htslib 0.2.8 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,11 +1,14 @@
 # ruby-htslib
 
 [![Gem Version](https://badge.fury.io/rb/htslib.svg)](https://badge.fury.io/rb/htslib)
-![CI](https://github.com/kojix2/ruby-htslib/workflows/CI/badge.svg)
+[![test](https://github.com/kojix2/ruby-htslib/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/ruby-htslib/actions/workflows/ci.yml)
 [![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)
 
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/kojix2/ruby-htslib)
+[![Lines of Code](https://img.shields.io/endpoint?url=https%3A%2F%2Ftokei.kojix2.net%2Fbadge%2Fgithub%2Fkojix2%2Fruby-htslib%2Flines)](https://tokei.kojix2.net/github/kojix2/ruby-htslib)
+
 Ruby-htslib is the [Ruby](https://www.ruby-lang.org) bindings to [HTSlib](https://github.com/samtools/htslib), a C library for high-throughput sequencing data formats. It allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/), in the Ruby language.
 
 :apple: Feel free to fork it!
@@ -162,6 +165,8 @@ Try Crystal. [HTS.cr](https://github.com/bio-cr/hts.cr) is implemented in Crysta
 
 ## Development
 
+![Diagram](diagram.svg)
+
 #### Compile from source code
 
 [GNU Autotools](https://en.wikipedia.org/wiki/GNU_Autotools) is required to compile htslib.

data/lib/hts/bam/auxi.rb

@@ -30,10 +30,10 @@ module HTS
       # which provides methods like `get_int`, `get_float`, etc.
       # I think they are better than `fetch_int`` and `fetch_float`.
       def get(key, type = nil)
-        aux = LibHTS.bam_aux_get(@record.struct, key)
-        return nil if aux.null?
+        aux_ptr = LibHTS.bam_aux_get(@record.struct, key)
+        return nil if aux_ptr.null?
 
-        get_ruby_aux(aux, type)
+        get_ruby_aux(aux_ptr, type)
       end
 
       # For compatibility with HTS.cr.
@@ -56,43 +56,47 @@ module HTS
       end
 
       def first
-        aux = LibHTS.bam_aux_first(@record.struct)
-        return nil if aux.null?
+        aux_ptr = first_pointer
+        return nil if aux_ptr.null?
 
-        get_ruby_aux(aux)
+        get_ruby_aux(aux_ptr)
       end
 
       def each
         return enum_for(__method__) unless block_given?
 
-        aux = LibHTS.bam_aux_first(@record.struct)
-        return nil if aux.null?
+        aux_ptr = first_pointer
+        return nil if aux_ptr.null?
 
         loop do
-          yield get_ruby_aux(aux)
-          aux = LibHTS.bam_aux_next(@record.struct, aux)
-          break if aux.null?
+          yield get_ruby_aux(aux_ptr)
+          aux_ptr = LibHTS.bam_aux_next(@record.struct, aux_ptr)
+          break if aux_ptr.null?
         end
       end
 
       def to_h
         h = {}
-        aux = LibHTS.bam_aux_first(@record.struct)
-        return h if aux.null?
+        aux_ptr = first_pointer
+        return h if aux_ptr.null?
 
         loop do
-          key = FFI::Pointer.new(aux.address - 2).read_string(2)
-          h[key] = get_ruby_aux(aux)
-          aux = LibHTS.bam_aux_next(@record.struct, aux)
-          break if aux.null?
+          key = FFI::Pointer.new(aux_ptr.address - 2).read_string(2)
+          h[key] = get_ruby_aux(aux_ptr)
+          aux_ptr = LibHTS.bam_aux_next(@record.struct, aux_ptr)
+          break if aux_ptr.null?
         end
         h
       end
 
       private
 
-      def get_ruby_aux(aux, type = nil)
-        type = type ? type.to_s : aux.read_string(1)
+      def first_pointer
+        LibHTS.bam_aux_first(@record.struct)
+      end
+
+      def get_ruby_aux(aux_ptr, type = nil)
+        type = type ? type.to_s : aux_ptr.read_string(1)
 
         # A (character), B (general array),
         # f (real number), H (hexadecimal array),
@@ -100,23 +104,23 @@ module HTS
 
         case type
         when "i", "I", "c", "C", "s", "S"
-          LibHTS.bam_aux2i(aux)
+          LibHTS.bam_aux2i(aux_ptr)
         when "f", "d"
-          LibHTS.bam_aux2f(aux)
+          LibHTS.bam_aux2f(aux_ptr)
         when "Z", "H"
-          LibHTS.bam_aux2Z(aux)
+          LibHTS.bam_aux2Z(aux_ptr)
         when "A" # char
-          LibHTS.bam_aux2A(aux).chr
+          LibHTS.bam_aux2A(aux_ptr).chr
         when "B" # array
-          t2 = aux.read_string(2)[1] # just a little less efficient
-          l = LibHTS.bam_auxB_len(aux)
+          t2 = aux_ptr.read_string(2)[1] # just a little less efficient
+          l = LibHTS.bam_auxB_len(aux_ptr)
           case t2
           when "c", "C", "s", "S", "i", "I"
             # FIXME : Not efficient.
-            Array.new(l) { |i| LibHTS.bam_auxB2i(aux, i) }
+            Array.new(l) { |i| LibHTS.bam_auxB2i(aux_ptr, i) }
           when "f", "d"
             # FIXME : Not efficient.
-            Array.new(l) { |i| LibHTS.bam_auxB2f(aux, i) }
+            Array.new(l) { |i| LibHTS.bam_auxB2f(aux_ptr, i) }
           else
             raise NotImplementedError, "type: #{type} #{t2}"
           end

data/lib/hts/bam/flag.rb

@@ -69,27 +69,29 @@ module HTS
       end
 
       def &(other)
-        Flag.new(@value & other.to_i)
+        self.class.new(@value & other.to_i)
       end
 
       def |(other)
-        Flag.new(@value | other.to_i)
+        self.class.new(@value | other.to_i)
       end
 
       def ^(other)
-        Flag.new(@value ^ other.to_i)
+        self.class.new(@value ^ other.to_i)
       end
 
       def ~
-        Flag.new(~@value)
+        # FIXME: Only 12bits are used for flags
+        # The result is different from the Crystal version.
+        self.class.new(~@value)
       end
 
       def <<(f)
-        Flag.new(@value << f.to_i)
+        self.class.new(@value << f.to_i)
       end
 
       def >>(other)
-        Flag.new(@value >> other.to_i)
+        self.class.new(@value >> other.to_i)
       end
 
       def to_i

data/lib/hts/bam/header.rb

@@ -6,8 +6,8 @@ module HTS
   class Bam < Hts
     # A class for working with alignment header.
     class Header
-      def self.parse(str)
-        new(LibHTS.sam_hdr_parse(str.size, str))
+      def self.parse(text)
+        new(LibHTS.sam_hdr_parse(text.size, text))
       end
 
       def initialize(arg = nil)
@@ -21,6 +21,8 @@ module HTS
         else
           raise TypeError, "Invalid argument"
         end
+
+        yield self if block_given?
       end
 
       def struct
@@ -31,11 +33,23 @@ module HTS
         @sam_hdr.to_ptr
       end
 
+      def targets
+        Array.new(target_count) do |i|
+          name = LibHTS.sam_hdr_tid2name(@sam_hdr, i)
+          len = LibHTS.sam_hdr_tid2len(@sam_hdr, i)
+          { name:, len: }
+        end
+      end
+
       def target_count
         # FIXME: sam_hdr_nref
         @sam_hdr[:n_targets]
       end
 
+      def target_name(tid)
+        tid2name(tid)
+      end
+
       def target_names
         Array.new(target_count) do |i|
           LibHTS.sam_hdr_tid2name(@sam_hdr, i)
@@ -48,15 +62,20 @@ module HTS
         end
       end
 
-      # experimental
-      def add_lines(str)
-        LibHTS.sam_hdr_add_lines(@sam_hdr, str, 0)
+      def write(...)
+        add_lines(...)
       end
 
       # experimental
-      def add_line(type, *args)
-        args = args.flat_map { |arg| [:string, arg] }
-        LibHTS.sam_hdr_add_line(@sam_hdr, type, *args, :pointer, FFI::Pointer::NULL)
+      def <<(obj)
+        case obj
+        when Array, Hash
+          args = obj.flatten(-1).map { |i| i.to_a if i.is_a?(Hash) }
+          add_line(*args)
+        else
+          add_lines(obj.to_s)
+        end
+        self
       end
 
       # experimental
@@ -87,6 +106,13 @@ module HTS
         LibHTS.sam_hdr_str(@sam_hdr)
       end
 
+      # experimental
+      def get_tid(name)
+        name2tid(name)
+      end
+
+      private
+
       def name2tid(name)
         LibHTS.sam_hdr_name2tid(@sam_hdr, name)
       end
@@ -95,7 +121,15 @@ module HTS
         LibHTS.sam_hdr_tid2name(@sam_hdr, tid)
       end
 
-      private
+      def add_lines(str)
+        LibHTS.sam_hdr_add_lines(@sam_hdr, str, 0)
+      end
+
+      def add_line(*args)
+        type = args.shift
+        args = args.flat_map { |arg| [:string, arg] }
+        LibHTS.sam_hdr_add_line(@sam_hdr, type, *args, :pointer, FFI::Pointer::NULL)
+      end
 
       def initialize_copy(orig)
         @sam_hdr = LibHTS.sam_hdr_dup(orig.struct)

data/lib/hts/bam/record.rb

@@ -12,9 +12,64 @@ module HTS
 
       attr_reader :header
 
-      def initialize(header, bam1_t = nil)
-        @bam1 = bam1_t || LibHTS.bam_init1
+      # Initialization API is experimental.
+
+      def initialize(
+        header,
+        bam1 = nil,
+        qname: nil,
+        flag: nil,
+        tid: nil,
+        pos: nil,
+        mapq: nil,
+        cigar: nil,
+        mtid: nil,
+        mpos: nil,
+        isize: nil,
+        seq: nil,
+        qual: nil,
+        l_aux: nil
+      )
+        @bam1 = bam1 || LibHTS.bam_init1
         @header = header
+
+        params = [qname, flag, tid, pos, mapq, cigar, mtid, mpos, isize, seq, qual, l_aux]
+        return if params.all? { |x| x.nil? }
+
+        if params.all?
+          c = FFI::MemoryPointer.new(:pointer)
+          m = FFI::MemoryPointer.new(:size_t)
+          LibHTS.sam_parse_cigar(cigar, FFI::Pointer::NULL, c, m)
+          cigar_array = c.read_pointer.read_array_of_uint32(m.read(:size_t))
+          cigar_pointer = FFI::MemoryPointer.new(:uint32, cigar_array.length)
+          cigar_pointer.write_array_of_uint32(cigar_array)
+          if qual.is_a?(Array)
+            qual = qual.pack("C*")
+          elsif qual.is_a?(String)
+            raise "Which implementation is better? +33 or not? Please tell me."
+          end
+          r = LibHTS.bam_set1(
+            @bam1,
+            qname.length,
+            qname,
+            flag,
+            tid,
+            pos,
+            mapq,
+            cigar_array.length,
+            cigar_pointer,
+            mtid,
+            mpos,
+            isize,
+            seq.length,
+            seq,
+            qual,
+            l_aux
+          )
+          raise "bam_set1 failed: #{r}" if r < 0
+        else
+          warn "Ignore bam_set1 because some arguments are missing."
+        end
       end
 
       # Return the FFI::Struct object.
@@ -158,6 +213,17 @@ module HTS
         Cigar.new(self)
       end
 
+      def cigar=(str)
+        if cigar.is_a? Cigar
+          raise "Not implemented yet."
+        elsif cigar.is_a? String
+          r = LibHTS.bam_parse_cigar(str, FFI::Pointer::NULL, @bam1)
+          raise "bam_parse_cigar failed: #{r}" if r != 0
+        else
+          raise ArgumentError, "cigar must be a String or Bam::Cigar"
+        end
+      end
+
       # Calculate query length from CIGAR.
       # @return [Integer] query length
       def qlen

data/lib/hts/bam.rb

@@ -7,6 +7,8 @@ require_relative "bam/header"
 require_relative "bam/cigar"
 require_relative "bam/flag"
 require_relative "bam/record"
+# require_relative "bam/pileup"
+# require_relative "bam/pileup_entry"
 
 module HTS
   # A class for working with SAM, BAM, CRAM files.
@@ -30,7 +32,7 @@ module HTS
     def initialize(file_name, mode = "r", index: nil, fai: nil, threads: nil,
                    build_index: false)
       if block_given?
-        message = "HTS::Bam.new() dose not take block; Please use HTS::Bam.open() instead"
+        message = "HTS::Bam.new() does not take block; Please use HTS::Bam.open() instead"
         raise message
       end
 
@@ -44,6 +46,17 @@ module HTS
 
       raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
 
+      # Auto-detect and set reference for CRAM files
+      if fai.nil? && @file_name.end_with?(".cram")
+        # Try to find reference file in the same directory
+        base_name = File.basename(@file_name, ".cram")
+        dir_name = File.dirname(@file_name)
+        potential_ref = File.join(dir_name, "#{base_name}.fa")
+
+        # For remote URLs, assume reference exists; for local files, check existence
+        fai = potential_ref if @file_name.start_with?("http") || File.exist?(potential_ref)
+      end
+
       if fai
         r = LibHTS.hts_set_fai_filename(@hts_file, fai)
         raise "Failed to load fasta index: #{fai}" if r < 0
@@ -67,7 +80,7 @@ module HTS
       else
         warn "Create index for #{@file_name}"
       end
-      case LibHTS.sam_index_build3(@file_name, index_name, min_shift, (@nthreads || threads))
+      case LibHTS.sam_index_build3(@file_name, index_name, min_shift, @nthreads || threads)
       when 0 # successful
       when -1 then raise "indexing failed"
       when -2 then raise "opening #{@file_name} failed"
@@ -95,7 +108,7 @@ module HTS
     end
 
     def close
-      LibHTS.hts_idx_destroy(@idx) if @idx&.null?
+      LibHTS.hts_idx_destroy(@idx) if @idx && !@idx.null?
       @idx = nil
       super
     end
@@ -141,7 +154,7 @@ module HTS
     alias isize insert_size
     alias mpos mate_pos
 
-    # FXIME: experimental
+    # FIXME: experimental
     def aux(tag)
       check_closed
 
@@ -194,7 +207,7 @@ module HTS
       raise "Index file is required to call the query method." unless index_loaded?
 
       if beg && end_
-        tid = header.name2tid(region)
+        tid = header.get_tid(region)
         queryi(tid, beg, end_, copy:, &block)
       elsif beg.nil? && end_.nil?
         querys(region, copy:, &block)
@@ -203,6 +216,10 @@ module HTS
       end
     end
 
+    # def pileup
+    #   Pileup.new(self)
+    # end
+
     private
 
     def queryi(tid, beg, end_, copy: false, &block)

data/lib/hts/bcf/header.rb

@@ -19,6 +19,8 @@ module HTS
         else
           raise TypeError, "Invalid argument"
         end
+
+        yield self if block_given?
       end
 
       def struct

data/lib/hts/bcf.rb

@@ -30,7 +30,7 @@ module HTS
     def initialize(file_name, mode = "r", index: nil, threads: nil,
                    build_index: false)
       if block_given?
-        message = "HTS::Bcf.new() dose not take block; Please use HTS::Bcf.open() instead"
+        message = "HTS::Bcf.new() does not take block; Please use HTS::Bcf.open() instead"
         raise message
       end
 
@@ -62,7 +62,7 @@ module HTS
       else
         warn "Create index for #{@file_name}"
       end
-      case LibHTS.bcf_index_build3(@file_name, index_name, min_shift, (@nthreads || threads))
+      case LibHTS.bcf_index_build3(@file_name, index_name, min_shift, @nthreads || threads)
       when 0 # successful
       when -1 then raise "indexing failed"
       when -2 then raise "opening #{@file_name} failed"
@@ -90,7 +90,7 @@ module HTS
     end
 
     def close
-      LibHTS.hts_idx_destroy(@idx) unless @idx&.null?
+      LibHTS.hts_idx_destroy(@idx) if @idx && !@idx.null?
       @idx = nil
       super
     end
@@ -185,7 +185,7 @@ module HTS
 
     def each_info(key)
       check_closed
-      return to_enum(__method__, key) unless block
+      return to_enum(__method__, key) unless block_given?
 
       each do |r|
         yield r.info(key)
@@ -194,7 +194,7 @@ module HTS
 
     def each_format(key)
       check_closed
-      return to_enum(__method__, key) unless block
+      return to_enum(__method__, key) unless block_given?
 
       each do |r|
         yield r.format(key)

data/lib/hts/faidx.rb

@@ -21,7 +21,7 @@ module HTS
 
     def initialize(file_name)
       if block_given?
-        message = "HTS::Faidx.new() dose not take block; Please use HTS::Faidx.open() instead"
+        message = "HTS::Faidx.new() does not take block; Please use HTS::Faidx.open() instead"
         raise message
       end
 

data/lib/hts/libhts/constants.rb

@@ -158,7 +158,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < FFI::Struct # FIXME: ManagedStruct
+    class HtsIdx < FFI::Struct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -189,9 +189,9 @@ module HTS
           :n_unmapped,   :uint64
         )
 
-      def self.release(ptr)
-        LibHTS.hts_idx_destroy(ptr) unless ptr.null?
-      end
+      # def self.release(ptr)
+      #   LibHTS.hts_idx_destroy(ptr) unless ptr.null?
+      # end
     end
 
     class HtsReglist < FFI::Struct
@@ -379,6 +379,10 @@ module HTS
                  :is_refskip, 1,
                  :_reserved,  1,
                  :aux,        27
+
+      # def self.release(ptr)
+      #   LibHTS.bam_plp_destroy(ptr) unless ptr.null?
+      # end
     end
 
     class TbxConf < FFI::Struct
@@ -570,5 +574,18 @@ module HTS
       :external,           4,
       :core,               5
     )
+
+    CramBlockMethod = enum(
+      :unknown,      -1,
+      :raw,          0,
+      :gzip,         1,
+      :bzip2,        2,
+      :lzma,         3,
+      :rans4x8,      4,
+      :ransnx16,     5,
+      :arith,        6,
+      :fqz,          7,
+      :tok3,         8
+    )
   end
 end

data/lib/hts/libhts/cram.rb

@@ -79,12 +79,27 @@ module HTS
       %i[cram_container int32 pointer],
       :void
 
+    attach_function \
+      :cram_container_get_num_records,
+      [:cram_container],
+      :int32
+
+    attach_function \
+      :cram_container_get_num_bases,
+      [:cram_container],
+      :int32
+
+    # Returns true if the container is empty (EOF marker)
     attach_function \
       :cram_container_is_empty,
       [:cram_fd],
       :int
 
-    # cram_block
+    # Returns chromosome and start/span from container struct
+    attach_function \
+      :cram_container_get_coords,
+      %i[cram_container pointer pointer],
+      :void
 
     attach_function \
       :cram_block_get_content_id,
@@ -116,6 +131,16 @@ module HTS
       [:cram_block],
       CramContentType
 
+    attach_function \
+      :cram_block_get_method,
+      [:cram_block],
+      CramBlockMethod
+
+    attach_function \
+      :cram_expand_method,
+      [:pointer, :int32, CramBlockMethod],
+      :pointer
+
     attach_function \
       :cram_block_set_content_id,
       %i[cram_block int32],
@@ -167,6 +192,18 @@ module HTS
       [:cram_block],
       :uint32
 
+    # Returns the Block Content ID values referred to by a cram_codec in ids[2].
+    attach_function \
+      :cram_codec_get_content_ids,
+      %i[pointer pointer],
+      :void
+
+    # Produces a human readable description of the codec parameters.
+    attach_function \
+      :cram_codec_describe,
+      [:pointer, KString.ptr],
+      :int
+
     # Renumbers RG numbers in a cram compression header.
     attach_function \
       :cram_transcode_rg,
@@ -180,6 +217,51 @@ module HTS
       %i[cram_fd cram_fd int32],
       :int
 
+    # Copies a container, but filtering it down to a specific region (as
+    # already specified in 'in'
+    attach_function \
+      :cram_filter_container,
+      %i[cram_fd cram_fd cram_container pointer],
+      :int
+
+    # Decodes a CRAM block compression header.
+    attach_function \
+      :cram_decode_compression_header,
+      %i[cram_fd cram_block],
+      :pointer # cram_block_compression_hdr
+
+    # Frees a cram_block_compression_hdr structure.
+    attach_function \
+      :cram_free_compression_header,
+      [:pointer],
+      :void
+
+    # Map cram block numbers to data-series.
+    attach_function \
+      :cram_update_cid2ds_map,
+      %i[pointer pointer],
+      :pointer
+
+    # Return a list of data series observed as belonging to a block with
+    # the specified content_id.
+    attach_function \
+      :cram_cid2ds_query,
+      %i[pointer int pointer],
+      :int
+
+    # Frees a cram_cid2ds_t allocated by cram_update_cid2ds_map
+    attach_function \
+      :cram_cid2ds_free,
+      [:pointer],
+      :void
+
+    # Produces a description of the record and tag encodings held within
+    # a compression header and appends to 'ks'.
+    attach_function \
+      :cram_describe_encodings,
+      [:pointer, KString.ptr],
+      :int
+
     # Returns the number of cram blocks within this slice.
     attach_function \
       :cram_slice_hdr_get_num_blocks,
@@ -360,5 +442,35 @@ module HTS
       :cram_get_refs,
       [HtsFile.by_ref],
       :pointer # refs_t
+
+    # Returns the file offsets of CRAM slices covering a specific region query.
+    attach_function \
+      :cram_index_extents,
+      %i[cram_fd int hts_pos_t hts_pos_t pointer pointer],
+      :int
+
+    # Returns the total number of containers in the CRAM index.
+    attach_function \
+      :cram_num_containers,
+      [:cram_fd],
+      :int64
+
+    # Returns the number of containers in the CRAM index within given offsets.
+    attach_function \
+      :cram_num_containers_between,
+      %i[cram_fd off_t off_t pointer pointer],
+      :int64
+
+    # Returns the byte offset for the start of the n^th container.
+    attach_function \
+      :cram_container_num2offset,
+      %i[cram_fd int64],
+      :off_t
+
+    # Returns the container number for the first container at offset >= pos.
+    attach_function \
+      :cram_container_offset2num,
+      %i[cram_fd off_t],
+      :int64
   end
 end

data/lib/hts/libhts/hts.rb

@@ -447,7 +447,7 @@ module HTS
     # Computes the final 128-bit MD5 hash from the given context
     attach_function \
       :hts_md5_final,
-      %i[pointer pointer], # unsinged char
+      %i[pointer pointer], # unsigned char
       :void
 
     #  Resets an md5_context to the initial state, as returned by hts_md5_init().

data/lib/hts/libhts/sam.rb

@@ -247,7 +247,7 @@ module HTS
        :hts_pos_t,
        :uint8,
        :size_t,
-       :string,
+       :pointer,
        :int32,
        :hts_pos_t,
        :hts_pos_t,
@@ -512,6 +512,12 @@ module HTS
       [Bam1, :pointer],
       :int
 
+    # Delete an aux field from a BAM record. Identical to @c bam_aux_del() apart from the return value
+    attach_function \
+      :bam_aux_remove,
+      [Bam1, :pointer],
+      :pointer
+
     # Update or add a string-type tag
     attach_function \
       :bam_aux_update_str,
@@ -674,12 +680,18 @@ module HTS
       [:pointer], # hts_base_mod_state
       :void
 
-    # Parses the Mm and Ml tags out of a bam record.
+    # Parses the MM and ML tags out of a bam record.
     attach_function \
       :bam_parse_basemod,
       [Bam1, :pointer],
       :int
 
+    # Parses the MM and ML tags out of a bam record.
+    attach_function \
+      :bam_parse_basemod2,
+      [Bam1, :pointer, :uint32],
+      :int
+
     # Returns modification status for the next base position in the query seq.
     attach_function \
       :bam_mods_at_next_pos,
@@ -704,6 +716,12 @@ module HTS
       %i[pointer int pointer pointer string],
       :int
 
+    # Returns data about the i^th modification type for the alignment record.
+    attach_function \
+      :bam_mods_queryi,
+      %i[pointer int pointer pointer string],
+      :int
+
     # Returns the list of base modification codes provided for this
     attach_function \
       :bam_mods_recorded,

data/lib/hts/libhts/sam_funcs.rb

@@ -105,7 +105,7 @@ module HTS
 
       # Modifies a single base in the bam structure.
       def bam_set_seqi(s, i, b)
-        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | ((b) << ((~i & 1) << 2))
+        s[i >> 1] = (s[i >> 1] & (0xf0 >> ((~i & 1) << 2))) | (b << ((~i & 1) << 2))
       end
 
       # Returns the SAM formatted text of the \@HD header line

data/lib/hts/libhts/tbx.rb

@@ -2,6 +2,13 @@
 
 module HTS
   module LibHTS
+    attach_variable :tbx_conf_gff, TbxConf
+    attach_variable :tbx_conf_bed, TbxConf
+    attach_variable :tbx_conf_psltbl, TbxConf
+    attach_variable :tbx_conf_sam, TbxConf
+    attach_variable :tbx_conf_vcf, TbxConf
+    attach_variable :tbx_conf_gaf, TbxConf
+
     attach_function \
       :tbx_name2id,
       [Tbx, :string],

data/lib/hts/libhts/tbx_funcs.rb

@@ -8,11 +8,16 @@ module HTS
       end
 
       def tbx_itr_queryi(tbx, tid, beg, end_)
-        hts_itr_query(tbx[:idx], tid, beg, end_, @@tbx_readrec)
+        hts_itr_query(tbx[:idx], tid, beg, end_, @ffi_functions[:tbx_readrec])
+      end
+
+      @@tbx_name2id = proc do |tbx, ss|
+        LibHTS.tbx_name2id(tbx, ss)
       end
 
       def tbx_itr_querys(tbx, s)
-        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @@hts_itr_query, @@tbx_readrec)
+        hts_itr_querys(tbx[:idx], s, @@tbx_name2id, tbx, @ffi_functions[:hts_itr_query],
+                       @ffi_functions[:tbx_readrec])
       end
 
       def tbx_itr_next(htsfp, tbx, itr, r)

data/lib/hts/libhts/vcf.rb

@@ -2,6 +2,12 @@
 
 module HTS
   module LibHTS
+    # Get error description for bcf error code
+    attach_function \
+      :bcf_strerror,
+      %i[int pointer size_t],
+      :string
+
     # Create an empty BCF header.
     attach_function \
       :bcf_hdr_init,

data/lib/hts/libhts/vcf_funcs.rb

@@ -167,7 +167,7 @@ module HTS
 
       # Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based)
       def bcf_alleles2gt(a, b)
-        ((a) > (b) ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
+        (a > b ? (a * (a + 1) / 2 + b) : (b * (b + 1) / 2 + a))
       end
 
       # Get INFO values
@@ -272,7 +272,7 @@ module HTS
       alias bcf_itr_destroy hts_itr_destroy
 
       def bcf_itr_queryi(idx, tid, beg, _end)
-        hts_itr_query(idx, tid, beg, _end, @@bcf_readrec)
+        hts_itr_query(idx, tid, beg, _end, @ffi_functions[:bcf_readrec])
       end
 
       @@bcf_hdr_name2id = proc do |hdr, id|
@@ -280,7 +280,7 @@ module HTS
       end
 
       def bcf_itr_querys(idx, hdr, s)
-        hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @@hts_itr_query, @@bcf_readrec)
+        hts_itr_querys(idx, s, @@bcf_hdr_name2id, hdr, @ffi_functions[:hts_itr_query], @ffi_functions[:bcf_readrec])
       end
 
       # Load a BCF index

data/lib/hts/tabix.rb

@@ -24,7 +24,7 @@ module HTS
 
     def initialize(file_name, index: nil, threads: nil, build_index: false)
       if block_given?
-        message = "HTS::Tabix.new() dose not take block; Please use HTS::Tabix.open() instead"
+        message = "HTS::Tabix.new() does not take block; Please use HTS::Tabix.open() instead"
         raise message
       end
 

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.8"
+  VERSION = "0.3.0"
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.8
+  version: 0.3.0
 platform: ruby
 authors:
 - kojix2
-autorequire:
 bindir: bin
 cert_chain: []
-date: 2023-05-17 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -52,77 +51,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: irb
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: minitest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: simplecov
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-description:
 email:
 - 2xijok@gmail.com
 executables: []
@@ -174,7 +102,6 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -189,8 +116,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.10
-signing_key:
+rubygems_version: 3.7.1
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []