htslib 0.0.2 → 0.0.6

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.6
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-06-18 00:00:00.000000000 Z
+date: 2022-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -24,6 +24,20 @@ 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
@@ -53,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: minitest
+  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: []
@@ -118,31 +132,38 @@ 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/vcf/header.rb
-- lib/hts/vcf/variant.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/sam_funcs.rb
+- lib/hts/libhts/tbx.rb
+- lib/hts/libhts/vcf.rb
+- lib/hts/libhts/vcf_funcs.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
@@ -150,15 +171,15 @@ 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: 3.2.15
-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

@@ -1,155 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  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

@@ -1,57 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-module HTS
-  class Fai
-    # FIXME: API
-    def self.open(path)
-      fai = new(path)
-      if block_given?
-        yield(fai)
-        fai.close
-      else
-        fai
-      end
-    end
-
-    def initialize(path)
-      @path = File.expand_path(path)
-      @path.delete_suffix!('.fai')
-      FFI.fai_build(@path) unless File.exist?("#{@path}.fai")
-      @fai = FFI.fai_load(@path)
-      raise if @fai.null?
-
-      # at_exit{FFI.fai_destroy(@fai)}
-    end
-
-    def close
-      FFI.fai_destroy(@fai)
-    end
-
-    # the number of sequences in the index.
-    def size
-      FFI.faidx_nseq(@fai)
-    end
-    alias length size
-
-    # return the length of the requested chromosome.
-    def chrom_size(chrom)
-      raise ArgumentError, 'Expect chrom to be String or Symbol' unless chrom.is_a?(String) || chrom.is_a?(Symbol)
-
-      chrom = chrom.to_s
-      result = FFI.faidx_seq_len(@fai, chrom)
-      result == -1 ? nil : result
-    end
-    alias chrom_length chrom_size
-
-    # FIXME: naming and syntax
-    def cget; end
-
-    # FIXME: naming and syntax
-    def get; end
-
-    # __iter__
-  end
-end

data/lib/hts/ffi.rb

@@ -1,85 +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
-    class << self
-      def union_layout(*args)
-        Class.new(FFI::Union) { layout(*args) }
-      end
-
-      def struct_layout(*args)
-        Class.new(FFI::Struct) { layout(*args) }
-      end
-    end
-  end
-
-  class BitStruct < Struct
-    class << self
-      module BitFieldsModule
-        def [](name)
-          bit_fields = self.class.bit_fields_hash_table
-          parent, start, width = bit_fields[name]
-          if parent
-            (super(parent) >> start) & ((1 << width) - 1)
-          else
-            super(name)
-          end
-        end
-      end
-      private_constant :BitFieldsModule
-
-      attr_reader :bit_fields_hash_table
-
-      def bitfields(*args)
-        unless instance_variable_defined?(:@bit_fields_hash_table)
-          @bit_fields_hash_table = {}
-          prepend BitFieldsModule
-        end
-
-        parent = args.shift
-        labels = []
-        widths = []
-        args.each_slice(2) do |l, w|
-          labels << l
-          widths << w
-        end
-        starts = widths.inject([0]) do |result, w|
-          result << (result.last + w)
-        end
-        labels.zip(starts, widths).each do |l, s, w|
-          @bit_fields_hash_table[l] = [parent, s, w]
-        end
-      end
-    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/header.rb

@@ -1,24 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  class VCF
-    class Header
-      attr_reader :h
-
-      def initialize(h)
-        @h = h
-      end
-
-      # FIXME: better name?
-      def seqs
-        Array.new(@h[:n_targets]) do |i|
-          FFI.sam_hdr_tid2name(@h, i)
-        end
-      end
-
-      def text
-        FFI.sam_hdr_str(@h)
-      end
-    end
-  end
-end

data/lib/hts/vcf/variant.rb

@@ -1,43 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  class VCF
-    class Variant
-      def initialize(bcf_t, vcf)
-        @c = bcf_t
-        FFI.bcf_unpack(@c, HTS::FFI::BCF_UN_ALL) # FIXME
-        @vcf = vcf
-      end
-
-      # def inspect; end
-
-      def formats; end
-
-      def genotypes; end
-
-      def pos
-        @c[:pos] + 1 # FIXME
-      end
-
-      def start
-        @c[:pos]
-      end
-
-      def stop
-        @c[:pos] + @c[:rlen]
-      end
-
-      def id
-        @c[:d][:id]
-      end
-
-      def qual
-        @c[:qual]
-      end
-
-      def ref
-        @c[:d][:allele].get_pointer(0).read_string
-      end
-    end
-  end
-end

data/lib/hts/vcf.rb

@@ -1,42 +0,0 @@
-# frozen_string_literal: true
-
-# Based on hts-python
-# https://github.com/quinlan-lab/hts-python
-
-require_relative 'vcf/header'
-require_relative 'vcf/variant'
-
-module HTS
-  class VCF
-    include Enumerable
-    attr_reader :file_path, :mode, :header, :htf
-
-    def initialize(file_path, mode = 'r')
-      @file_path = File.expand_path(file_path)
-      File.exist?(@file_path) || raise("No such VCF/BCF file - #{@file_path}")
-
-      @mode = mode
-      @htf = FFI.hts_open(@file_path, mode)
-
-      @header = VCF::Header.new(FFI.bcf_hdr_read(@htf))
-
-      @c = FFI.bcf_init
-    end
-
-    # def inspect; end
-
-    def each(&block)
-      block.call(Variant.new(@c, self)) while FFI.bcf_read(@htf, @header.h, @c) != -1
-    end
-
-    def seq(tid); end
-
-    def n_samples
-      FFI.bcf_hdr_nsamples(header.h)
-    end
-  end
-
-  class Format
-    def initialize; end
-  end
-end