bio-samtools 2.3.0 → 2.3.1
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.
- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bio-samtools.gemspec +3 -3
- data/ext/Rakefile +7 -7
- data/lib/bio/db/sam.rb +1 -2
- data/test/test_sam.rb +12 -0
- metadata +2 -2
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 8b8fc60d0e2728d7069923ed6c1efa52e5bafe85
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data.tar.gz: 3e190a21f82d735ddf376c85586df45bd7c60b28
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 999c438419b28abcab58633c24e16937ee267671384762a5d81d24650d95daa04a1789053302adc4eebf3984b9b8d4acbb72c604fedfc26c182c20216af704fb
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data.tar.gz: 048b2fb95ebbf7ada3f34ed1701f24bc4897a89da8efdfe018a9b441ae9cacb3d0e89b52affa38b779823f64167ad7dc15c99dd791e78b061f0df77f20cbd7b4
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data/VERSION
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@@ -1 +1 @@
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1
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2.3.
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2.3.1
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data/bio-samtools.gemspec
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@@ -2,17 +2,17 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: bio-samtools 2.3.
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# stub: bio-samtools 2.3.1 ruby lib
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# stub: ext/mkrf_conf.rb
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Gem::Specification.new do |s|
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s.name = "bio-samtools"
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s.version = "2.3.
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s.version = "2.3.1"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib"]
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s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
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s.date = "2015-02-
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s.date = "2015-02-25"
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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)."
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s.email = "ilpuccio.febo@gmail.com"
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s.executables = ["bam_consensus.rb"]
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data/ext/Rakefile
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@@ -24,24 +24,24 @@ task :compile do
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when /linux/
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#sh "CFLAGS='-g -Wall -O2 -fPIC' make -e"
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sh "make"
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cp("libbam.a","/
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cp("libbam.a","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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#sh "CFLAGS='-g -Wall -O2 -fPIC' make -e libbam.so.1-local"
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sh "make libbam.so.1-local"
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cp("samtools", "/
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cp("libbam.so.1","/
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cp("samtools", "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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cp("libbam.so.1","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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when /darwin/
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sh "make"
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cp("libbam.a","/
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cp("libbam.a","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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sh "make libbam.1.dylib-local"
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cp("libbam.1.dylib","/
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cp("libbam.1.dylib","/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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sh "make"
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cp('samtools', "/
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cp('samtools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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when /mswin|mingw/ then raise NotImplementedError, "BWA library is not available for Windows platform"
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end #case
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end #cd
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cd("samtools-0.1.19/bcftools") do
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sh "make"
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cp('bcftools', "/
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cp('bcftools', "/Users/ramirezr/Documents/public_code/helios/bioruby-samtools/ext/../lib/bio/db/sam/external")
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end
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end
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data/lib/bio/db/sam.rb
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require 'open3'
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module Bio
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class DB
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class Sam
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@last_command = nil
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raise ArgumentError, "Need Fasta and at least one BAM or SAM" if not @fasta or not @bam
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raise IOError, "File not found #{files}" if not files_ok?
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raise IOError, "File not found #{@files}" if not files_ok?
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@bams = [@bams] if @bams.instance_of? String
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end
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data/test/test_sam.rb
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@@ -43,6 +43,18 @@ class TestBioDbSam < Test::Unit::TestCase
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def test_new
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assert_kind_of(Bio::DB::Sam, @sam)
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assert_raise(IOError) do
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Bio::DB::Sam.new(
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:fasta => @testReference,
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:bam => @testBAMFile + "ads"
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)
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end
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assert_raise(ArgumentError) do
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Bio::DB::Sam.new()
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end
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end
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def test_index
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metadata
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--- !ruby/object:Gem::Specification
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name: bio-samtools
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version: !ruby/object:Gem::Version
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version: 2.3.
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version: 2.3.1
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platform: ruby
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authors:
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- Ricardo Ramirez-Gonzalez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2015-02-
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date: 2015-02-25 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio-svgenes
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