
 
126
130
  <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch_reference">#fetch_reference &mdash; Bio::DB::Sam</a>
127
131
 
128
132
  <li class="method"><a href="Bio/DB/Sam.html#method-i-fetch_with_function">#fetch_with_function &mdash; Bio::DB::Sam</a>
129
133
 
134
+ <li class="method"><a href="Bio/DB/Pileup.html#method-i-genotype_list">#genotype_list &mdash; Bio::DB::Pileup</a>
135
+
130
136
  <li class="method"><a href="Bio/DB/Sam.html#method-i-index_stats">#index_stats &mdash; Bio::DB::Sam</a>
131
137
 
132
138
  <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 @@
155
161
 
156
162
  <li class="method"><a href="Bio/DB/Alignment.html#method-i-sam-3D">#sam= &mdash; Bio::DB::Alignment</a>
157
163
 
158
- <li class="method"><a href="Bio/DB/Alignment.html#method-i-set">#set &mdash; Bio::DB::Alignment</a>
159
-
160
164
  <li class="method"><a href="Bio/DB/Tag.html#method-i-set">#set &mdash; Bio::DB::Tag</a>
161
165
 
166
+ <li class="method"><a href="Bio/DB/Alignment.html#method-i-set">#set &mdash; Bio::DB::Alignment</a>
167
+
162
168
  <li class="method"><a href="Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text">#text &mdash; Bio::DB::SAM::Tools::BamHeaderT</a>
163
169
 
164
170
  <li class="method"><a href="Bio/DB/SAM/Tools/BamHeaderT.html#method-i-text-3D">#text= &mdash; Bio::DB::SAM::Tools::BamHeaderT</a>
165
171
 
172
+ <li class="method"><a href="Bio/DB/Pileup.html#method-i-to_s">#to_s &mdash; Bio::DB::Pileup</a>
173
+
166
174
  <li class="method"><a href="Bio/DB/Sam.html#method-i-to_s">#to_s &mdash; Bio::DB::Sam</a>
167
175
 
176
+ <li class="method"><a href="Bio/DB/Pileup.html#method-i-to_vcf">#to_vcf &mdash; Bio::DB::Pileup</a>
177
+
168
178
  </ul>
169
179
 
170
180
 
171
181
  <footer id="validator-badges">
172
182
  <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
173
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.11.
183
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 3.12.
174
184
  <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
175
185
  </footer>
176
186
 
data/lib/bio/db/pileup.rb CHANGED
@@ -27,7 +27,7 @@
27
27
  module Bio
28
28
  class DB
29
29
  class Pileup
30
- attr_accessor :ref_name, :pos, :ref_base, :coverage, :read_bases, :read_quals, :consensus, :consensus_quality, :snp_quality, :rms_mapq, :ar1, :ar2, :ar3
30
+ 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
31
31
 
32
32
  #creates the Pileup object
33
33
  # pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
@@ -37,7 +37,11 @@ class Pileup
37
37
  if cols.length == 6 ##should only be able to get 6 lines from mpileup
38
38
  @ref_name, @pos, @ref_base, @coverage, @read_bases, @read_quals = cols
39
39
  elsif (10..13).include?(cols.length) ##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...
40
- @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @read_bases, @read_quals, @ar1, @ar2, @ar3 = cols
40
+ if cols[2] == '*' #indel
41
+ @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @indel_1, @indel_2, @ar1, @ar2, @ar3 = cols
42
+ else #snp / identity
43
+ @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @read_bases, @read_quals = cols
44
+ end
41
45
  @consensus_quality = @consensus_quality.to_f
42
46
  @snp_quality = @snp_quality.to_f
43
47
  @rms_mapq = @rms_mapq.to_f
@@ -77,7 +81,7 @@ class Pileup
77
81
  @ref_count
78
82
  end
79
83
 
80
- # 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
84
+ # 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
81
85
  def consensus
82
86
  if @consensus.nil?
83
87
  max = self.non_refs.values.max
@@ -95,6 +99,112 @@ class Pileup
95
99
  @consensus
96
100
  end
97
101
 
102
+ #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
103
+ def to_vcf
104
+
105
+ alt,g = self.genotype_list
106
+ alt = self.consensus.split(//).join(',') unless self.ref_base == '*'
107
+ alt = '.' if alt == self.ref_base
108
+ [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")
109
+ end
110
+
111
+ private
112
+ def Pileup.vcf_header
113
+ %{##fileformat=VCFv3.3
114
+ ##INFO=DP,1,Integer,"Total Depth"
115
+ ##FORMAT=GT,1,String,"Genotype"
116
+ ##FORMAT=GQ,1,Integer,"Genotype Quality"
117
+ ##FORMAT=DP,1,Integer,"Read Depth"
118
+ #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tDATA
119
+ }.join("\n")
120
+ end
121
+
122
+ def parse_indel(alt)
123
+
124
+ return "D#{$'.length}" if alt =~/^-/
125
+ if alt=~/^\+/
126
+ return "I#{$'}"
127
+ elsif alt == '*'
128
+ return nil
129
+ end
130
+ end
131
+
132
+ def indel_gt
133
+ return "undef" if self.consensus.instance_of?(Array)
134
+ al1, al2 = self.consensus.split(/\//)
135
+ if al1 == al2 && al1 == '*'
136
+ al1=self.indel_1
137
+ al2=self.indel_2
138
+ end
139
+ alt1 = parse_indel(al1)
140
+ alt2 = parse_indel(al2)
141
+ alt,gt = nil,nil
142
+
143
+ return nil if !alt1 and !alt2
144
+ if !alt1
145
+ alt = alt2
146
+ gt = '0/1'
147
+ elsif !alt2
148
+ alt = alt1
149
+ gt - '0/1'
150
+ elsif alt1 == alt2
151
+ alt = alt1
152
+ gt = '1/1'
153
+ else
154
+ alt="#{alt1},#{alt2}"
155
+ gt= '1/2'
156
+ end
157
+ return [alt, gt]
158
+
159
+ end
160
+
161
+ def snp_gt
162
+ return ['.','0/0'] if self.ref_base == self.consensus
163
+ bases = Pileup.iupac_to_base(self.consensus)
164
+ if bases[0] == self.ref_base
165
+ return [bases[1],'0/1']
166
+ elsif bases[1] == self.ref_base
167
+ return [bases[0],'0/1']
168
+ else
169
+ return ["#{bases[0]},#{bases[1]}",'1/2']
170
+ end
171
+ end
172
+
173
+ public
174
+ def genotype_list
175
+ if self.ref_base == '*'
176
+ return indel_gt
177
+ else
178
+ return snp_gt
179
+ end
180
+ end
181
+
182
+ public
183
+ #returns
184
+ def Pileup.iupac_to_base(alt_base)
185
+ case alt_base
186
+ when 'K' then ['G','T']
187
+ when 'M' then ['A','C']
188
+ when 'S' then ['C','G']
189
+ when 'R' then ['A','G']
190
+ when 'W' then ['A','T']
191
+ when 'Y' then ['C','T']
192
+ else alt_base.split(//)
193
+ end
194
+ end
195
+
196
+ #returns pileup format line
197
+ def to_s
198
+ if @read_quals and !@consensus_quality #6col
199
+ [@ref_name, @pos, @ref_base, @coverage.to_i, @read_bases, @read_quals].join("\t")
200
+ elsif @indel_1 #13 cols
201
+ [@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")
202
+ else #10 cols
203
+ [@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")
204
+ end
205
+
206
+ end
207
+
98
208
  end
99
209
  end
100
210
  end
data/lib/bio/db/sam.rb CHANGED
@@ -278,7 +278,7 @@ module Bio
278
278
  #the command line options that generate/affect BCF/VCF are ignored ie (g,u,e,h,I,L,o,p)
279
279
  #call the option as a symbol of the flag, eg -r for region is called :r => "some SAM compatible region"
280
280
  #eg bam.mpileup(:r => "chr1:1000-2000", :q => 50) gets the bases with quality > 50 on chr1 between 1000-5000
281
- def mpileup( opts )
281
+ def mpileup( opts={})
282
282
 
283
283
  raise SAMException.new(), "No BAMFile provided" unless @sam and @binary
284
284
  raise SAMException.new(), "No FastA provided" unless @fasta_path
@@ -531,7 +531,13 @@ module Bio
531
531
  index_stats
532
532
  end
533
533
 
534
-
534
+ ##yields each reference name and its length
535
+ def each_reference
536
+ refs = index_stats
537
+ refs.each_pair do |k, v|
538
+ yield k, v[:length]
539
+ end
540
+ end
535
541
 
536
542
  end
537
543
 
data/test/test_basic.rb CHANGED
@@ -329,6 +329,15 @@ class TestBioDbSam < Test::Unit::TestCase
329
329
  "*"=>{:length=>0, :mapped_reads=>0, :unmapped_reads=>0}
330
330
  }, sam.index_stats)
331
331
  end
332
+
333
+ def test_each_reference
334
+ sam = Bio::DB::Sam.new(:bam => @testBAMFile, :fasta => @testReference)
335
+ sam.each_reference do |name, length|
336
+ next if name == '*'
337
+ assert_equal name, "chr_1"
338
+ assert_equal length, 69930
339
+ end
340
+ end
332
341
  end
333
342
 
334
343
  class Feature
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-samtools
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.5.3
4
+ version: 0.6.0
5
5
  prerelease:
6
6
  platform: ruby
7
7
  authors:
@@ -11,11 +11,11 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2012-04-14 00:00:00.000000000Z
14
+ date: 2012-12-03 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: ffi
18
- requirement: &2155890140 !ruby/object:Gem::Requirement
18
+ requirement: !ruby/object:Gem::Requirement
19
19
  none: false
20
20
  requirements:
21
21
  - - ! '>='
@@ -23,10 +23,15 @@ dependencies:
23
23
  version: '0'
24
24
  type: :runtime
25
25
  prerelease: false
26
- version_requirements: *2155890140
26
+ version_requirements: !ruby/object:Gem::Requirement
27
+ none: false
28
+ requirements:
29
+ - - ! '>='
30
+ - !ruby/object:Gem::Version
31
+ version: '0'
27
32
  - !ruby/object:Gem::Dependency
28
33
  name: bio
29
- requirement: &2153046360 !ruby/object:Gem::Requirement
34
+ requirement: !ruby/object:Gem::Requirement
30
35
  none: false
31
36
  requirements:
32
37
  - - ! '>='
@@ -34,10 +39,15 @@ dependencies:
34
39
  version: 1.4.2
35
40
  type: :runtime
36
41
  prerelease: false
37
- version_requirements: *2153046360
42
+ version_requirements: !ruby/object:Gem::Requirement
43
+ none: false
44
+ requirements:
45
+ - - ! '>='
46
+ - !ruby/object:Gem::Version
47
+ version: 1.4.2
38
48
  - !ruby/object:Gem::Dependency
39
49
  name: shoulda
40
- requirement: &2153045200 !ruby/object:Gem::Requirement
50
+ requirement: !ruby/object:Gem::Requirement
41
51
  none: false
42
52
  requirements:
43
53
  - - ! '>='
@@ -45,10 +55,15 @@ dependencies:
45
55
  version: '0'
46
56
  type: :development
47
57
  prerelease: false
48
- version_requirements: *2153045200
58
+ version_requirements: !ruby/object:Gem::Requirement
59
+ none: false
60
+ requirements:
61
+ - - ! '>='
62
+ - !ruby/object:Gem::Version
63
+ version: '0'
49
64
  - !ruby/object:Gem::Dependency
50
65
  name: bundler
51
- requirement: &2153043840 !ruby/object:Gem::Requirement
66
+ requirement: !ruby/object:Gem::Requirement
52
67
  none: false
53
68
  requirements:
54
69
  - - ~>
@@ -56,10 +71,15 @@ dependencies:
56
71
  version: 1.0.0
57
72
  type: :development
58
73
  prerelease: false
59
- version_requirements: *2153043840
74
+ version_requirements: !ruby/object:Gem::Requirement
75
+ none: false
76
+ requirements:
77
+ - - ~>
78
+ - !ruby/object:Gem::Version
79
+ version: 1.0.0
60
80
  - !ruby/object:Gem::Dependency
61
81
  name: jeweler
62
- requirement: &2153042320 !ruby/object:Gem::Requirement
82
+ requirement: !ruby/object:Gem::Requirement
63
83
  none: false
64
84
  requirements:
65
85
  - - ! '>='
@@ -67,10 +87,15 @@ dependencies:
67
87
  version: '0'
68
88
  type: :development
69
89
  prerelease: false
70
- version_requirements: *2153042320
90
+ version_requirements: !ruby/object:Gem::Requirement
91
+ none: false
92
+ requirements:
93
+ - - ! '>='
94
+ - !ruby/object:Gem::Version
95
+ version: '0'
71
96
  - !ruby/object:Gem::Dependency
72
97
  name: rcov
73
- requirement: &2153039920 !ruby/object:Gem::Requirement
98
+ requirement: !ruby/object:Gem::Requirement
74
99
  none: false
75
100
  requirements:
76
101
  - - ! '>='
@@ -78,10 +103,15 @@ dependencies:
78
103
  version: '0'
79
104
  type: :development
80
105
  prerelease: false
81
- version_requirements: *2153039920
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ none: false
108
+ requirements:
109
+ - - ! '>='
110
+ - !ruby/object:Gem::Version
111
+ version: '0'
82
112
  - !ruby/object:Gem::Dependency
83
113
  name: bio
84
- requirement: &2153031660 !ruby/object:Gem::Requirement
114
+ requirement: !ruby/object:Gem::Requirement
85
115
  none: false
86
116
  requirements:
87
117
  - - ! '>='
@@ -89,10 +119,15 @@ dependencies:
89
119
  version: 1.4.2
90
120
  type: :development
91
121
  prerelease: false
92
- version_requirements: *2153031660
122
+ version_requirements: !ruby/object:Gem::Requirement
123
+ none: false
124
+ requirements:
125
+ - - ! '>='
126
+ - !ruby/object:Gem::Version
127
+ version: 1.4.2
93
128
  - !ruby/object:Gem::Dependency
94
129
  name: ffi
95
- requirement: &2153030200 !ruby/object:Gem::Requirement
130
+ requirement: !ruby/object:Gem::Requirement
96
131
  none: false
97
132
  requirements:
98
133
  - - ! '>='
@@ -100,10 +135,15 @@ dependencies:
100
135
  version: '0'
101
136
  type: :development
102
137
  prerelease: false
103
- version_requirements: *2153030200
138
+ version_requirements: !ruby/object:Gem::Requirement
139
+ none: false
140
+ requirements:
141
+ - - ! '>='
142
+ - !ruby/object:Gem::Version
143
+ version: '0'
104
144
  - !ruby/object:Gem::Dependency
105
145
  name: rdoc
106
- requirement: &2153028420 !ruby/object:Gem::Requirement
146
+ requirement: !ruby/object:Gem::Requirement
107
147
  none: false
108
148
  requirements:
109
149
  - - ! '>='
@@ -111,7 +151,12 @@ dependencies:
111
151
  version: '0'
112
152
  type: :development
113
153
  prerelease: false
114
- version_requirements: *2153028420
154
+ version_requirements: !ruby/object:Gem::Requirement
155
+ none: false
156
+ requirements:
157
+ - - ! '>='
158
+ - !ruby/object:Gem::Version
159
+ version: '0'
115
160
  description: ! "Binder of samtools for ruby, on the top of FFI. \n\n This project
116
161
  was born from the need to add support of BAM files to \n the gee_fu genome browser
117
162
  (http://github.com/danmaclean/gee_fu)."
@@ -310,7 +355,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
310
355
  version: '0'
311
356
  segments:
312
357
  - 0
313
- hash: -2712419178803943908
358
+ hash: 2827091236033561121
314
359
  required_rubygems_version: !ruby/object:Gem::Requirement
315
360
  none: false
316
361
  requirements:
@@ -319,7 +364,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
319
364
  version: '0'
320
365
  requirements: []
321
366
  rubyforge_project:
322
- rubygems_version: 1.8.6
367
+ rubygems_version: 1.8.24
323
368
  signing_key:
324
369
  specification_version: 3
325
370
  summary: Binder of samtools for ruby, on the top of FFI.