bio-samtools.gemspec in bio-samtools-0.6.2 vs bio-samtools.gemspec in bio-samtools-2.0.3
- old
+ new
@@ -1,20 +1,20 @@
# Generated by jeweler
# DO NOT EDIT THIS FILE DIRECTLY
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
# -*- encoding: utf-8 -*-
-# stub: bio-samtools 0.6.2 ruby lib
+# stub: bio-samtools 2.0.3 ruby lib
# stub: ext/mkrf_conf.rb
Gem::Specification.new do |s|
s.name = "bio-samtools"
- s.version = "0.6.2"
+ s.version = "2.0.3"
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 = "2014-02-25"
+ s.date = "2014-04-18"
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 = "ilpuccio.febo@gmail.com"
s.extensions = ["ext/mkrf_conf.rb"]
s.extra_rdoc_files = [
"LICENSE.txt",
@@ -34,84 +34,23 @@
"doc/Bio/DB/Alignment.html",
"doc/Bio/DB/Pileup.html",
"doc/Bio/DB/SAM.html",
"doc/Bio/DB/SAM/Library.html",
"doc/Bio/DB/SAM/Tools.html",
- "doc/Bio/DB/SAM/Tools/Bam1CoreT.html",
- "doc/Bio/DB/SAM/Tools/Bam1T.html",
- "doc/Bio/DB/SAM/Tools/BamHeaderT.html",
- "doc/Bio/DB/SAM/Tools/BamPileup1T.html",
- "doc/Bio/DB/SAM/Tools/SamfileT.html",
- "doc/Bio/DB/SAM/Tools/SamfileTX.html",
- "doc/Bio/DB/SAMException.html",
"doc/Bio/DB/Tag.html",
"doc/Bio/DB/Vcf.html",
"doc/LICENSE_txt.html",
- "doc/LibC.html",
- "doc/Pileup.html",
- "doc/Vcf.html",
- "doc/basic_styles.css",
- "doc/classes/Bio.html",
- "doc/classes/Bio/DB.html",
- "doc/classes/Bio/DB/Alignment.html",
- "doc/classes/Bio/DB/Alignment.src/M000012.html",
- "doc/classes/Bio/DB/Alignment.src/M000013.html",
- "doc/classes/Bio/DB/Alignment.src/M000014.html",
- "doc/classes/Bio/DB/Alignment.src/M000015.html",
- "doc/classes/Bio/DB/SAM.html",
- "doc/classes/Bio/DB/SAM/Library.html",
- "doc/classes/Bio/DB/SAM/Library.src/M000006.html",
- "doc/classes/Bio/DB/SAM/Tools.html",
- "doc/classes/Bio/DB/SAM/Tools.src/M000007.html",
- "doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html",
- "doc/classes/Bio/DB/SAM/Tools/Bam1T.html",
- "doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html",
- "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html",
- "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html",
- "doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html",
- "doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html",
- "doc/classes/Bio/DB/SAM/Tools/SamfileT.html",
- "doc/classes/Bio/DB/SAM/Tools/SamfileTX.html",
- "doc/classes/Bio/DB/SAMException.html",
- "doc/classes/Bio/DB/SAMException.src/M000016.html",
- "doc/classes/Bio/DB/Sam.src/M000017.html",
- "doc/classes/Bio/DB/Sam.src/M000018.html",
- "doc/classes/Bio/DB/Sam.src/M000019.html",
- "doc/classes/Bio/DB/Sam.src/M000020.html",
- "doc/classes/Bio/DB/Sam.src/M000021.html",
- "doc/classes/Bio/DB/Sam.src/M000022.html",
- "doc/classes/Bio/DB/Sam.src/M000023.html",
- "doc/classes/Bio/DB/Sam.src/M000024.html",
- "doc/classes/Bio/DB/Sam.src/M000025.html",
- "doc/classes/Bio/DB/Sam.src/M000026.html",
- "doc/classes/Bio/DB/Sam.src/M000027.html",
- "doc/classes/Bio/DB/Sam.src/M000028.html",
- "doc/classes/Bio/DB/Sam.src/M000029.html",
- "doc/classes/Bio/DB/Sam.src/M000030.html",
- "doc/classes/Bio/DB/Sam.src/M000031.html",
- "doc/classes/Bio/DB/Sam.src/M000032.html",
- "doc/classes/Bio/DB/Tag.html",
- "doc/classes/Bio/DB/Tag.src/M000011.html",
- "doc/classes/LibC.html",
- "doc/classes/Pileup.html",
- "doc/classes/Pileup.src/M000001.html",
- "doc/classes/Pileup.src/M000002.html",
- "doc/classes/Pileup.src/M000003.html",
- "doc/classes/Pileup.src/M000004.html",
- "doc/classes/Pileup.src/M000005.html",
"doc/created.rid",
- "doc/files/lib/bio-samtools_rb.html",
- "doc/files/lib/bio/db/sam/bam_rb.html",
- "doc/files/lib/bio/db/sam/faidx_rb.html",
- "doc/files/lib/bio/db/sam/library_rb.html",
- "doc/files/lib/bio/db/sam/pileup_rb.html",
- "doc/files/lib/bio/db/sam/sam_rb.html",
- "doc/files/lib/bio/db/sam_rb.html",
- "doc/fr_class_index.html",
- "doc/fr_file_index.html",
- "doc/fr_method_index.html",
+ "doc/fonts.css",
+ "doc/fonts/Lato-Light.ttf",
+ "doc/fonts/Lato-LightItalic.ttf",
+ "doc/fonts/Lato-Regular.ttf",
+ "doc/fonts/Lato-RegularItalic.ttf",
+ "doc/fonts/SourceCodePro-Bold.ttf",
+ "doc/fonts/SourceCodePro-Regular.ttf",
"doc/images/add.png",
+ "doc/images/arrow_up.png",
"doc/images/brick.png",
"doc/images/brick_link.png",
"doc/images/bug.png",
"doc/images/bullet_black.png",
"doc/images/bullet_toggle_minus.png",
@@ -138,112 +77,115 @@
"doc/js/jquery.js",
"doc/js/navigation.js",
"doc/js/search.js",
"doc/js/search_index.js",
"doc/js/searcher.js",
- "doc/lib/bio-samtools_rb.html",
- "doc/lib/bio/db/pileup_rb.html",
- "doc/lib/bio/db/sam/bam_rb.html",
- "doc/lib/bio/db/sam/faidx_rb.html",
- "doc/lib/bio/db/sam/library_rb.html",
- "doc/lib/bio/db/sam/pileup_rb.html",
- "doc/lib/bio/db/sam/sam_rb.html",
- "doc/lib/bio/db/sam/vcf_rb.html",
- "doc/lib/bio/db/sam_rb.html",
- "doc/lib/bio/db/vcf_rb.html",
- "doc/rdoc-style.css",
"doc/rdoc.css",
"doc/table_of_contents.html",
- "doc/tutorial.html",
- "doc/tutorial.pdf",
"ext/Makefile-bioruby.patch",
"ext/Makefile-suse.patch",
+ "ext/Rakefile",
"ext/mkrf_conf.rb",
"lib/bio-samtools.rb",
"lib/bio/.DS_Store",
+ "lib/bio/BIOExtensions.rb",
+ "lib/bio/db/alignment.rb",
+ "lib/bio/db/fastadb.rb",
"lib/bio/db/pileup.rb",
"lib/bio/db/sam.rb",
- "lib/bio/db/sam/bam.rb",
"lib/bio/db/sam/external/COPYING",
"lib/bio/db/sam/external/VERSION",
- "lib/bio/db/sam/faidx.rb",
+ "lib/bio/db/sam/faidx_old.rb",
"lib/bio/db/sam/library.rb",
- "lib/bio/db/sam/sam.rb",
"lib/bio/db/vcf.rb",
+ "test/.gitignore",
"test/helper.rb",
- "test/samples/pipe_char/test.bam",
- "test/samples/pipe_char/test.bam.bai",
- "test/samples/pipe_char/test.tam",
- "test/samples/pipe_char/test_chr.fasta",
- "test/samples/pipe_char/test_chr.fasta.fai",
+ "test/old_test_basic.rb",
+ "test/samples/small/dupes.bam",
+ "test/samples/small/dupes.sam",
"test/samples/small/ids2.txt",
+ "test/samples/small/map_for_reheader.sam",
+ "test/samples/small/map_to_merge1.bam",
+ "test/samples/small/map_to_merge1.bam.bai",
+ "test/samples/small/map_to_merge1.sam",
+ "test/samples/small/map_to_merge2.bam",
+ "test/samples/small/map_to_merge2.bam.bai",
+ "test/samples/small/map_to_merge2.sam",
+ "test/samples/small/no_md.sam",
"test/samples/small/sorted.bam",
"test/samples/small/sorted.bam.bai",
- "test/samples/small/test",
- "test/samples/small/test.bam",
- "test/samples/small/test.fa",
- "test/samples/small/test.fai",
"test/samples/small/test.sai",
"test/samples/small/test.tam",
"test/samples/small/test_chr.fasta",
+ "test/samples/small/test_chr.fasta.1.bt2",
+ "test/samples/small/test_chr.fasta.2.bt2",
+ "test/samples/small/test_chr.fasta.3.bt2",
+ "test/samples/small/test_chr.fasta.4.bt2",
"test/samples/small/test_chr.fasta.amb",
"test/samples/small/test_chr.fasta.ann",
"test/samples/small/test_chr.fasta.bwt",
"test/samples/small/test_chr.fasta.pac",
"test/samples/small/test_chr.fasta.rbwt",
+ "test/samples/small/test_chr.fasta.rev.1.bt2",
+ "test/samples/small/test_chr.fasta.rev.2.bt2",
"test/samples/small/test_chr.fasta.rpac",
"test/samples/small/test_chr.fasta.rsa",
"test/samples/small/test_chr.fasta.sa",
+ "test/samples/small/test_cov.svg",
"test/samples/small/testu.bam",
"test/samples/small/testu.bam.bai",
- "test/test_basic.rb",
+ "test/svg",
"test/test_bio-samtools.rb",
- "test/test_vcf.rb"
+ "test/test_pileup.rb",
+ "test/test_sam.rb",
+ "test/test_vcf.rb",
+ "tutorial/tutorial.html",
+ "tutorial/tutorial.pdf"
]
s.homepage = "http://github.com/helios/bioruby-samtools"
s.licenses = ["MIT"]
s.rubygems_version = "2.2.1"
s.summary = "Binder of samtools for ruby, on the top of FFI."
if s.respond_to? :specification_version then
s.specification_version = 4
if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
- s.add_runtime_dependency(%q<ffi>, [">= 0"])
+ s.add_runtime_dependency(%q<bio-svgenes>, [">= 0.4.1"])
s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
- s.add_runtime_dependency(%q<systemu>, [">= 2.5.2"])
s.add_development_dependency(%q<shoulda>, [">= 0"])
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<rdoc>, [">= 0"])
+ s.add_development_dependency(%q<test-unit>, [">= 0"])
else
- s.add_dependency(%q<ffi>, [">= 0"])
+ s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
s.add_dependency(%q<bio>, [">= 1.4.2"])
- s.add_dependency(%q<systemu>, [">= 2.5.2"])
s.add_dependency(%q<shoulda>, [">= 0"])
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<rdoc>, [">= 0"])
+ s.add_dependency(%q<test-unit>, [">= 0"])
end
else
- s.add_dependency(%q<ffi>, [">= 0"])
+ s.add_dependency(%q<bio-svgenes>, [">= 0.4.1"])
s.add_dependency(%q<bio>, [">= 1.4.2"])
- s.add_dependency(%q<systemu>, [">= 2.5.2"])
s.add_dependency(%q<shoulda>, [">= 0"])
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<rdoc>, [">= 0"])
+ s.add_dependency(%q<test-unit>, [">= 0"])
end
end