bio-samtools-wrapper 2.7.0

data/bio-samtools-wrapper.gemspec

@@ -0,0 +1,181 @@
+# Generated by juwelier
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: bio-samtools-wrapper 2.7.0 ruby lib
+# stub: ext/mkrf_conf.rb
+
+Gem::Specification.new do |s|
+  s.name = "bio-samtools-wrapper".freeze
+  s.version = "2.7.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Rob Ellis".freeze]
+  s.date = "2024-09-25"
+  s.description = "Wrapper of samtools for ruby. \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 = "rob.ellis@jic.ac.uk".freeze
+  s.executables = ["bam_consensus.rb".freeze]
+  s.extensions = ["ext/mkrf_conf.rb".freeze]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.md"
+  ]
+  s.files = [
+    ".document",
+    ".travis.yml",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.md",
+    "Rakefile",
+    "VERSION",
+    "bin/bam_consensus.rb",
+    "bio-samtools-wrapper.gemspec",
+    "doc/Bio.html",
+    "doc/Bio/DB.html",
+    "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/Tag.html",
+    "doc/Bio/DB/Vcf.html",
+    "doc/LICENSE_txt.html",
+    "doc/created.rid",
+    "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",
+    "doc/images/bullet_toggle_plus.png",
+    "doc/images/date.png",
+    "doc/images/delete.png",
+    "doc/images/find.png",
+    "doc/images/loadingAnimation.gif",
+    "doc/images/macFFBgHack.png",
+    "doc/images/package.png",
+    "doc/images/page_green.png",
+    "doc/images/page_white_text.png",
+    "doc/images/page_white_width.png",
+    "doc/images/plugin.png",
+    "doc/images/ruby.png",
+    "doc/images/tag_blue.png",
+    "doc/images/tag_green.png",
+    "doc/images/transparent.png",
+    "doc/images/wrench.png",
+    "doc/images/wrench_orange.png",
+    "doc/images/zoom.png",
+    "doc/index.html",
+    "doc/js/darkfish.js",
+    "doc/js/jquery.js",
+    "doc/js/navigation.js",
+    "doc/js/search.js",
+    "doc/js/search_index.js",
+    "doc/js/searcher.js",
+    "doc/rdoc.css",
+    "doc/table_of_contents.html",
+    "ext/Makefile-bioruby.patch",
+    "ext/Makefile-suse.patch",
+    "ext/mkrf_conf.rb",
+    "lib/bio-samtools-wrapper.rb",
+    "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/external/COPYING",
+    "lib/bio/db/sam/external/VERSION",
+    "lib/bio/db/sam/library.rb",
+    "lib/bio/db/vcf.rb",
+    "test/.gitignore",
+    "test/helper.rb",
+    "test/sample.vcf",
+    "test/samples/.gitignore",
+    "test/samples/LCI/NC_001988.ffn",
+    "test/samples/LCI/test.bam",
+    "test/samples/LCI/test.bam.bai",
+    "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.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/test_fastadb.fasta",
+    "test/samples/small/testu.bam",
+    "test/samples/small/testu.bed",
+    "test/test_bio-samtools-wrapper.rb",
+    "test/test_fastadb.rb",
+    "test/test_pileup.rb",
+    "test/test_sam.rb",
+    "test/test_vcf.rb",
+    "tutorial/tutorial.html",
+    "tutorial/tutorial.md",
+    "tutorial/tutorial.pdf"
+  ]
+  s.homepage = "http://github.com/helios/bioruby-samtools".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
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<bio-svgenes>.freeze, [">= 0.4.1"])
+      s.add_runtime_dependency(%q<bio>.freeze, [">= 1.4.2"])
+      s.add_development_dependency(%q<shoulda>.freeze, ["= 2.10"])
+      s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
+      s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
+      s.add_development_dependency(%q<rack>.freeze, ["= 1.6.4"])
+    else
+      s.add_dependency(%q<bio-svgenes>.freeze, [">= 0.4.1"])
+      s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
+      s.add_dependency(%q<shoulda>.freeze, ["= 2.10"])
+      s.add_dependency(%q<test-unit>.freeze, [">= 0"])
+      s.add_dependency(%q<juwelier>.freeze, [">= 0"])
+      s.add_dependency(%q<rack>.freeze, ["= 1.6.4"])
+    end
+  else
+    s.add_dependency(%q<bio-svgenes>.freeze, [">= 0.4.1"])
+    s.add_dependency(%q<bio>.freeze, [">= 1.4.2"])
+    s.add_dependency(%q<shoulda>.freeze, ["= 2.10"])
+    s.add_dependency(%q<test-unit>.freeze, [">= 0"])
+    s.add_dependency(%q<juwelier>.freeze, [">= 0"])
+    s.add_dependency(%q<rack>.freeze, ["= 1.6.4"])
+  end
+end
+