htslib 0.0.1 → 0.0.2

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data/README.md

@@ -4,12 +4,19 @@
 ![CI](https://github.com/kojix2/ruby-htslib/workflows/CI/badge.svg)
 [![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
 [![DOI](https://zenodo.org/badge/247078205.svg)](https://zenodo.org/badge/latestdoi/247078205)
+[![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/htslib)
 
 :dna: [HTSlib](https://github.com/samtools/htslib) - high-throughput sequencing data manipulation - for Ruby
 
 :apple: Feel free to fork it out if you can develop it! 
 
-:bowtie: Just a prototype. 
+:bowtie: Just a prototype. Pre-alpha stage.
+
+## Requirements
+
+* [htslib](https://github.com/samtools/htslib)
+  * Ubuntu : `apt install libhts-dev`
+  * macOS : `brew install htslib`
 
 ## Installation
 
@@ -17,16 +24,14 @@
 gem install htslib
 ```
 
-Set environment variable HTSLIBDIR. 
+If you installed htslib with Ubuntu/apt or Mac/homebrew, pkg-config will automatically detect the location of the shared library.
+
+Or you can set the environment variable `HTSLIBDIR`.
 
 ```sh
-export HTSLIBDIR="/your/path/to/htslib"
+export HTSLIBDIR="/your/path/to/htslib" # libhts.so
 ```
 
-## Requirements
-
-* [htslib](https://github.com/samtools/htslib)
-
 ## Usage
 
 HTS::FFI - Low-level API 
@@ -42,6 +47,23 @@ p b[:format]
 
 A high-level API based on [hts-python](https://github.com/quinlan-lab/hts-python) is under development.
 
+```ruby
+require 'htslib'
+
+bam = HTS::Bam.new("a.bam")
+
+bam.each do |aln|
+  p name:  aln.qname,
+    flag:  aln.flag,
+    start: aln.start + 1,
+    mpos:  aln.mate_pos + 1,
+    mqual: aln.mapping_quality,
+    seq:   aln.sequence,
+    cigar: aln.cigar.to_s,
+    qual:  aln.base_qualities.map { |i| (i + 33).chr }.join
+end
+```
+
 ## Documentation
 
 * [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
@@ -51,15 +73,17 @@ A high-level API based on [hts-python](https://github.com/quinlan-lab/hts-python
 To get started with development
 
 ```sh
-git clone --recurse-submodules https://github.com/kojix2/ruby-htslib
+git clone --recursive https://github.com/kojix2/ruby-htslib
 cd ruby-htslib
 bundle install
-bundle exec rake htslib:compile
-bundle exec rake spec
+bundle exec rake htslib:build
+bundle exec rake test
 ```
 
 ## Contributing
 
+Ruby-htslib is a library under development, so even small improvements like typofix are welcome! Please feel free to send us your pull requests.
+
 * [Report bugs](https://github.com/kojix2/ruby-htslib/issues)
 * Fix bugs and [submit pull requests](https://github.com/kojix2/ruby-htslib/pulls)
 * Write, clarify, or fix documentation

data/lib/hts/bam.rb

@@ -10,20 +10,20 @@ require_relative 'bam/alignment'
 module HTS
   class Bam
     include Enumerable
-    attr_reader :fname, :mode, :header, :htf
+    attr_reader :file_path, :mode, :header, :htf
 
-    def initialize(fname, mode = 'r', create_index: nil, header: nil, fasta: nil)
-      @fname = File.expand_path(fname)
-      File.exist?(@fname) || raise("No such SAM/BAM file - #{@fname}")
+    def initialize(file_path, mode = 'r', create_index: nil, header: nil, fasta: nil)
+      @file_path = File.expand_path(file_path)
+      File.exist?(@file_path) || raise("No such SAM/BAM file - #{@file_path}")
 
       @mode = mode
-      @htf = FFI.hts_open(@fname, mode)
+      @htf = FFI.hts_open(@file_path, mode)
 
       if mode[0] == 'r'
-        @idx = FFI.sam_index_load(@htf, @fname)
+        @idx = FFI.sam_index_load(@htf, @file_path)
         if (@idx.null? && create_index.nil?) || create_index
-          FFI.sam_index_build(fname, -1)
-          @idx = FFI.sam_index_load(@htf, @fname)
+          FFI.sam_index_build(file_path, -1)
+          @idx = FFI.sam_index_load(@htf, @file_path)
           warn 'NO querying'
         end
         @header = Bam::Header.new(FFI.sam_hdr_read(@htf))

data/lib/hts/bam/alignment.rb

@@ -4,7 +4,6 @@
 # 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)

data/lib/hts/fai.rb

@@ -5,13 +5,52 @@
 
 module HTS
   class Fai
-    def initialize; end
+    # FIXME: API
+    def self.open(path)
+      fai = new(path)
+      if block_given?
+        yield(fai)
+        fai.close
+      else
+        fai
+      end
+    end
 
-    # def call
+    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?
 
-    def nseqs; end
+      # at_exit{FFI.fai_destroy(@fai)}
+    end
 
-    def include?; 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

data/lib/hts/ffi.rb

@@ -20,12 +20,54 @@ end
 
 module FFI
   class Struct
-    def self.union_layout(*args)
-      Class.new(FFI::Union) { layout(*args) }
+    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
 
-    def self.struct_layout(*args)
-      Class.new(FFI::Struct) { layout(*args) }
+        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

data/lib/hts/ffi/bgzf.rb

@@ -120,7 +120,7 @@ module HTS
     # Read one line from a BGZF file. It is faster than bgzf_getc()
     attach_function \
       :bgzf_getline,
-      [BGZF, :int, Kstring],
+      [BGZF, :int, KString],
       :int
 
     # Read the next BGZF block.

data/lib/hts/ffi/constants.rb

@@ -8,13 +8,23 @@ module HTS
 
     # kstring
 
-    class Kstring < ::FFI::Struct
+    class KString < ::FFI::Struct
       layout \
         :l,              :size_t,
         :m,              :size_t,
         :s,              :string
     end
 
+    class KSeq < ::FFI::Struct
+      layout \
+        :name,           KString,
+        :comment,        KString,
+        :seq,            KString,
+        :qual,           KString,
+        :last_char,      :int,
+        :f,              :pointer # FIXME
+    end
+
     # BGZF
     class BGZF < ::FFI::Struct
       layout \
@@ -162,7 +172,7 @@ module HTS
       layout \
         :bitfields,      :uint32, # FIXME
         :lineno,         :int64,
-        :line,           Kstring,
+        :line,           KString,
         :fn,             :string,
         :fn_aux,         :string,
         :fp,
@@ -259,36 +269,6 @@ module HTS
     class BamMplp < ::FFI::Struct
     end
 
-    BAM_CMATCH     = 0
-    BAM_CINS       = 1
-    BAM_CDEL       = 2
-    BAM_CREF_SKIP  = 3
-    BAM_CSOFT_CLIP = 4
-    BAM_CHARD_CLIP = 5
-    BAM_CPAD       = 6
-    BAM_CEQUAL     = 7
-    BAM_CDIFF      = 8
-    BAM_CBACK      = 9
-
-    BAM_CIGAR_STR = 'MIDNSHP=XB'
-    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
-    BAM_CIGAR_SHIFT = 4
-    BAM_CIGAR_MASK  = 0xf
-    BAM_CIGAR_TYPE  = 0x3C1A7
-
-    BAM_FPAIRED        =    1
-    BAM_FPROPER_PAIR   =    2
-    BAM_FUNMAP         =    4
-    BAM_FMUNMAP        =    8
-    BAM_FREVERSE       =   16
-    BAM_FMREVERSE      =   32
-    BAM_FREAD1         =   64
-    BAM_FREAD2         =  128
-    BAM_FSECONDARY     =  256
-    BAM_FQCFAIL        =  512
-    BAM_FDUP           = 1024
-    BAM_FSUPPLEMENTARY = 2048
-
     class TbxConf < ::FFI::Struct
       layout \
         :preset,         :int32,
@@ -386,10 +366,10 @@ module HTS
         :nhrec,          :int,
         :dirty,          :int,
         :ntransl,        :int,
-        :transl,         :pointer,
+        :transl,         [:pointer, 2],
         :nsamples_ori,   :int,
         :keep_samples,   :pointer,
-        :mem,            Kstring,
+        :mem,            KString,
         :m,              [:int, 3]
     end
 
@@ -401,9 +381,10 @@ module HTS
         :m_als,          :int,
         :m_allele,       :int,
         :m_flt,          :int,
+        :n_flt,          :int,
         :flt,            :pointer,
         :id,             :string,
-        :als,            :string,
+        :als,            :pointer, # (\\0-separated string)
         :allele,         :pointer,
         :info,           BcfInfo.ptr,
         :fmt,            BcfFmt.ptr,
@@ -414,21 +395,29 @@ module HTS
         :indiv_dirty,    :int
     end
 
-    class Bcf1 < ::FFI::Struct
+    class Bcf1 < ::FFI::BitStruct
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
-        :rid,            :int,
+        :rid,            :int32_t,
         :qual,           :float,
-        :piyo,           :int, # FIXME
-        :fuga,           :int, # FIXME
-        :shared,         Kstring,
-        :indiv,          Kstring,
+        :n_info_allele,  :uint32_t, # FIXME
+        :n_fmt_sample,   :uint32_t, # FIXME
+        :shared,         KString,
+        :indiv,          KString,
         :d,              BcfDec,
         :max_unpack,     :int,
         :unpacked,       :int,
         :unpack_size,    [:int, 3],
         :errcode,        :int
+
+      bitfields :n_info_allele,
+                :n_info,   16,
+                :n_allele, 16
+
+      bitfields :n_fmt_sample,
+                :n_fmt,    8,
+                :n_sample, 24
     end
   end
 end

data/lib/hts/ffi/hfile.rb

@@ -23,7 +23,7 @@ module HTS
     # Append an extension or replace an existing extension
     attach_function \
       :haddextension,
-      [Kstring, :string, :int, :string],
+      [KString, :string, :int, :string],
       :string
 
     # Flush (for output streams) and close the stream

data/lib/hts/ffi/hts.rb

@@ -8,7 +8,7 @@ module HTS
 
     attach_function \
       :hts_lib_shutdown,
-      [:void],
+      [],
       :void
 
     attach_function \
@@ -110,7 +110,7 @@ module HTS
     # Read a line (and its \n or \r\n terminator) from a file
     attach_function \
       :hts_getline,
-      [HtsFile, :int, Kstring],
+      [HtsFile, :int, KString],
       :int
 
     attach_function \

data/lib/hts/ffi/sam.rb

@@ -2,6 +2,24 @@
 
 module HTS
   module FFI
+    # constants
+    BAM_CMATCH     = 0
+    BAM_CINS       = 1
+    BAM_CDEL       = 2
+    BAM_CREF_SKIP  = 3
+    BAM_CSOFT_CLIP = 4
+    BAM_CHARD_CLIP = 5
+    BAM_CPAD       = 6
+    BAM_CEQUAL     = 7
+    BAM_CDIFF      = 8
+    BAM_CBACK      = 9
+
+    BAM_CIGAR_STR = 'MIDNSHP=XB'
+    BAM_CIGAR_STR_PADDED = 'MIDNSHP=XB??????'
+    BAM_CIGAR_SHIFT = 4
+    BAM_CIGAR_MASK  = 0xf
+    BAM_CIGAR_TYPE  = 0x3C1A7
+
     # macros
     class << self
       def bam_cigar_op(c)
@@ -13,7 +31,7 @@ module HTS
       end
 
       def bam_cigar_opchr(c)
-        (BAM_CIGAR_STR + '??????')[bam_cigar_op(c)]
+        ("#{BAM_CIGAR_STR}??????")[bam_cigar_op(c)]
       end
 
       def bam_cigar_gen(l, o)
@@ -25,6 +43,19 @@ module HTS
       end
     end
 
+    BAM_FPAIRED        =    1
+    BAM_FPROPER_PAIR   =    2
+    BAM_FUNMAP         =    4
+    BAM_FMUNMAP        =    8
+    BAM_FREVERSE       =   16
+    BAM_FMREVERSE      =   32
+    BAM_FREAD1         =   64
+    BAM_FREAD2         =  128
+    BAM_FSECONDARY     =  256
+    BAM_FQCFAIL        =  512
+    BAM_FDUP           = 1024
+    BAM_FSUPPLEMENTARY = 2048
+
     # macros
     # function-like macros
     class << self
@@ -148,13 +179,13 @@ module HTS
     # Returns a complete line of formatted text for a given type and ID.
     attach_function \
       :sam_hdr_find_line_id,
-      [SamHdr, :string, :string, :string, Kstring],
+      [SamHdr, :string, :string, :string, KString],
       :int
 
     # Returns a complete line of formatted text for a given type and index.
     attach_function \
       :sam_hdr_find_line_pos,
-      [SamHdr, :string, :int, Kstring],
+      [SamHdr, :string, :int, KString],
       :int
 
     # Remove a line with given type / id from a header
@@ -208,13 +239,13 @@ module HTS
     # Return the value associated with a key for a header line identified by ID_key:ID_val
     attach_function \
       :sam_hdr_find_tag_id,
-      [SamHdr, :string, :string, :string, :string, Kstring],
+      [SamHdr, :string, :string, :string, :string, KString],
       :int
 
     # Return the value associated with a key for a header line identified by position
     attach_function \
       :sam_hdr_find_tag_pos,
-      [SamHdr, :string, :int, :string, Kstring],
+      [SamHdr, :string, :int, :string, KString],
       :int
 
     # Remove the key from the line identified by type, ID_key and ID_value.
@@ -445,12 +476,12 @@ module HTS
 
     attach_function \
       :sam_parse1,
-      [Kstring, SamHdr, Bam1],
+      [KString, SamHdr, Bam1],
       :int
 
     attach_function \
       :sam_format1,
-      [SamHdr, Bam1, Kstring],
+      [SamHdr, Bam1, KString],
       :int
 
     # Read a record from a file
@@ -598,7 +629,7 @@ module HTS
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
       :bam_plp_insertion,
-      [:pointer, Kstring, :pointer],
+      [:pointer, KString, :pointer],
       :int
 
     # sets a callback to initialise any per-pileup1_t fields.

data/lib/hts/ffi/vcf.rb

@@ -2,6 +2,75 @@
 
 module HTS
   module FFI
+    # constants
+    BCF_HL_FLT    = 0 # header line
+    BCF_HL_INFO   = 1
+    BCF_HL_FMT    = 2
+    BCF_HL_CTG    = 3
+    BCF_HL_STR    = 4 # structured header line TAG=<A=..,B=..>
+    BCF_HL_GEN    = 5 # generic header line
+    BCF_HT_FLAG   = 0 # header type
+
+    BCF_HT_INT    = 1
+    BCF_HT_REAL   = 2
+    BCF_HT_STR    = 3
+    BCF_HT_LONG   = (BCF_HT_INT | 0x100) # BCF_HT_INT, but for int64_t values; VCF only!
+
+    BCF_VL_FIXED  = 0 # variable length
+    BCF_VL_VAR    = 1
+    BCF_VL_A      = 2
+    BCF_VL_G      = 3
+    BCF_VL_R      = 4
+
+    BCF_DT_ID     = 0 # dictionary type
+    BCF_DT_CTG    = 1
+    BCF_DT_SAMPLE = 2
+
+    BCF_BT_NULL   = 0
+    BCF_BT_INT8   = 1
+    BCF_BT_INT16  = 2
+    BCF_BT_INT32  = 3
+    BCF_BT_INT64  = 4 # Unofficial, for internal use only.
+    BCF_BT_FLOAT  = 5
+    BCF_BT_CHAR   = 7
+
+    VCF_REF       = 0
+    VCF_SNP       = 1
+    VCF_MNP       = 2
+    VCF_INDEL     = 4
+    VCF_OTHER     = 8
+    VCF_BND       = 16 # breakend
+    VCF_OVERLAP   = 32 # overlapping deletion, ALT=*
+
+    BCF1_DIRTY_ID  = 1
+    BCF1_DIRTY_ALS = 2
+    BCF1_DIRTY_FLT = 4
+    BCF1_DIRTY_INF = 8
+
+    BCF_ERR_CTG_UNDEF   = 1
+    BCF_ERR_TAG_UNDEF   = 2
+    BCF_ERR_NCOLS       = 4
+    BCF_ERR_LIMITS      = 8
+    BCF_ERR_CHAR        = 16
+    BCF_ERR_CTG_INVALID = 32
+    BCF_ERR_TAG_INVALID = 64
+
+    # macros
+    class << self
+      def bcf_hdr_nsamples(hdr)
+        hdr[:n][BCF_DT_SAMPLE]
+      end
+    end
+
+    # constants
+    BCF_UN_STR  = 1 # up to ALT inclusive
+    BCF_UN_FLT  = 2 # up to FILTER
+    BCF_UN_INFO = 4 # up to INFO
+    BCF_UN_SHR  = (BCF_UN_STR | BCF_UN_FLT | BCF_UN_INFO) # all shared information
+    BCF_UN_FMT  = 8 # unpack format and each sample
+    BCF_UN_IND  = BCF_UN_FMT # a synonym of BCF_UN_FMT
+    BCF_UN_ALL  = (BCF_UN_SHR | BCF_UN_FMT) # everything
+
     attach_function \
       :bcf_hdr_init,
       [:string],
@@ -14,7 +83,7 @@ module HTS
 
     attach_function \
       :bcf_init,
-      [:void],
+      [],
       Bcf1.by_ref
 
     attach_function \
@@ -54,7 +123,7 @@ module HTS
 
     attach_function \
       :vcf_parse,
-      [Kstring, BcfHdr, Bcf1],
+      [KString, BcfHdr, Bcf1],
       :int
 
     attach_function \
@@ -64,7 +133,7 @@ module HTS
 
     attach_function \
       :vcf_format,
-      [BcfHdr, Bcf1, Kstring],
+      [BcfHdr, Bcf1, KString],
       :int
 
     attach_function \
@@ -119,7 +188,7 @@ module HTS
 
     attach_function \
       :vcf_write_line,
-      [HtsFile, Kstring],
+      [HtsFile, KString],
       :int
 
     attach_function \
@@ -144,7 +213,7 @@ module HTS
 
     attach_function \
       :bcf_hdr_format,
-      [BcfHdr, :int, Kstring],
+      [BcfHdr, :int, KString],
       :int
 
     attach_function \
@@ -204,7 +273,7 @@ module HTS
 
     attach_function \
       :bcf_hrec_format,
-      [BcfHrec, Kstring],
+      [BcfHrec, KString],
       :int
 
     attach_function \
@@ -369,27 +438,27 @@ module HTS
 
     attach_function \
       :bcf_fmt_array,
-      [Kstring, :int, :int, :pointer],
+      [KString, :int, :int, :pointer],
       :int
 
     attach_function \
       :bcf_fmt_sized_array,
-      [Kstring, :pointer],
+      [KString, :pointer],
       :uint8_t
 
     attach_function \
       :bcf_enc_vchar,
-      [Kstring, :int, :string],
+      [KString, :int, :string],
       :int
 
     attach_function \
       :bcf_enc_vint,
-      [Kstring, :int, :pointer, :int],
+      [KString, :int, :pointer, :int],
       :int
 
     attach_function \
       :bcf_enc_vfloat,
-      [Kstring, :int, :pointer],
+      [KString, :int, :pointer],
       :int
 
     attach_function \

data/lib/hts/vcf.rb

@@ -3,27 +3,37 @@
 # Based on hts-python
 # https://github.com/quinlan-lab/hts-python
 
+require_relative 'vcf/header'
+require_relative 'vcf/variant'
+
 module HTS
   class VCF
-    def initialize; end
+    include Enumerable
+    attr_reader :file_path, :mode, :header, :htf
 
-    def inspect; end
+    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 each; end
+      @mode = mode
+      @htf = FFI.hts_open(@file_path, mode)
 
-    def seq; end
+      @header = VCF::Header.new(FFI.bcf_hdr_read(@htf))
 
-    def n_samples; end
-  end
+      @c = FFI.bcf_init
+    end
 
-  class Variant
-    def initialize; end
+    # def inspect; end
 
-    def inspect; end
+    def each(&block)
+      block.call(Variant.new(@c, self)) while FFI.bcf_read(@htf, @header.h, @c) != -1
+    end
 
-    def formats; end
+    def seq(tid); end
 
-    def genotypes; end
+    def n_samples
+      FFI.bcf_hdr_nsamples(header.h)
+    end
   end
 
   class Format

data/lib/hts/vcf/header.rb

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

@@ -0,0 +1,43 @@
+# 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/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = '0.0.1'
+  VERSION = '0.0.2'
 end

data/lib/htslib.rb

@@ -9,15 +9,33 @@ module HTS
 
   class << self
     attr_accessor :ffi_lib
-  end
-
-  suffix = ::FFI::Platform::LIBSUFFIX
 
-  self.ffi_lib = if ENV['HTSLIBDIR']
-                   File.expand_path("libhts.#{suffix}", ENV['HTSLIBDIR'])
+    def search_htslib(name = nil)
+      name ||= "libhts.#{::FFI::Platform::LIBSUFFIX}"
+      lib_path = if ENV['HTSLIBDIR']
+                   File.expand_path(name, ENV['HTSLIBDIR'])
                  else
-                   File.expand_path("../vendor/libhts.#{suffix}", __dir__)
+                   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')
+        lib_path = File.expand_path(name, lib_dir)
+      rescue PackageConfig::NotFoundError
+        warn "htslib.pc was not found in the pkg-config search path."
+      end
+      return lib_path if File.exist?(lib_path)
+
+      warn "htslib shared library '#{name}' not found."
+    end
+  end
+
+  self.ffi_lib = search_htslib
+
+  # You can change the path of the shared library with `HTS.ffi_lib=`
+  # before calling the FFI module.
   autoload :FFI, 'hts/ffi'
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - kojix2
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-01-25 00:00:00.000000000 Z
+date: 2021-06-18 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: pkg-config
   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 +39,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: minitest
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -53,7 +53,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: minitest
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -108,7 +108,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description:
+description: 
 email:
 - 2xijok@gmail.com
 executables: []
@@ -134,13 +134,15 @@ files:
 - 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/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
@@ -155,8 +157,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
-signing_key:
+rubygems_version: 3.2.15
+signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []