bio-twobit 0.1.3 → 0.2.0
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/LICENSE.txt +11 -0
- data/README.md +42 -4
- data/ext/bio/twobit/twobit.c +409 -412
- data/lib/bio/twobit/cache_path.rb +32 -0
- data/lib/bio/twobit/downloader.rb +282 -0
- data/lib/bio/twobit/metadata.rb +9 -0
- data/lib/bio/twobit/reference_genome.rb +24 -0
- data/lib/bio/twobit/references/danrer10.rb +16 -0
- data/lib/bio/twobit/references/danrer11.rb +16 -0
- data/lib/bio/twobit/references/dm6.rb +16 -0
- data/lib/bio/twobit/references/hg19.rb +16 -0
- data/lib/bio/twobit/references/hg38.rb +16 -0
- data/lib/bio/twobit/references/hs1.rb +16 -0
- data/lib/bio/twobit/references/mm10.rb +16 -0
- data/lib/bio/twobit/references/mm39.rb +16 -0
- data/lib/bio/twobit/references/mm9.rb +16 -0
- data/lib/bio/twobit/version.rb +1 -1
- data/lib/bio/twobit.rb +55 -9
- metadata +16 -7
- data/.rubocop.yml +0 -13
- data/Gemfile +0 -14
- data/Rakefile +0 -25
- data/bio-twobit.gemspec +0 -25
data/Gemfile
DELETED
data/Rakefile
DELETED
|
@@ -1,25 +0,0 @@
|
|
|
1
|
-
# frozen_string_literal: true
|
|
2
|
-
|
|
3
|
-
require "bundler/gem_tasks"
|
|
4
|
-
require "rake/testtask"
|
|
5
|
-
|
|
6
|
-
Rake::TestTask.new(:test) do |t|
|
|
7
|
-
t.libs << "test"
|
|
8
|
-
t.libs << "lib"
|
|
9
|
-
t.test_files = FileList["test/**/*_test.rb"]
|
|
10
|
-
end
|
|
11
|
-
|
|
12
|
-
require "rubocop/rake_task"
|
|
13
|
-
|
|
14
|
-
RuboCop::RakeTask.new
|
|
15
|
-
|
|
16
|
-
require "rake/extensiontask"
|
|
17
|
-
|
|
18
|
-
task build: :compile
|
|
19
|
-
|
|
20
|
-
Rake::ExtensionTask.new("twobit") do |ext|
|
|
21
|
-
ext.lib_dir = "lib/bio/twobit"
|
|
22
|
-
ext.ext_dir = "ext/bio/twobit"
|
|
23
|
-
end
|
|
24
|
-
|
|
25
|
-
task default: %i[clobber compile test rubocop]
|
data/bio-twobit.gemspec
DELETED
|
@@ -1,25 +0,0 @@
|
|
|
1
|
-
# frozen_string_literal: true
|
|
2
|
-
|
|
3
|
-
require_relative "lib/bio/twobit/version"
|
|
4
|
-
|
|
5
|
-
Gem::Specification.new do |spec|
|
|
6
|
-
spec.name = "bio-twobit"
|
|
7
|
-
spec.version = Bio::TwoBit::VERSION
|
|
8
|
-
spec.authors = ["kojix2"]
|
|
9
|
-
spec.email = ["2xijok@gmail.com"]
|
|
10
|
-
|
|
11
|
-
spec.summary = "A ruby library for accessing 2bit files"
|
|
12
|
-
spec.description = "This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit), " \
|
|
13
|
-
"which provides high-speed access to genomic data in 2bit file format."
|
|
14
|
-
spec.homepage = "https://github.com/ruby-on-bioc/bio-twobit"
|
|
15
|
-
spec.license = "MIT"
|
|
16
|
-
spec.required_ruby_version = ">= 2.6.0"
|
|
17
|
-
|
|
18
|
-
spec.files = Dir.chdir(File.expand_path(__dir__)) do
|
|
19
|
-
`git ls-files -z`.split("\x0").reject do |f|
|
|
20
|
-
(f == __FILE__) || f.match(%r{\A(?:(?:test|spec|features)/|\.(?:git|travis|circleci)|appveyor)})
|
|
21
|
-
end
|
|
22
|
-
end
|
|
23
|
-
spec.require_paths = ["lib"]
|
|
24
|
-
spec.extensions = ["ext/bio/twobit/extconf.rb"]
|
|
25
|
-
end
|