bio-samtools 2.6.1 → 2.6.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 5c7c1107bfac77e9b61fd5e5c42858b1f9a47343
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data/.travis.yml

@@ -6,13 +6,22 @@ addons:
     - zlib1g-dev
     - libncurses5-dev
     - libtinfo-dev   
+before_install:
+  - gem update --system
+  - if [ $TRAVIS_OS_NAME = osx ]; then brew update; brew install xz ; fi
 before_script:
   - cd ext
   - ruby mkrf_conf.rb
   - rake -f Rakefile
   - cd ../
+os:
+  - linux
+  - osx
 rvm:
   - 2.1.10
   - 2.2.5
   - 2.3.5
   - 2.4.2
+  - 2.5.0
+
+

data/README.md

@@ -438,17 +438,14 @@ Each test file tests different aspects of the code.
 
 ## Dependencies
 
-* BioRuby >= 1.4.3 [https://github.com/bioruby/bioruby](https://github.com/bioruby/bioruby)
-* Ruby 1.9 and above. 
+* BioRuby >= 1.5 [https://github.com/bioruby/bioruby](https://github.com/bioruby/bioruby)
+* Ruby 2.1.10 and above. 
+
 	
 ## FAQ
-* I´m getting a **segmentation Fault**, what did I do wrong?
-
-	[Answer] You are using an old version of bio-samtools, the current version doesn't link directly to the library. 
+* I want to use Ruby 1.x, what can I do? 
 
-* I keep seeing this **Invalid gemspec in [some ruby gem path…]**, what is wrong?
-	
-	[Answer] This appears to be a bug in RubyGems that doesn't affect the running of the tools. It will keep happening until someone updates RubyGems. If it really bugs you, downgrade RubyGems.
+We try to ensure backwards compatibility with old rubies. However we only officially support current versions of [https://www.ruby-lang.org/en/downloads/](Ruby). The code should work however the testing suites used in earlier versions are not currently supported and don't work in modern rubies. This decision ensures compatibility with maintained versions of Ruby.  
 
 
 ## Contributing to bio-samtools

data/Rakefile

@@ -27,7 +27,7 @@ end
   # 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"
-  gem.license = "MIT"
+  gem.license = "GPL-3.0"
   gem.summary = %Q{Binder of samtools for ruby, on the top of FFI.}
   gem.description = %Q{Binder of samtools for ruby, on the top of FFI. 
 

data/VERSION

@@ -1 +1 @@
-2.6.1
+2.6.2

data/bio-samtools.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.6.1 ruby lib
+# stub: bio-samtools 2.6.2 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools".freeze
-  s.version = "2.6.1"
+  s.version = "2.6.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo Ramirez-Gonzalez".freeze, "Dan MacLean".freeze, "Raoul J.P. Bonnal".freeze]
-  s.date = "2017-11-30"
+  s.date = "2018-01-11"
   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).".freeze
   s.email = "Ricardo.Ramirez-Gonzalez@tgac.ac.uk".freeze
   s.executables = ["bam_consensus.rb".freeze]
@@ -147,8 +147,8 @@ Gem::Specification.new do |s|
     "tutorial/tutorial.pdf"
   ]
   s.homepage = "http://github.com/helios/bioruby-samtools".freeze
-  s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.6.10".freeze
+  s.licenses = ["GPL-3.0".freeze]
+  s.rubygems_version = "2.6.14".freeze
   s.summary = "Binder of samtools for ruby, on the top of FFI.".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/db/fastadb.rb

@@ -13,7 +13,7 @@ module Bio::DB::Fasta
 
     #This doesnt validate if you are adding the same entry twice. I may add
     #a validation for that. 
-    def << (entry)
+    def <<(entry)
       @entries << entry
       @entries_map[entry.id] = entry
     end
@@ -252,7 +252,7 @@ module Bio::DB::Fasta
       query = region.to_s
       query = region.to_region.to_s if region.respond_to?(:to_region) 
       command = "#{@samtools} faidx #{@fasta_path} '#{query}'"
-      puts "Running: #{command}"  if $VERBOSE
+      puts "Running: #{command}"  if $DEBUG
       @last_command = command
       seq = ""
       yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
@@ -294,7 +294,7 @@ module Bio::DB::Fasta
     end
 
     private
-    #Returns Process::Status with the execution status. If run in a $VERBOSE environment, stderr of the process
+    #Returns Process::Status with the execution status. If run in a $DEBUG environment, stderr of the process
     #is forwarded to the default stdout
     def yield_from_pipe(command, klass, type=:text, skip_comments=true, comment_char="#", &block)
       stdin, pipe, stderr, wait_thr = Open3.popen3(command)
@@ -310,7 +310,7 @@ module Bio::DB::Fasta
         end
       end
       exit_status = wait_thr.value  # Process::Status object returned.
-      puts stderr.read if $VERBOSE 
+      puts stderr.read if $DEBUG 
       stdin.close
       pipe.close
       stderr.close

data/lib/bio/db/sam.rb

@@ -276,7 +276,7 @@ module Bio
         end
 
         command = form_opt_string(@samtools, "mpileup", opts, [:R, :B, :E, "6", :A, :g, :u, :I] )
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         if opts[:u]
           command = command + " | #{@bcftools} view -cg -"
         end
@@ -299,7 +299,7 @@ module Bio
           seq = "n" * (stop-start)
         else
           command = "#{@samtools} faidx \"#{@fasta}\" '#{chr}:#{start}-#{stop}'"
-          puts "Running: #{command}" if $VERBOSE
+          puts "Running: #{command}" if $DEBUG
           @last_command = command
           seq = ""
           yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
@@ -331,7 +331,7 @@ module Bio
       #* out_index - [STRING] name of index
       def index(opts={})
         command = "#{@samtools} index \"#{@bam}\" #{opts[:out_index]}"
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -346,7 +346,7 @@ module Bio
           remove_reads = "-r"
         end
         command = "#{@samtools} fixmate #{remove_reads} \"#{@bam}\" #{opts[:out_bam]}"
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -356,7 +356,7 @@ module Bio
       #generate simple stats with regard to the number and pairing of reads mapped to a reference
       def flag_stats(opts={})
         command = form_opt_string(@samtools, "flagstat", opts, [])
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         strings = []
         yield_from_pipe(command,String) {|line| strings << line.chomp}
@@ -371,7 +371,7 @@ module Bio
         stats = {}
         command = form_opt_string(@samtools, "idxstats", {}, [])
         @last_command = command
-        puts "Running: #{command}" if $VERBOSE
+        #puts "Running: #{command}" if $DEBUG
         yield_from_pipe(command, String, :text, true, "#") do |line|
           info = line.chomp.split(/\t/)
           stats[ info[0] ] = {:length => info[1].to_i, :mapped_reads => info[2].to_i, :unmapped_reads => info[3].to_i }
@@ -452,7 +452,7 @@ module Bio
         command = "#{@samtools} merge #{options} #{out} #{bam_list}"
 
         @last_command = command
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         system(command)
 
       end
@@ -468,7 +468,7 @@ module Bio
         opts.delete(:bams)
         options = commandify(opts, [:h] )
         command = "#{@samtools} cat #{options} -o #{out} #{bam_list}"
-        puts command if $VERBOSE
+        puts command if $DEBUG
         @last_command = command
         system(command)
 
@@ -515,7 +515,7 @@ module Bio
         command = form_opt_string(@samtools, "sort", opts, [:n, :f])
         command = command + " "
         @last_command = command
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         #if opts[:o]
         #  yield_from_pipe(command, Bio::DB::Alignment)
         #else
@@ -541,7 +541,7 @@ module Bio
           opts.delete(:s)
         end
         command = "#{form_opt_string(@samtools, "tview", opts)}"
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -556,7 +556,7 @@ module Bio
         else
           command = "#{@samtools} reheader #{header_sam} \"#{@bam}\""
         end
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -572,7 +572,7 @@ module Bio
       #* E - Extended BAQ calculation. This option trades specificity for sensitivity, though the effect is minor.
       def calmd(opts={}, &block)
         command = form_opt_string(@samtools, "calmd",  opts, [:E, :e, :u, :b, :S, :r] )+ " " + @fasta
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         type = :text
         klass = Bio::DB::Alignment
@@ -593,7 +593,7 @@ module Bio
         end
 
         command = "#{form_opt_string(@samtools, "targetcut", opts, [] )}"
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -607,7 +607,7 @@ module Bio
       #* Q - [INT] Minimum base quality to be used in het calling. [13]
       def phase(opts={})
         command = "#{form_opt_string(@samtools, "phase", opts, [:A, :F] )}"
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         @last_command = command
         system(command)
       end
@@ -651,7 +651,7 @@ module Bio
       #We asume that the options (other than the region) are constant. If they are not, the cache mechanism may not be consistent.
       #
       #TODO: It may be good to load partially the pileup
-      def mpileup_cached (opts={})
+      def mpileup_cached(opts={})
         raise SamException.new(), "A region must be provided" unless opts[:r] or opts[:region]
         @cached_regions = Hash.new unless @cached_regions
         region = opts[:r] ? opts[:r] : opts[:region]
@@ -667,7 +667,7 @@ module Bio
 
       #Clears the pileup cache. If a region is passed as argument, just the specified region is removed
       #If no region is passed, the hash is emptied
-      def mpileup_clear_cache (region)
+      def mpileup_clear_cache(region)
         return unless @cached_regions
         if region
           @cached_regions[region.to_s] = nil
@@ -685,7 +685,7 @@ module Bio
         else
           command = "#{@samtools} bedcov \"#{bed}\" \"#{@bam}\""
         end
-         puts "Running: #{command}" if $VERBOSE
+         puts "Running: #{command}" if $DEBUG
         #puts command
         @last_command = command
         system(command)
@@ -724,14 +724,14 @@ module Bio
 
       #Returns true if the .bai exists. It doesn't validate if it is valid.
       def indexed?
-        File.exists? @bam and File.exist? "#{@bam}.bai"
+        File.exist? @bam and File.exist? "#{@bam}.bai"
       end
 
       private
-      #Returns Process::Status with the execution status. If run in a $VERBOSE environment, stderr of the process
+      #Returns Process::Status with the execution status. If run in a $DEBUG environment, stderr of the process
       #is forwarded to the default stdout
       def yield_from_pipe(command, klass, type=:text, skip_comments=true, comment_char="#", &block)
-        puts "[yield_from_pipe] #{command}" if $VERBOSE
+        puts "[yield_from_pipe] #{command}" if $DEBUG
         stdin, pipe, stderr, wait_thr = Open3.popen3(command)
         #pid = wait_thr[:pid]  # pid of the started process.
         if type == :text
@@ -745,7 +745,7 @@ module Bio
           end
         end
         exit_status = wait_thr.value  # Process::Status object returned.
-        puts "Running: #{command}" if $VERBOSE
+        puts "Running: #{command}" if $DEBUG
         stdin.close
         pipe.close
         stderr.close

data/tutorial/tutorial.md

@@ -18,7 +18,7 @@ connection.
 
 bio-samtools relies on the following other rubygems:
 
--   [bio \>= 1.4.2](http://rubygems.org/gems/bio)
+-   [bio \>= 1.5](http://rubygems.org/gems/bio)
 -   [bio-svgenes >= 0.4.1](https://rubygems.org/gems/bio-svgenes)
 
 Once these are installed, bio-samtools can be installed with

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 2.6.1
+  version: 2.6.2
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-11-30 00:00:00.000000000 Z
+date: 2018-01-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-svgenes
@@ -233,7 +233,7 @@ files:
 - tutorial/tutorial.pdf
 homepage: http://github.com/helios/bioruby-samtools
 licenses:
-- MIT
+- GPL-3.0
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -251,7 +251,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.10
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: Binder of samtools for ruby, on the top of FFI.