htslib 0.0.2 → 0.0.3

data/lib/hts/{ffi → libhts}/faidx.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Build index for a FASTA or FASTQ or bgzip-compressed FASTA or FASTQ file.
     attach_function \
       :fai_build3,

data/lib/hts/{ffi → libhts}/hfile.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Open the named file or URL as a stream
     attach_function \
       :hopen,

data/lib/hts/{ffi → libhts}/hts.rb

@@ -1,11 +1,17 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # hts_expand
     # hts_expand3
     # hts_resize
 
+    # hts_log.h
+    attach_function \
+      :hts_get_log_level,
+      [],
+      HtsLogLevel
+
     attach_function \
       :hts_lib_shutdown,
       [],

data/lib/hts/{ffi → libhts}/kfunc.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # Log gamma function
     attach_function \
       :kf_lgamma,

data/lib/hts/{ffi → libhts}/sam.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # constants
     BAM_CMATCH     = 0
     BAM_CINS       = 1
@@ -14,8 +14,8 @@ module HTS
     BAM_CDIFF      = 8
     BAM_CBACK      = 9
 
-    BAM_CIGAR_STR = 'MIDNSHP=XB'
-    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
+    BAM_CIGAR_STR = "MIDNSHP=XB"
+    BAM_CIGAR_STR_PADDED = "MIDNSHP=XB??????"
     BAM_CIGAR_SHIFT = 4
     BAM_CIGAR_MASK  = 0xf
     BAM_CIGAR_TYPE  = 0x3C1A7
@@ -441,7 +441,7 @@ module HTS
     # Get the next read from a SAM/BAM/CRAM iterator
     def self.sam_itr_next(htsfp, itr, r)
       # FIXME: check if htsfp is compressed BGZF
-      hts_log_error('Null iterator') if itr.null?
+      hts_log_error("Null iterator") if itr.null?
       # FIXME: check multi
       hts_itr_next(htsfp[:fp][:bgzf], itr, r, htsfp)
     end
@@ -584,52 +584,52 @@ module HTS
     attach_function \
       :bam_plp_init,
       %i[bam_plp_auto_f pointer],
-      BamPlp
+      :bam_plp
 
     attach_function \
       :bam_plp_destroy,
-      [BamPlp],
+      [:bam_plp],
       :void
 
     attach_function \
       :bam_plp_push,
-      [BamPlp, Bam1],
+      [:bam_plp, Bam1],
       :int
 
     attach_function \
       :bam_plp_next,
-      [BamPlp, :pointer, :pointer, :pointer],
-      :pointer
+      %i[bam_plp pointer pointer pointer],
+      BamPileup1.by_ref
 
     attach_function \
       :bam_plp_auto,
-      [BamPlp, :pointer, :pointer, :pointer],
-      :pointer
+      %i[bam_plp pointer pointer pointer],
+      BamPileup1.by_ref
 
     attach_function \
       :bam_plp64_next,
-      [BamPlp, :pointer, :pointer, :pointer],
-      :pointer
+      %i[bam_plp pointer pointer pointer],
+      BamPileup1.by_ref
 
     attach_function \
       :bam_plp64_auto,
-      [BamPlp, :pointer, :pointer, :pointer],
-      :pointer
+      %i[bam_plp pointer pointer pointer],
+      BamPileup1.by_ref
 
     attach_function \
       :bam_plp_set_maxcnt,
-      [BamPlp, :int],
+      %i[bam_plp int],
       :void
 
     attach_function \
       :bam_plp_reset,
-      [BamPlp],
+      [:bam_plp],
       :void
 
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
       :bam_plp_insertion,
-      [:pointer, KString, :pointer],
+      [BamPileup1, KString, :pointer],
       :int
 
     # sets a callback to initialise any per-pileup1_t fields.
@@ -643,36 +643,36 @@ module HTS
     attach_function \
       :bam_mplp_init,
       %i[int bam_plp_auto_f pointer],
-      BamMplp.by_ref
+      :bam_mplp
 
     attach_function \
       :bam_mplp_init_overlaps,
-      [BamMplp],
+      [:bam_mplp],
       :int
 
     attach_function \
       :bam_mplp_destroy,
-      [BamMplp],
+      [:bam_mplp],
       :void
 
     attach_function \
       :bam_mplp_set_maxcnt,
-      [BamMplp, :int],
+      %i[bam_mplp int],
       :void
 
     attach_function \
       :bam_mplp_auto,
-      [BamMplp, :pointer, :pointer, :pointer, :pointer],
+      %i[bam_mplp pointer pointer pointer pointer], # BamPileup1T
       :int
 
     attach_function \
       :bam_mplp64_auto,
-      [BamMplp, :pointer, :pointer, :pointer, :pointer],
+      %i[bam_mplp pointer pointer pointer pointer], # BamPileup1T
       :int
 
     attach_function \
       :bam_mplp_reset,
-      [BamMplp],
+      [:bam_mplp],
       :void
 
     # bam_mplp_constructor

data/lib/hts/{ffi → libhts}/tbx.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     attach_function \
       :tbx_name2id,
       [Tbx, :string],

data/lib/hts/{ffi → libhts}/vcf.rb

@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 module HTS
-  module FFI
+  module LibHTS
     # constants
     BCF_HL_FLT    = 0 # header line
     BCF_HL_INFO   = 1

data/lib/hts/vcf.rb

@@ -3,40 +3,40 @@
 # Based on hts-python
 # https://github.com/quinlan-lab/hts-python
 
-require_relative 'vcf/header'
-require_relative 'vcf/variant'
+require_relative "vcf/header"
+require_relative "vcf/record"
 
 module HTS
   class VCF
     include Enumerable
-    attr_reader :file_path, :mode, :header, :htf
+    attr_reader :file_path, :mode, :htf, :header
 
-    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}")
+    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)
 
-      @mode = mode
-      @htf = FFI.hts_open(@file_path, mode)
+      @file_path = file_path
+      @mode      = mode
+      @htf       = LibHTS.hts_open(file_path, mode)
+      @header = VCF::Header.new(LibHTS.bcf_hdr_read(htf))
 
-      @header = VCF::Header.new(FFI.bcf_hdr_read(@htf))
-
-      @c = FFI.bcf_init
+      # FIXME: should be defined here?
+      @c = LibHTS.bcf_init
     end
 
     # def inspect; end
 
     def each(&block)
-      block.call(Variant.new(@c, self)) while FFI.bcf_read(@htf, @header.h, @c) != -1
+      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
-      FFI.bcf_hdr_nsamples(header.h)
+      LibHTS.bcf_hdr_nsamples(header.h)
     end
   end
-
-  class Format
-    def initialize; end
-  end
 end

data/lib/hts/vcf/format.rb

@@ -0,0 +1,24 @@
+# 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

@@ -12,12 +12,12 @@ module HTS
       # FIXME: better name?
       def seqs
         Array.new(@h[:n_targets]) do |i|
-          FFI.sam_hdr_tid2name(@h, i)
+          LibHTS.sam_hdr_tid2name(@h, i)
         end
       end
 
       def text
-        FFI.sam_hdr_str(@h)
+        LibHTS.sam_hdr_str(@h)
       end
     end
   end

data/lib/hts/vcf/info.rb

@@ -0,0 +1,24 @@
+# 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/{variant.rb → record.rb}

@@ -2,10 +2,10 @@
 
 module HTS
   class VCF
-    class Variant
+    class Record
       def initialize(bcf_t, vcf)
         @c = bcf_t
-        FFI.bcf_unpack(@c, HTS::FFI::BCF_UN_ALL) # FIXME
+        LibHTS.bcf_unpack(@c, LibHTS::BCF_UN_ALL) # FIXME
         @vcf = vcf
       end
 

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = '0.0.2'
+  VERSION = "0.0.3"
 end

data/lib/htslib.rb

@@ -1,27 +1,27 @@
 # frozen_string_literal: true
 
-require 'ffi'
+require "ffi"
 
-require 'hts/version'
+require "hts/version"
 
 module HTS
   class Error < StandardError; end
 
   class << self
-    attr_accessor :ffi_lib
+    attr_accessor :lib_path
 
     def search_htslib(name = nil)
-      name ||= "libhts.#{::FFI::Platform::LIBSUFFIX}"
-      lib_path = if ENV['HTSLIBDIR']
-                   File.expand_path(name, ENV['HTSLIBDIR'])
+      name ||= "libhts.#{FFI::Platform::LIBSUFFIX}"
+      lib_path = if ENV["HTSLIBDIR"]
+                   File.expand_path(name, ENV["HTSLIBDIR"])
                  else
                    File.expand_path("../vendor/#{name}", __dir__)
                  end
       return lib_path if File.exist?(lib_path)
 
       begin
-        require 'pkg-config'
-        lib_dir = PKGConfig.variable('htslib', 'libdir')
+        require "pkg-config"
+        lib_dir = PKGConfig.variable("htslib", "libdir")
         lib_path = File.expand_path(name, lib_dir)
       rescue PackageConfig::NotFoundError
         warn "htslib.pc was not found in the pkg-config search path."
@@ -32,17 +32,14 @@ module HTS
     end
   end
 
-  self.ffi_lib = search_htslib
+  self.lib_path = search_htslib
 
-  # You can change the path of the shared library with `HTS.ffi_lib=`
-  # before calling the FFI module.
-  autoload :FFI, 'hts/ffi'
+  # You can change the path of the shared library with `HTS.lib_path=`
+  # before calling the LibHTS module.
+  autoload :LibHTS, "hts/libhts"
 end
 
-# alias
-HTSlib = HTS
-
-require_relative 'hts/bam'
-require_relative 'hts/fai'
-require_relative 'hts/tbx'
-require_relative 'hts/vcf'
+require_relative "hts/bam"
+require_relative "hts/fai"
+require_relative "hts/tbx"
+require_relative "hts/vcf"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-06-18 00:00:00.000000000 Z
+date: 2021-07-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -53,7 +53,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: minitest
+  name: irb
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -67,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rake
+  name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -81,7 +81,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: rubocop
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -118,24 +118,27 @@ 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/bam/record.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/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/tbx.rb
 - lib/hts/vcf.rb
+- lib/hts/vcf/format.rb
 - lib/hts/vcf/header.rb
-- lib/hts/vcf/variant.rb
+- lib/hts/vcf/info.rb
+- lib/hts/vcf/record.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib