bio-twobit 0.1.3 → 0.2.0
Sign up to get free protection for your applications and to get access to all the features.
- 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
|