htslib 0.0.0 → 0.0.4

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.0.4
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-10-21 00:00:00.000000000 Z
+date: 2021-12-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -24,6 +24,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: ffi-bitfield
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pkg-config
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -39,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: irb
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -53,7 +81,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -67,7 +95,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -81,7 +109,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rubocop
+  name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -104,20 +132,30 @@ files:
 - LICENSE.txt
 - README.md
 - lib/hts/bam.rb
-- lib/hts/fai.rb
-- lib/hts/ffi.rb
-- lib/hts/ffi/bgzf.rb
-- lib/hts/ffi/faidx.rb
-- lib/hts/ffi/hfile.rb
-- lib/hts/ffi/hts.rb
-- lib/hts/ffi/kfunc.rb
-- lib/hts/ffi/sam.rb
-- lib/hts/ffi/struct.rb
-- lib/hts/ffi/tbx.rb
-- lib/hts/ffi/vcf.rb
-- lib/hts/ffi_constants.rb
-- lib/hts/tbx.rb
-- lib/hts/vcf.rb
+- lib/hts/bam/cigar.rb
+- lib/hts/bam/flag.rb
+- lib/hts/bam/header.rb
+- lib/hts/bam/record.rb
+- lib/hts/bcf.rb
+- lib/hts/bcf/format.rb
+- lib/hts/bcf/header.rb
+- lib/hts/bcf/info.rb
+- lib/hts/bcf/record.rb
+- lib/hts/faidx.rb
+- lib/hts/ffi_ext/README.md
+- lib/hts/ffi_ext/struct.rb
+- lib/hts/libhts.rb
+- lib/hts/libhts/bgzf.rb
+- lib/hts/libhts/constants.rb
+- lib/hts/libhts/faidx.rb
+- lib/hts/libhts/hfile.rb
+- lib/hts/libhts/hts.rb
+- lib/hts/libhts/kfunc.rb
+- lib/hts/libhts/sam.rb
+- lib/hts/libhts/tbx.rb
+- lib/hts/libhts/vcf.rb
+- lib/hts/tabix.rb
+- lib/hts/utils/open_method.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
@@ -132,14 +170,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.4'
+      version: '2.7'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.4
+rubygems_version: 3.2.26
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby

data/lib/hts/fai.rb

@@ -1,16 +0,0 @@
-# frozen_string_literal: true
-
-# Create a skeleton using hts-python as a reference.
-# https://github.com/quinlan-lab/hts-python
-
-class Fai
-  def initialize; end
-
-  # def call
-
-  def nseqs; end
-
-  def include?; end
-
-  # __iter__
-end

data/lib/hts/ffi/struct.rb

@@ -1,14 +0,0 @@
-# frozen_string_literal: true
-
-# This should be removed if you get the better way...
-module FFI
-  class Struct
-    def self.union_layout(*args)
-      Class.new(FFI::Union) { layout(*args) }
-    end
-
-    def self.struct_layout(*args)
-      Class.new(FFI::Struct) { layout(*args) }
-    end
-  end
-end

data/lib/hts/ffi.rb

@@ -1,32 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module FFI
-    extend ::FFI::Library
-
-    begin
-      ffi_lib HTS.ffi_lib
-    rescue LoadError => e
-      raise LoadError, "Could not find HTSlib.#{FFI::Platform::LIBSUFFIX}"
-    end
-
-    def self.attach_function(*)
-      super
-    rescue ::FFI::NotFoundError => e
-      warn e.message
-    end
-  end
-end
-
-require_relative 'ffi/struct'
-require_relative 'ffi_constants'
-
-# alphabetical order
-require_relative 'ffi/bgzf'
-require_relative 'ffi/faidx'
-require_relative 'ffi/hfile'
-require_relative 'ffi/hts'
-require_relative 'ffi/sam'
-require_relative 'ffi/kfunc'
-require_relative 'ffi/tbx'
-require_relative 'ffi/vcf'

data/lib/hts/tbx.rb

@@ -1,14 +0,0 @@
-# frozen_string_literal: true
-
-# Create a skeleton using hts-python as a reference.
-# https://github.com/quinlan-lab/hts-python
-
-class Tbx
-  def initialize; end
-
-  def build; end
-
-  def sequences; end
-
-  # def __call__\
-end

data/lib/hts/vcf.rb

@@ -1,30 +0,0 @@
-# frozen_string_literal: true
-
-# Create a skeleton using hts-python as a reference.
-# https://github.com/quinlan-lab/hts-python
-
-class VCF
-  def initialize; end
-
-  def inspect; end
-
-  def each; end
-
-  def seq; end
-
-  def n_samples; end
-end
-
-class Variant
-  def initialize; end
-
-  def inspect; end
-
-  def formats; end
-
-  def genotypes; end
-end
-
-class Format
-  def initialize; end
-end