htslib 0.2.5 → 0.2.8

data/lib/hts/libhts/constants.rb

@@ -158,7 +158,7 @@ module HTS
         :specific,          :pointer
     end
 
-    class HtsIdx < FFI::Struct
+    class HtsIdx < FFI::Struct # FIXME: ManagedStruct
       layout \
         :fmt,            :int,
         :min_shift,      :int,
@@ -205,7 +205,7 @@ module HTS
     end
 
     # HtsFile
-    class SamHdr < FFI::Struct
+    class SamHdr < FFI::ManagedStruct
       layout \
         :n_targets,      :int32,
         :ignore_sam_err, :int32,
@@ -255,7 +255,7 @@ module HTS
 
     SamFile = HtsFile
 
-    class HtsTpool < FFI::Struct
+    class HtsTpool < FFI::ManagedStruct
       layout \
         :pool,           :pointer,
         :qsize,          :int
@@ -277,7 +277,7 @@ module HTS
         :next,           HtsOpt.ptr
     end
 
-    class HtsItr < FFI::BitStruct
+    class HtsItr < FFI::BitStruct # FIXME: ManagedBitStruct
       layout \
         :_flags,         :uint32, # bit_fields
         :tid,            :int,
@@ -358,14 +358,14 @@ module HTS
     class BamPileupCd < FFI::Union
       layout \
         :p,               :pointer,
-        :i,               :int64_t,
+        :i,               :int64,
         :f,               :double
     end
 
     class BamPileup1 < FFI::BitStruct
       layout \
         :b,              Bam1.ptr,
-        :qpos,           :int32_t,
+        :qpos,           :int32,
         :indel,          :int,
         :level,          :int,
         :_flags,         :uint32, # bit_fields
@@ -391,9 +391,9 @@ module HTS
         :line_skip,      :int32
     end
 
-    class Tbx < FFI::Struct
+    class Tbx < FFI::ManagedStruct
       layout \
-        :conf,           TbxConf.ptr,
+        :conf,           TbxConf,
         :idx,            HtsIdx.ptr,
         :dict,           :pointer
 
@@ -406,8 +406,8 @@ module HTS
 
     FaiFormatOptions = enum(:FAI_NONE, :FAI_FASTA, :FAI_FASTQ)
 
-    class Faidx < FFI::Struct
-      layout :bgzf,      BGZF,
+    class Faidx < FFI::Struct # FIXME: ManagedStruct
+      layout :bgzf,      BGZF.ptr,
              :n,         :int,
              :m,         :int,
              :name,      :pointer,
@@ -428,7 +428,7 @@ module HTS
     end
 
     # Complete textual representation of a header line
-    class BcfHrec < FFI::Struct
+    class BcfHrec < FFI::ManagedStruct
       layout \
         :type,           :int,
         :key,            :string,
@@ -463,7 +463,7 @@ module HTS
 
     class BcfIdinfo < FFI::Struct
       layout \
-        :info,           [:uint64_t, 3],
+        :info,           [:uint64, 3],
         :hrec,           [BcfHrec.ptr, 3],
         :id,             :int
     end
@@ -474,7 +474,7 @@ module HTS
         :val,            BcfIdinfo.ptr
     end
 
-    class BcfHdr < FFI::Struct
+    class BcfHdr < FFI::ManagedStruct
       layout \
         :n,              [:int, 3],
         :id,             [:pointer, 3], # BcfIdpair.ptr
@@ -536,7 +536,7 @@ module HTS
       layout \
         :pos,            :hts_pos_t,
         :rlen,           :hts_pos_t,
-        :rid,            :int32_t,
+        :rid,            :int32,
         :qual,           :float,
         :_n_info_allele, :uint32,
         :_n_fmt_sample,  :uint32,

data/lib/hts/libhts/cram.rb

@@ -352,7 +352,7 @@ module HTS
     # As int32_decoded/encode, but from/to blocks instead of cram_fd
     attach_function \
       :int32_put_blk,
-      %i[cram_block int32_t],
+      %i[cram_block int32],
       :int
 
     # Returns the refs_t structure used by a cram file handle.

data/lib/hts/libhts/sam.rb

@@ -242,13 +242,13 @@ module HTS
       [Bam1,
        :size_t,
        :string,
-       :uint16_t,
-       :int32_t,
+       :uint16,
+       :int32,
        :hts_pos_t,
-       :uint8_t,
+       :uint8,
        :size_t,
        :string,
-       :int32_t,
+       :int32,
        :hts_pos_t,
        :hts_pos_t,
        :size_t,
@@ -440,10 +440,22 @@ module HTS
       [SamHdr, Bam1, :pointer], # hts_filter_t
       :int
 
+    # Return a pointer to a BAM record's first aux field
+    attach_function \
+      :bam_aux_first,
+      [Bam1],
+      :pointer
+
+    # Return a pointer to a BAM record's next aux field
+    attach_function \
+      :bam_aux_next,
+      [Bam1, :pointer],
+      :pointer
+
     # Return a pointer to an aux record
     attach_function \
       :bam_aux_get,
-      [Bam1, :string], # FIXME
+      [Bam1, :string], # const char tag[2]
       :pointer
 
     # Get an integer aux value
@@ -570,17 +582,17 @@ module HTS
       [:bam_plp],
       :void
 
-    callback :bam_plp_callback_funcion, [:pointer, Bam1, BamPileupCd], :int
+    callback :bam_plp_callback_function, [:pointer, Bam1, BamPileupCd], :int
 
     # sets a callback to initialise any per-pileup1_t fields.
     attach_function \
       :bam_plp_constructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_plp_destructor,
-      %i[bam_plp bam_plp_callback_funcion],
+      %i[bam_plp bam_plp_callback_function],
       :void
 
     # Get pileup padded insertion sequence
@@ -632,12 +644,12 @@ module HTS
 
     attach_function \
       :bam_mplp_constructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \
       :bam_mplp_destructor,
-      %i[bam_mplp bam_plp_callback_funcion],
+      %i[bam_mplp bam_plp_callback_function],
       :void
 
     attach_function \

data/lib/hts/libhts/tbx.rb

@@ -68,3 +68,5 @@ module HTS
       :void
   end
 end
+
+require_relative "tbx_funcs"

data/lib/hts/libhts/tbx_funcs.rb

@@ -8,7 +8,7 @@ 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_, @@tbx_readrec)
       end
 
       def tbx_itr_querys(tbx, s)

data/lib/hts/libhts/vcf.rb

@@ -469,7 +469,7 @@ module HTS
     attach_function \
       :bcf_fmt_sized_array,
       [KString, :pointer],
-      :uint8_t
+      :uint8
 
     # Encode a variable-length char array in BCF format
     attach_function \

data/lib/hts/libhts.rb

@@ -37,5 +37,5 @@ require_relative "libhts/sam"
 require_relative "libhts/cram"
 require_relative "libhts/vcf"
 require_relative "libhts/tbx"
-require_relative "libhts/faidx"
+require_relative "libhts/fai"
 require_relative "libhts/thread_pool"

data/lib/hts/tabix.rb

@@ -0,0 +1,116 @@
+# frozen_string_literal: true
+
+require_relative "../htslib"
+
+require_relative "hts"
+
+module HTS
+  class Tabix < Hts
+    include Enumerable
+
+    attr_reader :file_name, :index_name, :mode, :nthreads
+
+    def self.open(*args, **kw)
+      file = new(*args, **kw) # do not yield
+      return file unless block_given?
+
+      begin
+        yield file
+      ensure
+        file.close
+      end
+      file
+    end
+
+    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"
+        raise message
+      end
+
+      # NOTE: Do not check for the existence of local files, since file_names may be remote URIs.
+
+      @file_name  = file_name
+      @index_name = index
+      @mode       = "r"
+      @nthreads   = threads
+      @hts_file   = LibHTS.hts_open(@file_name, @mode)
+
+      raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
+
+      set_threads(threads) if threads
+
+      # build_index(index) if build_index
+      @idx = load_index(index)
+    end
+
+    def build_index
+      raise "Not implemented yet"
+    end
+
+    def load_index(index_name = nil)
+      if index_name
+        LibHTS.tbx_index_load2(@file_name, index_name)
+      else
+        LibHTS.tbx_index_load3(@file_name, nil, 2)
+      end
+    end
+
+    def index_loaded?
+      !@idx.null?
+    end
+
+    def name2id(name)
+      LibHTS.tbx_name2id(@idx, name)
+    end
+
+    def seqnames
+      nseq = FFI::MemoryPointer.new(:int)
+      LibHTS.tbx_seqnames(@idx, nseq).then do |pts|
+        pts.read_array_of_pointer(nseq.read_int).map(&:read_string)
+      end
+    end
+
+    def query(region, start = nil, end_ = nil, &block)
+      check_closed
+      raise "Index file is required to call the query method." unless index_loaded?
+
+      if start && end_
+        queryi(name2id(region), start, end_, &block)
+      else
+        querys(region, &block)
+      end
+    end
+
+    private
+
+    def queryi(id, start, end_, &block)
+      return to_enum(__method__, id, start, end_) unless block_given?
+
+      qiter = LibHTS.tbx_itr_queryi(@idx, id, start, end_)
+      raise "Failed to query region: #{id}:#{start}-#{end_}" if qiter.null?
+
+      query_yield(qiter, &block)
+      self
+    end
+
+    def querys(region, &block)
+      return to_enum(__method__, region) unless block_given?
+
+      qiter = LibHTS.tbx_itr_querys(@idx, region)
+      raise "Failed to query region: #{region}" if qiter.null?
+
+      query_yield(qiter, &block)
+      self
+    end
+
+    def query_yield(qiter)
+      r = LibHTS::KString.new
+      begin
+        yield r[:s].split("\t") while LibHTS.tbx_itr_next(@hts_file, @idx, qiter, r) > 0
+      ensure
+        LibHTS.hts_itr_destroy(qiter)
+      end
+    end
+  end
+end

data/lib/hts/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module HTS
-  VERSION = "0.2.5"
+  VERSION = "0.2.8"
 end

data/lib/htslib.rb

@@ -55,6 +55,6 @@ module HTS
   autoload :Hts,    "hts/hts"
   autoload :Bam,    "hts/bam"
   autoload :Bcf,    "hts/bcf"
-  autoload :Tbx,    "hts/tbx"
   autoload :Faidx,  "hts/faidx"
+  autoload :Tabix,  "hts/tabix"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.2.5
+  version: 0.2.8
 platform: ruby
 authors:
 - kojix2
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-10-27 00:00:00.000000000 Z
+date: 2023-05-17 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: []
@@ -131,6 +131,7 @@ extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
+- TUTORIAL.md
 - lib/hts/bam.rb
 - lib/hts/bam/auxi.rb
 - lib/hts/bam/cigar.rb
@@ -145,6 +146,7 @@ files:
 - lib/hts/bcf/info.rb
 - lib/hts/bcf/record.rb
 - lib/hts/faidx.rb
+- lib/hts/faidx/sequence.rb
 - lib/hts/ffi_ext/README.md
 - lib/hts/ffi_ext/pointer.rb
 - lib/hts/ffi_ext/struct.rb
@@ -153,7 +155,7 @@ files:
 - lib/hts/libhts/bgzf.rb
 - lib/hts/libhts/constants.rb
 - lib/hts/libhts/cram.rb
-- lib/hts/libhts/faidx.rb
+- lib/hts/libhts/fai.rb
 - lib/hts/libhts/hfile.rb
 - lib/hts/libhts/hts.rb
 - lib/hts/libhts/kfunc.rb
@@ -164,7 +166,7 @@ files:
 - lib/hts/libhts/thread_pool.rb
 - lib/hts/libhts/vcf.rb
 - lib/hts/libhts/vcf_funcs.rb
-- lib/hts/tbx.rb
+- lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
 homepage: https://github.com/kojix2/ruby-htslib
@@ -172,7 +174,7 @@ licenses:
 - MIT
 metadata:
   msys2_mingw_dependencies: htslib
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -187,8 +189,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.7
-signing_key: 
+rubygems_version: 3.4.10
+signing_key:
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []

data/lib/hts/tbx.rb

@@ -1,73 +0,0 @@
-# frozen_string_literal: true
-
-require_relative "../htslib"
-
-require_relative "hts"
-
-module HTS
-  class Tbx < Hts
-    include Enumerable
-
-    attr_reader :file_name, :index_name, :mode, :nthreads
-
-    def self.open(*args, **kw)
-      file = new(*args, **kw) # do not yield
-      return file unless block_given?
-
-      begin
-        yield file
-      ensure
-        file.close
-      end
-      file
-    end
-
-    def initialize(file_name, mode = "r", index: nil, threads: nil, build_index: false)
-      if block_given?
-        message = "HTS::Tbx.new() dose not take block; Please use HTS::Tbx.open() instead"
-        raise message
-      end
-
-      # NOTE: Do not check for the existence of local files, since file_names may be remote URIs.
-
-      @file_name  = file_name
-      @index_name = index
-      @mode       = mode
-      @nthreads   = threads
-      @hts_file = LibHTS.hts_open(@file_name, @mode)
-
-      raise Errno::ENOENT, "Failed to open #{@file_name}" if @hts_file.null?
-
-      set_threads(threads) if threads
-
-      # return if @mode[0] == "w"
-      raise "Not implemented" if @mode[0] == "w"
-
-      # build_index(index) if build_index
-      @idx = load_index(index)
-    end
-
-    def build_index
-      raise "Not implemented yet"
-    end
-
-    def load_index(index_name = nil)
-      if index_name
-        LibHTS.tbx_index_load2(@file_name, index_name)
-      else
-        LibHTS.tbx_index_load3(@file_name, nil, 2)
-      end
-    end
-
-    def tid(name)
-      LibHTS.tbx_name2id(@idx, name)
-    end
-
-    def seqnames
-      nseq = FFI::MemoryPointer.new(:int)
-      LibHTS.tbx_seqnames(@idx, nseq).then do |pts|
-        pts.read_array_of_pointer(nseq.read_int).map(&:read_string)
-      end
-    end
-  end
-end