htslib 0.0.6 → 0.0.8

checksums.yaml

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data/README.md

@@ -39,26 +39,12 @@ export HTSLIBDIR="/your/path/to/htslib" # libhts.so
 
 ## Overview
 
-### Low level API
-
-`HTS::LibHTS` provides native functions. 
-
-```ruby
-require 'htslib'
-
-a = HTS::LibHTS.hts_open("a.bam", "r")
-b = HTS::LibHTS.hts_get_format(a)
-p b[:category]
-p b[:format]
-```
+### High level API
 
-Note: Managed struct is not used in ruby-htslib. You may need to free the memory by yourself.
+A high-level API is under development. 
+Classes such as `Cram` `Bam` `Bcf` `Faidx` `Tabix` are partially implemented.
 
-### High level API (Plan)
-
-`Cram` `Bam` `Bcf` `Faidx` `Tabix`
-
-A high-level API is under development. We will change and improve the API to make it better.
+Read SAM / BAM - Sequence Alignment Map file
 
 ```ruby
 require 'htslib'
@@ -68,15 +54,56 @@ bam = HTS::Bam.new("a.bam")
 bam.each do |r|
   p name:  r.qname,
     flag:  r.flag,
-    start: r.start + 1,
-    mpos:  r.mate_pos + 1,
+    pos:   r.start + 1,
+    mpos:  r.mate_start + 1,
     mqual: r.mapping_quality,
     seq:   r.sequence,
     cigar: r.cigar.to_s,
     qual:  r.base_qualities.map { |i| (i + 33).chr }.join
 end
+
+bam.close
 ```
 
+Read VCF / BCF - Variant Call Format
+
+```ruby
+bcf = HTS::Bcf.new("b.bcf")
+
+bcf.each do |r|
+  p chrom:  r.chrom,
+    pos:    r.pos,
+    id:     r.id,
+    qual:   r.qual.round(2),
+    ref:    r.ref,
+    alt:    r.alt,
+    filter: r.filter
+end
+
+bcf.close
+```
+
+The methods for reading are implemented first. Methods for writing will be implemented in the coming days.
+
+### Low level API
+
+`HTS::LibHTS` provides native functions. 
+
+```ruby
+require 'htslib'
+
+a = HTS::LibHTS.hts_open("a.bam", "r")
+b = HTS::LibHTS.hts_get_format(a)
+p b[:category]
+p b[:format]
+```
+
+Note: Only some C structs are implemented with FFI's ManagedStruct, which frees memory when Ruby's garbage collection fires. Other structs will need to be freed manually.
+
+### Need more speed?
+
+Try [htslib.cr](https://github.com/bio-crystal/htslib.cr). htslib.cr is implemented in Crystal language and provides an API compatible with ruby-htslib. crsytal language is not as flexible as Ruby language. If you have a clear idea of the manipulation you want to do and need to perform it many times, then by all means try to implement a command line tool using htslib.cr. The Crystal language is very fast and can perform almost as well as the Rust and C languages.
+
 ## Documentation
 
 * [RubyDoc.info - HTSlib](https://rdoc.info/gems/htslib)
@@ -93,6 +120,8 @@ bundle exec rake htslib:build
 bundle exec rake test
 ```
 
+Many macro functions are used in HTSlib. Since these macro functions cannot be called using FFI, they must be reimplemented in Ruby.
+
 * Actively use the advanced features of Ruby.
 * Consider compatibility with [htslib.cr](https://github.com/bio-crystal/htslib.cr) to some extent.
 
@@ -102,6 +131,7 @@ bundle exec rake test
 
 #### Automatic generation or automatic validation (Future plan)
 
+
 + [c2ffi](https://github.com/rpav/c2ffi) is a tool to create JSON format metadata from C header files. It is planned to use c2ffi to automatically generate bindings or tests.
 
 ## Contributing
@@ -114,6 +144,16 @@ Ruby-htslib is a library under development, so even small improvements like typo
 * Suggest or add new features
 * [financial contributions](https://github.com/sponsors/kojix2)
 
+```
+Do you need commit rights to my repository?
+Do you want to get admin rights and take over the project?
+If so, please feel free to contact us @kojix2.
+```
+
+#### Why do you implement htslib in a language like Ruby, which is not widely used in the bioinformatics?
+
+One of the greatest joys of using a minor language like Ruby in bioinformatics is that there is nothing stopping you from reinventing the wheel. Reinventing the wheel can be fun. But with languages like Python and R, where many bioinformatics masters work, there is no chance left for beginners to create htslib bindings. Bioinformatics file formats, libraries and tools are very complex and I don't know how to understand them. So I wanted to implement the HTSLib binding to better understand how to use the file formats and tools. And that effort is still going on today...
+
 ## Links
 
 * [samtools/hts-spec](https://github.com/samtools/hts-specs)

data/lib/hts/bam/header.rb

@@ -6,8 +6,8 @@
 module HTS
   class Bam
     class Header
-      def initialize(pointer)
-        @sam_hdr = pointer
+      def initialize(hts_file)
+        @sam_hdr = LibHTS.sam_hdr_read(hts_file)
       end
 
       def struct
@@ -22,16 +22,27 @@ module HTS
         @sam_hdr[:n_targets]
       end
 
-      # FIXME: better name?
-      def seqs
-        Array.new(@sam_hdr[:n_targets]) do |i|
+      def target_names
+        Array.new(target_count) do |i|
           LibHTS.sam_hdr_tid2name(@sam_hdr, i)
         end
       end
 
+      def target_lengths
+        Array.new(target_count) do |i|
+          LibHTS.sam_hdr_tid2len(@sam_hdr, i)
+        end
+      end
+
       def to_s
         LibHTS.sam_hdr_str(@sam_hdr)
       end
+
+      private
+
+      def initialize_copy(orig)
+        @sam_hdr = LibHTS.sam_hdr_dup(orig.struct)
+      end
     end
   end
 end

data/lib/hts/bam/record.rb

@@ -74,6 +74,11 @@ module HTS
         LibHTS.sam_hdr_tid2name(@header, tid)
       end
 
+      # returns the chromosome or '' if not mapped.
+      def contig
+        chrom
+      end
+
       # returns the chromosome of the mate or '' if not mapped.
       def mate_chrom
         mtid = mate_tid
@@ -91,7 +96,7 @@ module HTS
       # end
 
       # insert size
-      def isize
+      def insert_size
         @bam1[:core][:isize]
       end
 
@@ -191,9 +196,12 @@ module HTS
         kstr[:s]
       end
 
-      # TODO:
-      # def eql?
-      # def hash
+      private
+
+      def initialize_copy(orig)
+        @header = orig.header
+        @bam = LibHTS.bam_dup1(orig.struct)
+      end
     end
   end
 end

data/lib/hts/bam.rb

@@ -13,98 +13,133 @@ module HTS
     include Enumerable
 
     attr_reader :file_path, :mode, :header
-    # HtfFile is FFI::BitStruct
-    attr_reader :htf_file
 
-    class << self
-      alias open new
+    def self.open(...)
+      file = new(...)
+      return file unless block_given?
+
+      begin
+        yield file
+      ensure
+        file.close
+      end
+      file
     end
 
-    def initialize(file_path, mode = "r", create_index: nil)
-      file_path = File.expand_path(file_path)
+    def initialize(filename, mode = "r", fai: nil, threads: nil, index: nil)
+      raise "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead" if block_given?
 
-      unless File.exist?(file_path)
+      @file_path = filename == "-" ? "-" : File.expand_path(filename)
+
+      if mode[0] == "r" && !File.exist?(file_path)
         message = "No such SAM/BAM file - #{file_path}"
         raise message
       end
 
-      @file_path = file_path
       @mode      = mode
-      @htf_file  = LibHTS.hts_open(file_path, mode)
-      @header    = Bam::Header.new(LibHTS.sam_hdr_read(htf_file))
-
-      # read
-      if mode[0] == "r"
-        # load index
-        @idx = LibHTS.sam_index_load(htf_file, file_path)
-        # create index
-        if create_index || (@idx.null? && create_index.nil?)
-          warn "Create index for #{file_path}"
-          LibHTS.sam_index_build(file_path, -1)
-          @idx = LibHTS.sam_index_load(htf_file, file_path)
-        end
-      else
-        # FIXME: implement
-        raise "not implemented yet."
+      @hts_file  = LibHTS.hts_open(file_path, mode)
+
+      if fai
+        fai_path = File.expand_path(fai)
+        r = LibHTS.hts_set_fai_filename(@hts_file, fai_path)
+        raise "Failed to load fasta index: #{fai}" if r < 0
       end
 
-      # IO like API
-      if block_given?
-        begin
-          yield self
-        ensure
-          close
-        end
+      if threads&.> 0
+        r = LibHTS.hts_set_threads(@hts_file, threads)
+        raise "Failed to set number of threads: #{threads}" if r < 0
       end
+
+      return if mode[0] == "w"
+
+      @header = Bam::Header.new(@hts_file)
+
+      create_index if index
+
+      # load index
+      @idx = LibHTS.sam_index_load(@hts_file, file_path)
     end
 
-    def struct
-      htf_file
+    def create_index
+      warn "Create index for #{file_path}"
+      LibHTS.sam_index_build(file_path, -1)
+      idx = LibHTS.sam_index_load(@hts_file, file_path)
+      raise "Failed to load index: #{file_path}" if idx.null?
     end
 
-    def to_ptr
-      htf_file.to_ptr
+    def struct
+      @hts_file
     end
 
-    def write(alns)
-      alns.each do
-        LibHTS.sam_write1(htf_file, header, alns.b) > 0 || raise
-      end
+    def to_ptr
+      @hts_file.to_ptr
     end
 
     # Close the current file.
     def close
-      LibHTS.hts_close(htf_file)
+      LibHTS.hts_idx_destroy(@idx) if @idx
+      @idx = nil
+      LibHTS.hts_close(@hts_file)
+      @hts_file = nil
+    end
+
+    def closed?
+      @hts_file.nil?
+    end
+
+    def write_header(header)
+      @header = header.dup
+      LibHTS.hts_set_fai_filename(@hts_file, @file_path)
+      LibHTS.sam_hdr_write(@hts_file, header)
+    end
+
+    def write(aln)
+      aln_dup = aln.dup
+      LibHTS.sam_write1(@hts_file, header, aln_dup) > 0 || raise
     end
 
     # Flush the current file.
     def flush
-      # LibHTS.bgzf_flush(@htf_file.fp.bgzf)
+      # LibHTS.bgzf_flush(@@hts_file.fp.bgzf)
     end
 
+    # Iterate over each record.
+    # Record object is reused.
+    # Faster than each_copy.
     def each
       # Each does not always start at the beginning of the file.
       # This is the common behavior of IO objects in Ruby.
       # This may change in the future.
       return to_enum(__method__) unless block_given?
 
-      while LibHTS.sam_read1(htf_file, header, bam1 = LibHTS.bam_init1) > 0
+      bam1 = LibHTS.bam_init1
+      record = Record.new(bam1, header)
+      yield record while LibHTS.sam_read1(@hts_file, header, bam1) > 0
+    end
+
+    # Iterate over each record.
+    # Generate a new Record object each time.
+    # Slower than each.
+    def each_copy
+      return to_enum(__method__) unless block_given?
+
+      while LibHTS.sam_read1(@hts_file, header, bam1 = LibHTS.bam_init1) > 0
         record = Record.new(bam1, header)
         yield record
       end
-      self
     end
 
     # query [WIP]
     def query(region)
+      # FIXME: when @idx is nil
       qiter = LibHTS.sam_itr_querys(@idx, header, region)
       begin
         bam1 = LibHTS.bam_init1
-        slen = LibHTS.sam_itr_next(htf_file, qiter, bam1)
+        slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
         while slen > 0
           yield Record.new(bam1, header)
           bam1 = LibHTS.bam_init1
-          slen = LibHTS.sam_itr_next(htf_file, qiter, bam1)
+          slen = LibHTS.sam_itr_next(@hts_file, qiter, bam1)
         end
       ensure
         LibHTS.hts_itr_destroy(qiter)

data/lib/hts/bcf/format.rb

@@ -12,10 +12,30 @@ module HTS
         @p1 = FFI::MemoryPointer.new(:pointer) # FIXME: naming
       end
 
+      # For compatibility with htslib.cr.
+      def get_int(key)
+        get(key, :int)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_float(key)
+        get(key, :float)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_flag(key)
+        get(key, :flag)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_string(key)
+        get(key, :string)
+      end
+
       def get(key, type = nil)
         n = FFI::MemoryPointer.new(:int)
         p1 = @p1
-        h = @record.bcf.header.struct
+        h = @record.header.struct
         r = @record.struct
 
         format_values = proc do |type|
@@ -33,12 +53,13 @@ module HTS
           format_values.call(LibHTS::BCF_HT_REAL)
                        .read_array_of_float(n.read_int)
         when :flag
-          format_values.call(LibHTS::BCF_HT_FLAG)
-                       .read_int == 1
+          raise NotImplementedError, "Flag type not implemented yet."
+          # format_values.call(LibHTS::BCF_HT_FLAG)
+          #              .read_int == 1
         when :string, :str
           raise NotImplementedError, "String type not implemented yet."
-          format_values.call(LibHTS::BCF_HT_STR)
-                       .read_string
+          # format_values.call(LibHTS::BCF_HT_STR)
+          #              .read_string
         end
       end
 

data/lib/hts/bcf/header.rb

@@ -3,8 +3,8 @@
 module HTS
   class Bcf
     class Header
-      def initialize(bcf_hdr)
-        @bcf_hdr = bcf_hdr
+      def initialize(hts_file)
+        @bcf_hdr = LibHTS.bcf_hdr_read(hts_file)
       end
 
       def struct
@@ -15,12 +15,33 @@ module HTS
         @bcf_hdr.to_ptr
       end
 
+      def get_version
+        LibHTS.bcf_hdr_get_version(@bcf_hdr)
+      end
+
+      def sample_count
+        LibHTS.bcf_hdr_nsamples(@bcf_hdr)
+      end
+
+      def sample_names
+        # bcf_hdr_id2name is macro function
+        @bcf_hdr[:samples]
+          .read_array_of_pointer(sample_count)
+          .map(&:read_string)
+      end
+
       def to_s
         kstr = LibHTS::KString.new
         raise "Failed to get header string" unless LibHTS.bcf_hdr_format(@bcf_hdr, 0, kstr)
 
         kstr[:s]
       end
+
+      private
+
+      def initialize_copy(orig)
+        @bcf_hdr = LibHTS.bcf_hdr_dup(orig.struct)
+      end
     end
   end
 end

data/lib/hts/bcf/info.rb

@@ -5,13 +5,34 @@ module HTS
     class Info
       def initialize(record)
         @record = record
+        @p1 = FFI::MemoryPointer.new(:pointer) # FIXME: naming
+      end
+
+      # For compatibility with htslib.cr.
+      def get_int(key)
+        get(key, :int)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_float(key)
+        get(key, :float)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_string(key)
+        get(key, :string)
+      end
+
+      # For compatibility with htslib.cr.
+      def get_flag(key)
+        get(key, :flag)
       end
 
       # @note Specify the type. If you don't specify a type, it will still work, but it will be slower.
       def get(key, type = nil)
         n = FFI::MemoryPointer.new(:int)
-        p1 = @record.p1
-        h = @record.bcf.header.struct
+        p1 = @p1
+        h = @record.header.struct
         r = @record.struct
 
         info_values = proc do |type|
@@ -54,10 +75,10 @@ module HTS
           )
           {
             name: LibHTS.bcf_hdr_int2id(
-              @record.bcf.header.struct, LibHTS::BCF_DT_ID, fld[:key]
+              @record.header.struct, LibHTS::BCF_DT_ID, fld[:key]
             ),
             n: LibHTS.bcf_hdr_id2number(
-              @record.bcf.header.struct, LibHTS::BCF_HL_INFO, fld[:key]
+              @record.header.struct, LibHTS::BCF_HL_INFO, fld[:key]
             ),
             vtype: fld[:type], i: fld[:key]
           }
@@ -73,7 +94,7 @@ module HTS
             i * LibHTS::BcfInfo.size
           )
           id = LibHTS.bcf_hdr_int2id(
-            @record.bcf.header.struct, LibHTS::BCF_DT_ID, fld[:key]
+            @record.header.struct, LibHTS::BCF_DT_ID, fld[:key]
           )
           return fld[:type] if id == key
         end

data/lib/hts/bcf/record.rb

@@ -3,13 +3,12 @@
 module HTS
   class Bcf
     class Record
-      def initialize(bcf_t, bcf)
+      def initialize(bcf_t, header)
         @bcf1 = bcf_t
-        @bcf = bcf
-        @p1 = FFI::MemoryPointer.new(:pointer) # FIXME: naming
+        @header = header
       end
 
-      attr_reader :p1, :bcf
+      attr_reader :header
 
       def struct
         @bcf1
@@ -26,10 +25,9 @@ module HTS
       def genotypes; end
 
       def chrom
-        hdr = @bcf.header.struct
         rid = @bcf1[:rid]
 
-        LibHTS.bcf_hdr_id2name(hdr, rid)
+        LibHTS.bcf_hdr_id2name(@header.struct, rid)
       end
 
       def pos
@@ -59,10 +57,10 @@ module HTS
           "PASS"
         when 1
           i = d[:flt].read_int
-          LibHTS.bcf_hdr_int2id(@bcf.header.struct, LibHTS::BCF_DT_ID, i)
+          LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
         when 2
           d[:flt].get_array_of_int(0, n_flt).map do |i|
-            LibHTS.bcf_hdr_int2id(@bcf.header.struct, LibHTS::BCF_DT_ID, i)
+            LibHTS.bcf_hdr_int2id(@header.struct, LibHTS::BCF_DT_ID, i)
           end
         else
           raise "Unexpected number of filters. n_flt: #{n_flt}"
@@ -104,10 +102,16 @@ module HTS
 
       def to_s
         ksr = LibHTS::KString.new
-        raise "Failed to format record" if LibHTS.vcf_format(@bcf.header.struct, @bcf1, ksr) == -1
+        raise "Failed to format record" if LibHTS.vcf_format(@header.struct, @bcf1, ksr) == -1
 
         ksr[:s]
       end
+
+      private
+
+      def initialize_copy
+        raise "Not implemented"
+      end
     end
   end
 end

data/lib/hts/bcf.rb

@@ -13,61 +13,87 @@ module HTS
     include Enumerable
 
     attr_reader :file_path, :mode, :header
-    # HtfFile is FFI::BitStruct
-    attr_reader :htf_file
 
-    class << self
-      alias open new
+    def self.open(...)
+      file = new(...)
+      return file unless block_given?
+
+      begin
+        yield file
+      ensure
+        file.close
+      end
+      file
     end
 
-    def initialize(file_path, mode = "r")
-      file_path = File.expand_path(file_path)
+    def initialize(filename, mode = "r", threads: nil)
+      raise "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead" if block_given?
+
+      @file_path = filename == "-" ? "-" : File.expand_path(filename)
 
-      unless File.exist?(file_path)
+      if mode[0] == "r" && !File.exist?(file_path)
         message = "No such VCF/BCF file - #{file_path}"
         raise message
       end
 
-      @file_path = file_path
       @mode      = mode
-      @htf_file  = LibHTS.hts_open(file_path, mode)
-      @header    = Bcf::Header.new(LibHTS.bcf_hdr_read(htf_file))
-
-      # IO like API
-      if block_given?
-        begin
-          yield self
-        ensure
-          close
-        end
+      @hts_file  = LibHTS.hts_open(file_path, mode)
+
+      if threads&.> 0
+        r = LibHTS.hts_set_threads(@hts_file, threads)
+        raise "Failed to set number of threads: #{threads}" if r < 0
       end
+
+      return if mode[0] == "w"
+
+      @header = Bcf::Header.new(@hts_file)
     end
 
     def struct
-      htf_file
+      @hts_file
     end
 
     def to_ptr
-      htf_file.to_ptr
+      @hts_file.to_ptr
+    end
+
+    def write_header
+      @header = header.dup
+      LibHTS.hts_set_fai_filename(header, @file_path)
+      LibHTS.bcf_hdr_write(@hts_file, header.struct)
+    end
+
+    def write(var)
+      var_dup = var.dup = var.dup
+      LibHTS.bcf_write(@hts_file, header, var_dup) > 0 || raise
     end
 
     # Close the current file.
     def close
-      LibHTS.hts_close(htf_file)
+      LibHTS.hts_close(@hts_file)
+      @hts_file = nil
+    end
+
+    def closed?
+      @hts_file.nil?
+    end
+
+    def sample_count
+      header.sample_count
+    end
+
+    def sample_names
+      header.sample_names
     end
 
     def each
       return to_enum(__method__) unless block_given?
 
-      while LibHTS.bcf_read(htf_file, header, bcf1 = LibHTS.bcf_init) != -1
-        record = Record.new(bcf1, self)
+      while LibHTS.bcf_read(@hts_file, header, bcf1 = LibHTS.bcf_init) != -1
+        record = Record.new(bcf1, header)
         yield record
       end
       self
     end
-
-    def sample_count
-      LibHTS.bcf_hdr_nsamples(header.struct)
-    end
   end
 end

data/lib/hts/libhts/constants.rb

@@ -218,7 +218,7 @@ module HTS
 
     SamFile = HtsFile
 
-    class HtsThreadPool < FFI::Struct
+    class HtsTpool < FFI::Struct
       layout \
         :pool,           :pointer,
         :qsize,          :int

data/lib/hts/libhts/hts.rb

@@ -145,7 +145,7 @@ module HTS
     # Create extra threads to aid compress/decompression for this file
     attach_function \
       :hts_set_thread_pool,
-      [HtsFile, HtsThreadPool],
+      [HtsFile, HtsTpool],
       :int
 
     # Adds a cache of decompressed blocks, potentially speeding up seeks.

data/lib/hts/libhts/thread_pool.rb

@@ -0,0 +1,139 @@
+# frozen_string_literal: true
+
+module HTS
+  module LibHTS
+    attach_function \
+      :hts_tpool_init,
+      [:int],
+      HtsTpool.by_ref
+
+    attach_function \
+      :hts_tpool_size,
+      [HtsTpool],
+      :int
+
+    # FIXME: struct
+    HtsTpoolProcess = :pointer
+    HtsTpoolResult  = :pointer
+
+    attach_function \
+      :hts_tpool_dispatch,
+      [HtsTpool, HtsTpoolProcess, :pointer, :pointer],
+      :int
+
+    attach_function \
+      :hts_tpool_dispatch2,
+      [HtsTpool, HtsTpoolProcess, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :hts_tpool_dispatch3,
+      [HtsTpool, HtsTpoolProcess, :pointer, :pointer, :pointer, :pointer, :int],
+      :int
+
+    attach_function \
+      :hts_tpool_wake_dispatch,
+      [HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_flush,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_process_reset,
+      [HtsTpoolProcess, :int],
+      :int
+
+    attach_function \
+      :hts_tpool_process_qsize,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_destroy,
+      [HtsTpool],
+      :void
+
+    attach_function \
+      :hts_tpool_kill,
+      [HtsTpool],
+      :void
+
+    attach_function \
+      :hts_tpool_next_result,
+      [HtsTpoolProcess],
+      HtsTpoolResult # .by_ref
+
+    attach_function \
+      :hts_tpool_next_result_wait,
+      [HtsTpoolProcess],
+      HtsTpoolResult # .by_ref
+
+    attach_function \
+      :hts_tpool_delete_result,
+      [HtsTpoolResult, :int],
+      :void
+
+    attach_function \
+      :hts_tpool_result_data,
+      [HtsTpoolResult],
+      :pointer
+
+    attach_function \
+      :hts_tpool_process_init,
+      [HtsTpool, :int, :int],
+      HtsTpoolProcess # .by_ref
+
+    attach_function \
+      :hts_tpool_process_destroy,
+      [HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_empty,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_process_len,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_process_sz,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_process_shutdown,
+      [HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_is_shutdown,
+      [HtsTpoolProcess],
+      :int
+
+    attach_function \
+      :hts_tpool_process_attach,
+      [HtsTpool, HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_detach,
+      [HtsTpool, HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_ref_incr,
+      [HtsTpoolProcess],
+      :void
+
+    attach_function \
+      :hts_tpool_process_ref_decr,
+      [HtsTpoolProcess],
+      :void
+  end
+end

data/lib/hts/libhts.rb

@@ -31,3 +31,4 @@ require_relative "libhts/sam"
 require_relative "libhts/kfunc"
 require_relative "libhts/tbx"
 require_relative "libhts/vcf"
+require_relative "libhts/thread_pool"

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.0.6"
+  VERSION = "0.0.8"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.8
 platform: ruby
 authors:
 - kojix2
-autorequire:
+autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-01-03 00:00:00.000000000 Z
+date: 2022-03-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -122,7 +122,7 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description:
+description: 
 email:
 - 2xijok@gmail.com
 executables: []
@@ -154,6 +154,7 @@ files:
 - lib/hts/libhts/sam.rb
 - lib/hts/libhts/sam_funcs.rb
 - lib/hts/libhts/tbx.rb
+- lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
 - lib/hts/tabix.rb
@@ -163,7 +164,7 @@ homepage: https://github.com/kojix2/ruby-htslib
 licenses:
 - MIT
 metadata: {}
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -178,8 +179,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
-signing_key:
+rubygems_version: 3.3.7
+signing_key: 
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []