bio-samtools 2.4.0 → 2.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 251a8a0a110617d3894cfa6e287bc06bbd24ed89
+  metadata.gz: 536e4a02119f2315755d2768e868ca21b29213ac
+  data.tar.gz: 6b4c39ca800763b7f654d4d04994338ea9b809a1
 SHA512:
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+  data.tar.gz: 1cce66d5dbab92a6fc1ccd167b5df3827d8f44efac002fd970c789335abf6dace5ea32aab75e82a6a977b47241da967531660131059ddc8224cdaaff0bb8f3f2

data/.travis.yml

@@ -12,8 +12,9 @@ before_script:
   - rake -f Rakefile
   - cd ../
 rvm:
-  - 1.9.3
   - 2.0.0
-  - 2.1.0
+  - 2.1.10
   - 2.2.2
   - 2.2.3
+  - 2.2.5
+  - 2.3.1

data/Gemfile

@@ -1,22 +1,21 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-#   gem "activesupport", ">= 2.3.5"
 gem "bio-svgenes", ">= 0.4.1"
 gem "bio", ">= 1.4.2"
-gem 'open_uri_redirections'
+#gem 'open_uri_redirections'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", "> 2.10"
-  gem "shoulda-context"
-  gem  "shoulda-matchers"
-  gem "bundler", "> 1.0.21"
-  gem "jeweler"
-  gem "rcov", ">=0", :platforms => :ruby_18
-  gem "simplecov", ">= 0",   :platforms => :ruby_19
-  gem "ruby-prof"
-  gem 'rdoc'
+  gem "shoulda", "= 2.10"
   gem 'test-unit'
+if RUBY_VERSION.start_with?("2.1") or RUBY_VERSION.start_with?("2.2") or RUBY_VERSION.start_with?("2.0")
+  gem "jeweler", "= 2.0.1"
+else
+	gem "juwelier" ,  :platforms => :ruby_23 #jeweler support is being dropped
+end
+  gem "rack", "1.6.4",  :platforms => :ruby_21
+
+
 end

data/Rakefile

@@ -11,8 +11,19 @@ rescue Bundler::BundlerError => e
 end
 require 'rake'
 
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
+
+if RUBY_VERSION.start_with?("2.1") or RUBY_VERSION.start_with?("2.2") or RUBY_VERSION.start_with?("2.0")
+  require 'jeweler'
+  @taskClass = Jeweler
+else
+  require 'juwelier'
+  @taskClass = Juwelier
+end
+
+
+#Juwelier
+
+@taskClass::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "bio-samtools"
   gem.homepage = "http://github.com/helios/bioruby-samtools"
@@ -30,7 +41,7 @@ Jeweler::Tasks.new do |gem|
   #  gem.add_development_dependency 'rspec', '> 1.2.3'
   gem.extensions = "ext/mkrf_conf.rb"
 end
-Jeweler::RubygemsDotOrgTasks.new
+@taskClass::RubygemsDotOrgTasks.new
 
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|

data/VERSION

@@ -1 +1 @@
-2.4.0
+2.5.1

data/bio-samtools.gemspec

@@ -1,18 +1,18 @@
-# Generated by jeweler
+# Generated by juwelier
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.4.0 ruby lib
+# stub: bio-samtools 2.5.1 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "2.4.0"
+  s.version = "2.5.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2016-05-25"
+  s.date = "2016-11-04"
   s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
   s.email = "Ricardo.Ramirez-Gonzalez@tgac.ac.uk"
   s.executables = ["bam_consensus.rb"]
@@ -135,9 +135,11 @@ Gem::Specification.new do |s|
     "test/samples/small/test_chr.fasta.rsa",
     "test/samples/small/test_chr.fasta.sa",
     "test/samples/small/test_cov.svg",
+    "test/samples/small/test_fastadb.fasta",
     "test/samples/small/testu.bam",
     "test/samples/small/testu.bed",
     "test/test_bio-samtools.rb",
+    "test/test_fastadb.rb",
     "test/test_pileup.rb",
     "test/test_sam.rb",
     "test/test_vcf.rb",
@@ -147,7 +149,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/helios/bioruby-samtools"
   s.licenses = ["MIT"]
-  s.rubygems_version = "2.2.2"
+  s.rubygems_version = "2.5.1"
   s.summary = "Binder of samtools for ruby, on the top of FFI."
 
   if s.respond_to? :specification_version then
@@ -156,46 +158,25 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_runtime_dependency(%q<open_uri_redirections>, [">= 0"])
-      s.add_development_dependency(%q<shoulda>, ["> 2.10"])
-      s.add_development_dependency(%q<shoulda-context>, [">= 0"])
-      s.add_development_dependency(%q<shoulda-matchers>, [">= 0"])
-      s.add_development_dependency(%q<bundler>, ["> 1.0.21"])
-      s.add_development_dependency(%q<jeweler>, [">= 0"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
-      s.add_development_dependency(%q<simplecov>, [">= 0"])
-      s.add_development_dependency(%q<ruby-prof>, [">= 0"])
-      s.add_development_dependency(%q<rdoc>, [">= 0"])
+      s.add_development_dependency(%q<shoulda>, ["= 2.10"])
       s.add_development_dependency(%q<test-unit>, [">= 0"])
+      s.add_development_dependency(%q<juwelier>, [">= 0"])
+      s.add_development_dependency(%q<rack>, ["= 1.6.4"])
     else
       s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
-      s.add_dependency(%q<open_uri_redirections>, [">= 0"])
-      s.add_dependency(%q<shoulda>, ["> 2.10"])
-      s.add_dependency(%q<shoulda-context>, [">= 0"])
-      s.add_dependency(%q<shoulda-matchers>, [">= 0"])
-      s.add_dependency(%q<bundler>, ["> 1.0.21"])
-      s.add_dependency(%q<jeweler>, [">= 0"])
-      s.add_dependency(%q<rcov>, [">= 0"])
-      s.add_dependency(%q<simplecov>, [">= 0"])
-      s.add_dependency(%q<ruby-prof>, [">= 0"])
-      s.add_dependency(%q<rdoc>, [">= 0"])
+      s.add_dependency(%q<shoulda>, ["= 2.10"])
       s.add_dependency(%q<test-unit>, [">= 0"])
+      s.add_dependency(%q<juwelier>, [">= 0"])
+      s.add_dependency(%q<rack>, ["= 1.6.4"])
     end
   else
     s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
-    s.add_dependency(%q<open_uri_redirections>, [">= 0"])
-    s.add_dependency(%q<shoulda>, ["> 2.10"])
-    s.add_dependency(%q<shoulda-context>, [">= 0"])
-    s.add_dependency(%q<shoulda-matchers>, [">= 0"])
-    s.add_dependency(%q<bundler>, ["> 1.0.21"])
-    s.add_dependency(%q<jeweler>, [">= 0"])
-    s.add_dependency(%q<rcov>, [">= 0"])
-    s.add_dependency(%q<simplecov>, [">= 0"])
-    s.add_dependency(%q<ruby-prof>, [">= 0"])
-    s.add_dependency(%q<rdoc>, [">= 0"])
+    s.add_dependency(%q<shoulda>, ["= 2.10"])
     s.add_dependency(%q<test-unit>, [">= 0"])
+    s.add_dependency(%q<juwelier>, [">= 0"])
+    s.add_dependency(%q<rack>, ["= 1.6.4"])
   end
 end
 

data/lib/bio/db/fastadb.rb

@@ -45,11 +45,25 @@ module Bio::DB::Fasta
   end
 
   class Entry
-    attr_reader :id, :length
-
-    def initialize(id, length)
+    attr_reader :id, :length, :line_bases, :line_length, :offset
+    alias_method :size, :length
+    def initialize(id, length, offset = 0 , line_bases= 0 , line_length = 0 )
       @id=id
       @length=length.to_i
+      @offset = offset.to_i
+      @line_bases  = line_bases.to_i
+      @line_length = line_length.to_i
+    end
+
+    def get_base_coordinate(coordinate)
+      lines_for_offset = coordinate / line_bases
+      line_offset = coordinate % line_bases
+      #puts "get_base_coordinate"
+      #puts "Coordinate: #{coordinate}"
+      #puts "lines_for_offset: #{lines_for_offset}"
+      #puts "line pffset: #{line_offset}"
+      #puts self.inspect
+      pointer = offset + (line_length * lines_for_offset) + line_offset - 1
     end
 
     def get_full_region
@@ -79,9 +93,6 @@ module Bio::DB::Fasta
       @orientation = args[:orientation]
     end
   
-
-  
-
     #TODO: Debug, as it hasnt been tested in the actual code. 
     def allele_freq_for_base(base)
       @all_ratios = Hash.new unless @all_ratios
@@ -144,8 +155,9 @@ module Bio::DB::Fasta
     def self.parse_region(reg_str)
       string = reg_str.delete("'")
       fields_1 = string.split(":")
+      raise FastaDBException.new(), "Invalid region. #{string}" if fields_1.length != 2
       fields_2 = fields_1[1].split("-")
-      raise FastaDBException.new(), "Invalid region. #{string}" if fields_1.length != 2 || fields_2.length != 2
+      raise FastaDBException.new(), "Invalid region. #{string}" if fields_2.length != 2
 
       reg = Region.new(:entry=> fields_1[0], :start=>fields_2[0].to_i, :end=>fields_2[1].to_i)
 
@@ -174,9 +186,11 @@ module Bio::DB::Fasta
     #Initialize the fasta file. If the fai file doesn't exists, it is generated at startup
     #* fasta path to the fasta file
     #* samtools path to samtools, if it is not provided, use the bundled version
-    def initialize(args)
-      @fasta_path = args[:fasta]
-      @samtools = args[:samtools] || File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')
+    def initialize(fasta: nil, samtools: false)
+      #puts "The arguments are: '#{fasta}':'#{samtools}'"
+      @fasta_path = fasta
+      @samtools = samtools  
+      @samtools = File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools') if samtools == true
       raise FastaDBException.new(), "No path for the refernce fasta file. " if @fasta_path.nil?
       @fai_file = @fasta_path + ".fai" 
       unless File.file?(@fai_file) then
@@ -184,7 +198,6 @@ module Bio::DB::Fasta
         @last_command = command
         system(command)
       end
-
     end
 
     #Loads the fai entries 
@@ -194,7 +207,7 @@ module Bio::DB::Fasta
       fai_file = @fai_file
       File.open(fai_file).each do | line |
         fields = line.split("\t")
-        @index << Entry.new(fields[0], fields[1])
+        @index << Entry.new(fields[0], fields[1], fields[2], fields[3], fields[4])
       end     
       @index.length
     end
@@ -217,9 +230,22 @@ module Bio::DB::Fasta
       end
     end
 
+    def index
+      return @index if @index
+      if @samtools
+        faidx
+      else
+        samtools = File.join(File.expand_path(File.dirname(__FILE__)),'sam','external','samtools')
+        #TODO: make a ruby implementations 
+        command = "#{samtools} faidx #{@fasta_path}"
+        @last_command = command
+        system(command)
+      end
+        load_fai_entries
+      return @index
+    end
 
-    #The region needs to have a method to_region or a method to_s that ha the format "chromosome:start-end" as in samtools
-    def fetch_sequence(region)
+    def fetch_sequence_samtools(region)
       query = region.to_s
       query = region.to_region.to_s if region.respond_to?(:to_region) 
       command = "#{@samtools} faidx #{@fasta_path} '#{query}'"
@@ -227,11 +253,38 @@ module Bio::DB::Fasta
       @last_command = command
       seq = ""
       yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
+      seq
+    end
 
-      reference = Bio::Sequence::NA.new(seq)
+    def fetch_sequence_native(region)
+      query = region
+      query = Region.parse_region(region) unless region.is_a?(Region) 
+      seq = ""
+      #In order to make this reentrant, if we want to make a multithreaded
+      #version of this function, we need to get a lock. Currently, only one thred
+      #can be assosiated with eache fastadb object
+      @fasta_file = File.open(@fasta_path) unless @fasta_file
+      entry = index.region_for_entry(query.entry)
+     
+      start_pointer  =  entry.get_base_coordinate(query.start)
+      @fasta_file.seek(start_pointer, IO::SEEK_SET)
+      end_pointer  =  entry.get_base_coordinate(query.end)
+      to_read = end_pointer - start_pointer + 1
+      seq = @fasta_file.read(to_read)
+      seq.gsub!(/\s+/, '')
+      seq 
+    end
 
-      if region.orientation == :reverse
-        #puts "reversing! #{reference.to_s}"
+    #The region needs to have a method to_region or a method to_s that ha the format "chromosome:start-end" as in samtools
+    def fetch_sequence(region)
+      load_fai_entries
+      region = Region.parse_region(region.to_s) unless region.is_a?(Region) 
+      entry = index.region_for_entry(region.entry)
+      raise FastaDBException.new "Entry (#{region.entry})not found in reference" unless entry
+      raise FastaDBException.new "Region in invalid range (#{region}): Valid range: #{entry.to_region.to_s} has a size of #{entry.size}." if region.end > entry.size or region.start < 1
+      seq = @samtools ?  fetch_sequence_samtools(region): fetch_sequence_native(region)
+      reference = Bio::Sequence::NA.new(seq)
+      if region.respond_to? :orientation and region.orientation == :reverse
         reference.reverse_complement!()
       end
       reference

data/test/samples/small/test_fastadb.fasta

@@ -0,0 +1,34 @@
+>chr_1
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
+ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC
+TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
+CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
+ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACGTGAATGCCGAGGA
+TTATACCGATGTTGTTGGTCAGCTTGCCCGCGGACATATGGATGAAGAGGAGAAGATTCTTGAGGTGGCC
+AAGAAGCTTATGCCTTCTAAGCCAACAACCCTCAAGGATATGAGCAAGTGGCGTTCCTTCTTTGAAAACT
+GGAACTTGTACATGAGTCAGTGTCGCGGTGCTGCGGCTATCCCTCTTTCGTACGTTTACCGTACCAACGA
+GCAGCCCGAGACCGCTTTGGTCGGAACCTATGTGAATATGGATGCCTATTTGGTTGCCCAGACAGTACTG
+TCTGGTTCCAACTTTGAGATCGATAATCAATGGGTTTTTGACGAATTCAAGGAAGCAATCACTACAACCG
+GACCTGGTTGGTCTTTCATCAAGACGTACAACCGAAGCAAGGACGGTCGTGCTGCCATTTTGAAATTAAA
+GGAACAGGCGGAAGGAACATTAAACGAGTCCGTTCGCCGTGATGATGCCATCAAGATCCTGTCAACTACG
+>chr.2
+ACATACAATGGTCCGAGTTGTAACTGGAATATTGATATGCTGTTGCAGAAATTTCAGTATGCCATCTCGG
+AATTGGTCGAAATTGACGGAGTCGCGTTGCCGGATGGGCAGCTTGTGACTTATTTGGTCCAGGCATTGAA
+GCGCAGCTTTTTGTGAAGACTTTTGTGTCTTCGTCCACGAGCAAATCCGAAAACACGCCTCGACAGGTCA
+ATGATGTGCAAACATCAGGTAGTGGGGCCTCCGGTGGGAGTAAGAAAGGAGGTACCGGGAAAGGAGCCAG
+CAAGCAGACTCCCTTCAAGGGTGCAGTCACGGCTCGCAGTTATACTCCGGGAGAATGGAAAAGATTGTCC
+AAGGACCAACAGGAAAAAGTGCGATCGCTGCGTAATAAAAAGAAGCAAGGAGGGAAACCCGAGGAATCAG
+AGAGGAGTGTTGACAGTGTAGCACGGGATGAGCCTGTGGACACTAAGGAAGTCCATACCAGCAGTGATAT
+GGAACCGACTTCAGATGCGGCTGGCCTGCAATTTGGCCGTGGTGCGTATAAGAAATCGGTCGGATTCACT
+GCGGACACCGCTTCTCCTTCAGAAAACGGAACGAAGAAGCAGAAAACGCATCACGATGCGTGAAACGCGG
+CACCCAATGCCAGTGTTTCGGGGACTAAGCAATGCATTTTACCAGATCGAGTGATATTGAGCCTCACCTC
+TACACGCAGCATTTGTGATCTCAACGCATGCACTCATCTTGGTGAGGGCCGCTGCGAGTTGGATTCACAT
+>chr_3
+GCAGACACATGCGTGGCTGGGGCAAACACTGTCTTGATTGGTGAATCGCAGAAGTCCGTAACTGTGCG
+CTTTCTCCGGTGAATATTCTGCACTGAAGAATATCCCCATTGGAACGGTTGCCACAGCTTACACAGCC
+AGAAGACGGGAGAGTGGTGCTTCTTATTATTAATCAGGCCCTATTCTTTGGGGACAGATTGAAACACC
+CTAGACCCCCAACCAGATGCGAGACTTTGGCATTGAAGTTGACGATGCCCCTCGGCAGTACGTCGCCA
+ACCAAGCACTCTTTGTATGTTCCTGACTCCCAACTTCGGATTCCGCTGCAGCTGCGCGGTATATTCTC
+GTTTTTGGAGTCGGAAGCCCACGCAACAGGAACTTGACGAGTGTGAGCATATCATACTCACCTCTGAT
+GTGCCGTGGGACTTGCTCAACGGACTTTGCCCGTCGAGAAGAAGAGGCCGCTAAGAGAGACCGGAGCG
+TATCATTGACACAACGGGACTTTCCACTGGCCACGCAATCCTATCAGCACACCCATATGGTATACG

data/test/test_fastadb.rb

@@ -0,0 +1,87 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+
+require 'rubygems'
+require 'bio/db/sam'
+require "test/unit"
+#gem 'ruby-prof'
+gem 'test-unit'
+#require "ruby-prof"
+
+
+class TestBioDbfastaDB < Test::Unit::TestCase
+
+	def setup
+		@test_folder                = "test/samples/small"
+		@testReference  = @test_folder + "/test_fastadb.fasta"
+		@fasta_local = Bio::DB::Fasta::FastaFile.new(
+        	fasta: @testReference,
+        	samtools: false
+    	)
+
+    	@fasta_samtools = Bio::DB::Fasta::FastaFile.new(
+        	:fasta => @testReference,
+        	samtools: true
+    	)
+	end
+     class << self    
+        def shutdown
+            File.delete("test/samples/small/test_fastadb.fasta.fai")
+        end
+    end
+
+	def test_faidx
+		@fasta_samtools.index()
+    	test_fai_file = @testReference+".fai"
+    	#test that the .fai file exists
+    	assert_nothing_thrown do
+      		File.open(test_fai_file, "r")
+    	end
+    	#test that the file is not empty
+    	assert(File.size(test_fai_file) > 0, "From test_faidx: .fai file is empty")
+	end
+
+
+
+	def test_fetch_reference
+    	#this is the first 70 nucleotides of the test seqeunce
+    	@fasta_samtools.faidx()
+
+    	test_regions = { "chr_1:1-70" => "CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA", 
+    		"chr_1:68-74" => "CTAACCC",
+    		"chr.2:300-450" => "GGTGCAGTCACGGCTCGCAGTTATACTCCGGGAGAATGGAAAAGATTGTCCAAGGACCAA\
+CAGGAAAAAGTGCGATCGCTGCGTAATAAAAAGAAGCAAGGAG\
+GGAAACCCGAGGAATCAGAGAGGAGTGTTGACAGTGTAGCACGGGATG",
+			"chr_3:536-542" => "GTATACG", 
+			"chr.2:765-770" => "TCACAT"
+    	}
+
+    	test_regions.each_pair do |region, seq_expected|  
+    		seq_fetched = @fasta_samtools.fetch_sequence(region)
+    		assert_equal(seq_expected, seq_fetched.upcase)
+
+    		seq_fetched_local = @fasta_local.fetch_sequence(region)
+    		assert_equal(seq_expected, seq_fetched_local.upcase)
+    	end
+
+    	test_regions = {
+    		"chr_3:772-780" => Bio::DB::Fasta::FastaDBException,
+            "chr_3:-1-10" => Bio::DB::Fasta::FastaDBException,
+            "chr_3:0-10" => Bio::DB::Fasta::FastaDBException,
+            "bfafdaads" => Bio::DB::Fasta::FastaDBException,
+            "chr.2:765-771" => Bio::DB::Fasta::FastaDBException,
+            "chr_2:765-770" => Bio::DB::Fasta::FastaDBException,
+
+    	}
+    	test_regions.each_pair do |region, expected_eception|  
+            assert_raise expected_eception do
+                seq_fetched = @fasta_samtools.fetch_sequence(region)
+            end
+
+            assert_raise expected_eception do
+    	       seq_fetched_local = @fasta_local.fetch_sequence(region)
+    	   end
+        end
+    end
+
+end

data/test/test_sam.rb

@@ -343,7 +343,7 @@ class TestBioDbSam < Test::Unit::TestCase
     bam_files = [bam_to_merge1, bam_to_merge2]
     
     merged_bam_file = @test_folder + "/maps_merged.bam"
-    File.delete merged_bam_file if File.exists?(merged_bam_file)
+    File.delete merged_bam_file if File.exist?(merged_bam_file)
 #    File.delete("test/samples/small/maps_merged.bam")
     @sam.merge(:out=>merged_bam_file, :bams=>bam_files, :n=>true)
     merged_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => merged_bam_file)
@@ -364,7 +364,7 @@ class TestBioDbSam < Test::Unit::TestCase
     bam_files = [bam1, bam2]
     
     cat_bam_file = @test_folder + "/maps_cated.bam"
-    File.delete cat_bam_file if File.exists?(cat_bam_file)
+    File.delete cat_bam_file if File.exist?(cat_bam_file)
     @sam.merge(:out=>cat_bam_file, :bams=>bam_files)
     cated_bam = Bio::DB::Sam.new(:fasta => @testReference, :bam => cat_bam_file)
     

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 2.4.0
+  version: 2.5.1
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-25 00:00:00.000000000 Z
+date: 2016-11-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-svgenes
@@ -40,120 +40,22 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.2
-- !ruby/object:Gem::Dependency
-  name: open_uri_redirections
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
+    - - '='
       - !ruby/object:Gem::Version
         version: '2.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">"
+    - - '='
       - !ruby/object:Gem::Version
         version: '2.10'
 - !ruby/object:Gem::Dependency
-  name: shoulda-context
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: shoulda-matchers
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.21
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.21
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: simplecov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: ruby-prof
+  name: test-unit
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -167,7 +69,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: juwelier
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -181,19 +83,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: test-unit
+  name: rack
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.6.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '='
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 1.6.4
 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)."
@@ -319,9 +221,11 @@ files:
 - test/samples/small/test_chr.fasta.rsa
 - test/samples/small/test_chr.fasta.sa
 - test/samples/small/test_cov.svg
+- test/samples/small/test_fastadb.fasta
 - test/samples/small/testu.bam
 - test/samples/small/testu.bed
 - test/test_bio-samtools.rb
+- test/test_fastadb.rb
 - test/test_pileup.rb
 - test/test_sam.rb
 - test/test_vcf.rb
@@ -348,7 +252,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Binder of samtools for ruby, on the top of FFI.