htslib 0.0.3 → 0.0.4

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-08 00:00:00.000000000 Z
+date: 2021-12-22 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
@@ -122,7 +136,14 @@ files:
 - lib/hts/bam/flag.rb
 - lib/hts/bam/header.rb
 - lib/hts/bam/record.rb
-- lib/hts/fai.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
@@ -133,12 +154,8 @@ files:
 - lib/hts/libhts/sam.rb
 - lib/hts/libhts/tbx.rb
 - lib/hts/libhts/vcf.rb
-- lib/hts/tbx.rb
-- lib/hts/vcf.rb
-- lib/hts/vcf/format.rb
-- lib/hts/vcf/header.rb
-- lib/hts/vcf/info.rb
-- lib/hts/vcf/record.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
@@ -153,14 +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: 3.2.15
+rubygems_version: 3.2.26
 signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby

data/lib/hts/vcf/format.rb

@@ -1,24 +0,0 @@
-# frozen_string_literal: true
-
-# https://github.com/brentp/hts-nim/blob/master/src/hts/vcf.nim
-# This is a port from Nim.
-# TODO: Make it more like Ruby.
-
-module HTS
-  class VCF
-    class Format
-      def initialize; end
-
-      def delete; end
-
-      def get; end
-
-      def set; end
-
-      # def fields # iterator
-      # end
-
-      def genotypes; end
-    end
-  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|
-          LibHTS.sam_hdr_tid2name(@h, i)
-        end
-      end
-
-      def text
-        LibHTS.sam_hdr_str(@h)
-      end
-    end
-  end
-end

data/lib/hts/vcf/info.rb

@@ -1,24 +0,0 @@
-# frozen_string_literal: true
-
-# https://github.com/brentp/hts-nim/blob/master/src/hts/vcf.nim
-# This is a port from Nim.
-# TODO: Make it more like Ruby.
-
-module HTS
-  class VCF
-    class Info
-      def initialize; end
-
-      def has_flag?; end
-
-      def get; end
-
-      def set; end
-
-      def delete; end
-
-      # def fields # iterator
-      # end
-    end
-  end
-end

data/lib/hts/vcf/record.rb

@@ -1,43 +0,0 @@
-# frozen_string_literal: true
-
-module HTS
-  class VCF
-    class Record
-      def initialize(bcf_t, vcf)
-        @c = bcf_t
-        LibHTS.bcf_unpack(@c, LibHTS::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/record"
-
-module HTS
-  class VCF
-    include Enumerable
-    attr_reader :file_path, :mode, :htf, :header
-
-    def initialize(file_path, mode = "r")
-      file_path = File.expand_path(file_path)
-      raise("No such VCF/BCF file - #{file_path}") unless File.exist?(file_path)
-
-      @file_path = file_path
-      @mode      = mode
-      @htf       = LibHTS.hts_open(file_path, mode)
-      @header = VCF::Header.new(LibHTS.bcf_hdr_read(htf))
-
-      # FIXME: should be defined here?
-      @c = LibHTS.bcf_init
-    end
-
-    # def inspect; end
-
-    def each(&block)
-      while LibHTS.bcf_read(htf, header.h, @c) != -1
-        record = Record.new(@c, self)
-        block.call(record)
-      end
-    end
-
-    def seq(tid); end
-
-    def n_samples
-      LibHTS.bcf_hdr_nsamples(header.h)
-    end
-  end
-end