htslib 0.0.1 → 0.0.5

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.5
 platform: ruby
 authors:
 - kojix2
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-01-25 00:00:00.000000000 Z
+date: 2021-12-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -25,13 +25,13 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: ffi-bitfield
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-  type: :development
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
@@ -39,7 +39,21 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: minitest
+  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
     requirements:
     - - ">="
@@ -53,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: irb
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -67,7 +81,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -81,7 +95,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rubocop
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -108,7 +122,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description:
+description: 
 email:
 - 2xijok@gmail.com
 executables: []
@@ -118,29 +132,36 @@ files:
 - LICENSE.txt
 - README.md
 - lib/hts/bam.rb
-- lib/hts/bam/alignment.rb
 - lib/hts/bam/cigar.rb
+- lib/hts/bam/flag.rb
 - lib/hts/bam/header.rb
-- lib/hts/fai.rb
-- lib/hts/ffi.rb
-- lib/hts/ffi/bgzf.rb
-- lib/hts/ffi/constants.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/tbx.rb
-- lib/hts/ffi/vcf.rb
-- lib/hts/tbx.rb
-- lib/hts/vcf.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/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -148,15 +169,15 @@ 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: 3.0.3
-signing_key:
+rubygems_version: 3.3.3
+signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []

data/lib/hts/bam/alignment.rb

@@ -1,156 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  # A cigar object usually created from `Alignment`.
-  class Bam
-    class Alignment
-      def initialize(bam1_t, bam_hdr_t)
-        @b = bam1_t
-        @h = bam_hdr_t
-      end
-
-      # def initialize_copy
-      #   super
-      # end
-
-      def self.rom_sam_str; end
-
-      def tags; end
-
-      # Read (query) name.
-      def qname
-        FFI.bam_get_qname(@b).read_string
-      end
-
-      # Set (query) name.
-      # def qname=(name)
-      #   raise 'Not Implemented'
-      # end
-
-      # returns the chromosome of the mate or '' if not mapped.
-      def mate_chrom
-        tid = @b[:core][:mtid]
-        return '' if tid == -1
-
-        FFI.sam_hdr_tid2name(@h, tid)
-      end
-
-      # returns the tid of the mate or -1 if not mapped.
-      def mate_tid
-        @b[:core][:mtid]
-      end
-
-      # returns the tid of the alignment or -1 if not mapped.
-      def tid
-        @b[:core][:tid]
-      end
-
-      # mate position
-      def mate_pos
-        @b[:core][:mpos]
-      end
-
-      # returns 0-based start position.
-      def start
-        @b[:core][:pos]
-      end
-
-      # returns end position of the read.
-      def stop
-        FFI.bam_endpos @b
-      end
-
-      # returns the chromosome or '' if not mapped.
-      def chrom
-        tid = @b[:core][:tid]
-        return '' if tid == -1
-
-        FFI.sam_hdr_tid2name(@h, tid)
-      end
-
-      def strand
-        FFI.bam_is_rev(@b) ? '-' : '+'
-      end
-
-      # def start=(v)
-      #   raise 'Not Implemented'
-      # end
-
-      # insert size
-      def isize
-        @b[:core][:isize]
-      end
-
-      # mapping quality
-      def mapping_quality
-        @b[:core][:qual]
-      end
-
-      # returns a `Cigar` object.
-      def cigar
-        Cigar.new(FFI.bam_get_cigar(@b), @b[:core][:n_cigar])
-      end
-
-      def qlen
-        FFI.bam_cigar2qlen(
-          @b[:core][:n_cigar],
-          FFI.bam_get_cigar(@b)
-        )
-      end
-
-      def rlen
-        FFI.bam_cigar2rlen(
-          @b[:core][:n_cigar],
-          FFI.bam_get_cigar(@b)
-        )
-      end
-
-      # return the read sequence
-      def sequence
-        seq_nt16_str = '=ACMGRSVTWYHKDBN'
-        r = FFI.bam_get_seq(@b)
-        Array.new(@b[:core][:l_qseq]) do |i|
-          seq_nt16_str[FFI.bam_seqi(r, i)]
-        end.join
-      end
-
-      def base_at(n)
-        n += @b[:core][:l_qseq] if n < 0
-        seq_nt16_str = '=ACMGRSVTWYHKDBN'
-        return '.' if (n >= @b[:core][:l_qseq]) || (n < 0) # eg. base_at(-1000)
-
-        r = FFI.bam_get_seq(@b)
-        seq_nt16_str[FFI.bam_seqi(r, n)]
-      end
-
-      def base_qualities
-        q_ptr = FFI.bam_get_qual(@b)
-        q_ptr.read_array_of_uint8(@b[:core][:l_qseq])
-      end
-
-      def base_quality_at(n)
-        n += @b[:core][:l_qseq] if n < 0 # eg. base_quality_at(-1000)
-        return 0 if (n >= @b[:core][:l_qseq]) || (n < 0)
-
-        q_ptr = FFI.bam_get_qual(@b)
-        q_ptr.get_uint8(n)
-      end
-
-      def flag_str
-        FFI.bam_flag2str(flag)
-      end
-
-      # returns a `Flag` object.
-      def flag
-        @b[:core][:flag]
-      end
-
-      # TODO:
-      # def eql?
-      # def hash
-    end
-  end
-end

data/lib/hts/fai.rb

@@ -1,18 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  class Fai
-    def initialize; end
-
-    # def call
-
-    def nseqs; end
-
-    def include?; end
-
-    # __iter__
-  end
-end

data/lib/hts/ffi.rb

@@ -1,43 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  module FFI
-    extend ::FFI::Library
-
-    begin
-      ffi_lib HTS.ffi_lib
-    rescue LoadError => e
-      raise LoadError, "#{e}\nCould not find #{HTS.ffi_lib}"
-    end
-
-    def self.attach_function(*)
-      super
-    rescue ::FFI::NotFoundError => e
-      warn e.message
-    end
-  end
-end
-
-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
-
-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

@@ -1,16 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  class Tbx
-    def initialize; end
-
-    def build; end
-
-    def sequences; end
-
-    # def __call__\
-  end
-end

data/lib/hts/vcf.rb

@@ -1,32 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  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
-end