bio-twobit 0.1.1

data/lib/bio/twobit.rb

@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+require_relative "twobit/version"
+require_relative "twobit/twobit"
+
+module Bio
+  class TwoBit
+    class << self
+      alias open new
+    end
+
+    def initialize(fname, masked: false)
+      mskd = masked ? 1 : 0
+      initialize_raw(fname, mskd)
+      if block_given?
+        begin
+          yield self
+        ensure
+          close
+        end
+      end
+    end
+
+    def sequence(chrom, start = 0, stop = 0)
+      sequence_raw(chrom, start, stop)
+    end
+
+    def bases(chrom, start = 0, stop = 0, fraction: true)
+      bases_raw(chrom, start, stop, fraction ? 1 : 0)
+    end
+
+    def hard_masked_blocks(chrom, start = 0, stop = 0)
+      hard_masked_blocks_raw(chrom, start, stop)
+    end
+
+    def soft_masked_blocks(chrom, start = 0, stop = 0)
+      soft_masked_blocks_raw(chrom, start, stop)
+    end
+  end
+end

metadata

@@ -0,0 +1,59 @@
+--- !ruby/object:Gem::Specification
+name: bio-twobit
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+platform: ruby
+authors:
+- kojix2
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2021-12-18 00:00:00.000000000 Z
+dependencies: []
+description: This is a Ruby binding for lib2bit(https://github.com/dpryan79/lib2bit),
+  which provides high-speed access to genomic data in 2bit file format.
+email:
+- 2xijok@gmail.com
+executables: []
+extensions:
+- ext/bio/twobit/extconf.rb
+extra_rdoc_files: []
+files:
+- ".rubocop.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bio-twobit.gemspec
+- ext/bio/twobit/2bit.c
+- ext/bio/twobit/2bit.h
+- ext/bio/twobit/LICENSE
+- ext/bio/twobit/extconf.rb
+- ext/bio/twobit/twobit.c
+- ext/bio/twobit/twobit.h
+- lib/bio/twobit.rb
+- lib/bio/twobit/version.rb
+homepage: https://github.com/ruby-on-bioc/bio-twobit
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 2.6.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.2.22
+signing_key: 
+specification_version: 4
+summary: A ruby library for accessing 2bit files
+test_files: []