htslib 0.4.1 → 0.5.0

metadata

@@ -1,65 +1,31 @@
 --- !ruby/object:Gem::Specification
 name: htslib
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.5.0
 platform: ruby
 authors:
 - kojix2
 bindir: bin
 cert_chain: []
 date: 1980-01-02 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: ffi
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: ffi-bitfield
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: pkg-config
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+dependencies: []
 email:
 - 2xijok@gmail.com
 executables: []
-extensions: []
+extensions:
+- ext/htslib_native/extconf.rb
 extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
 - TUTORIAL.md
+- ext/htslib_native/extconf.rb
+- ext/htslib_native/htslib_native.h
+- ext/htslib_native/htslib_native_ext.c
+- ext/htslib_native/native_bam.c
+- ext/htslib_native/native_bcf.c
+- ext/htslib_native/native_faidx.c
+- ext/htslib_native/native_tabix.c
 - lib/hts/bam.rb
 - lib/hts/bam/auxi.rb
 - lib/hts/bam/base_mod.rb
@@ -78,25 +44,8 @@ files:
 - lib/hts/bcf/info.rb
 - lib/hts/bcf/record.rb
 - lib/hts/faidx.rb
-- lib/hts/ffi_ext/README.md
-- lib/hts/ffi_ext/pointer.rb
-- lib/hts/ffi_ext/struct.rb
 - lib/hts/hts.rb
-- lib/hts/libhts.rb
-- lib/hts/libhts/bgzf.rb
-- lib/hts/libhts/constants.rb
-- lib/hts/libhts/cram.rb
-- lib/hts/libhts/fai.rb
-- lib/hts/libhts/hfile.rb
-- lib/hts/libhts/hts.rb
-- lib/hts/libhts/kfunc.rb
-- lib/hts/libhts/sam.rb
-- lib/hts/libhts/sam_funcs.rb
-- lib/hts/libhts/tbx.rb
-- lib/hts/libhts/tbx_funcs.rb
-- lib/hts/libhts/thread_pool.rb
-- lib/hts/libhts/vcf.rb
-- lib/hts/libhts/vcf_funcs.rb
+- lib/hts/native.rb
 - lib/hts/tabix.rb
 - lib/hts/version.rb
 - lib/htslib.rb
@@ -119,7 +68,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 4.0.10
+rubygems_version: 4.0.3
 specification_version: 4
 summary: HTSlib bindings for Ruby
 test_files: []

data/lib/hts/ffi_ext/README.md

@@ -1,8 +0,0 @@
-# Ruby-FFI extensions
-
-* Add syntax sugar
-  * union_layout
-  * struct_layout
-
-* Support for bit fields
-  * [ffi-bitfield](https://github.com/kojix2/ffi-bitfield)

data/lib/hts/ffi_ext/pointer.rb

@@ -1,18 +0,0 @@
-# frozen_string_literal: true
-
-module FFI
-  class Pointer
-    unless method_defined?(:read_array_of_struct)
-      def read_array_of_struct(type, length)
-        ary = []
-        size = type.size
-        tmp = self
-        length.times do |j|
-          ary << type.new(tmp)
-          tmp += size unless j == length - 1 # avoid OOB
-        end
-        ary
-      end
-    end
-  end
-end

data/lib/hts/ffi_ext/struct.rb

@@ -1,45 +0,0 @@
-# frozen_string_literal: true
-
-require "ffi/bit_field"
-
-module FFI
-  class Struct
-    class << self
-      # @example HtsOpt
-      #   class HtsOpt < FFI::Struct
-      #     layout \
-      #       :arg,            :string,
-      #       :opt,            HtsFmtOption,
-      #       :val,
-      #       union_layout(
-      #         :i,            :int,
-      #         :s,            :string
-      #       ),
-      #       :next,           HtsOpt.ptr
-      #   end
-
-      def union_layout(*args)
-        Class.new(FFI::Union) { layout(*args) }
-      end
-
-      # @example HtsFormat
-      #   class HtsFormat < FFI::Struct
-      #     layout \
-      #       :category,          HtsFormatCategory,
-      #       :format,            HtsExactFormat,
-      #       :version,
-      #       struct_layout(
-      #         :major,           :short,
-      #         :minor,           :short
-      #       ),
-      #       :compression,       HtsCompression,
-      #       :compression_level, :short,
-      #       :specific,          :pointer
-      #   end
-
-      def struct_layout(*args)
-        Class.new(FFI::Struct) { layout(*args) }
-      end
-    end
-  end
-end

data/lib/hts/libhts/bgzf.rb

@@ -1,199 +0,0 @@
-# frozen_string_literal: true
-
-# BGZF
-module HTS
-  module LibHTS
-    # Open an existing file descriptor for reading or writing.
-    attach_function \
-      :bgzf_dopen,
-      %i[int string],
-      BGZF.by_ref
-
-    # Open the specified file for reading or writing.
-    attach_function \
-      :bgzf_open,
-      %i[string string],
-      BGZF.by_ref
-
-    # Open an existing hFILE stream for reading or writing.
-    attach_function \
-      :bgzf_hopen,
-      [HFile, :string],
-      BGZF.by_ref
-
-    # Close the BGZF and free all associated resources.
-    attach_function \
-      :bgzf_close,
-      [HFile],
-      :int
-
-    # Read up to _length_ bytes from the file storing into _data_.
-    attach_function \
-      :bgzf_read,
-      [HFile, :pointer, :size_t],
-      :ssize_t
-
-    # Write _length_ bytes from _data_ to the file. If no I/O errors occur,
-    # the complete _length_ bytes will be written (or queued for writing).
-    attach_function \
-      :bgzf_write,
-      [BGZF, :pointer, :size_t],
-      :ssize_t
-
-    # Write _length_ bytes from _data_ to the file, the index will be used to
-    # decide the amount of uncompressed data to be written to each bgzip block.
-    attach_function \
-      :bgzf_block_write,
-      [BGZF, :pointer, :size_t],
-      :ssize_t
-
-    # Returns the next byte in the file without consuming it.
-    attach_function \
-      :bgzf_peek,
-      [BGZF],
-      :int
-
-    # Read up to _length_ bytes directly from the underlying stream without
-    # decompressing.  Bypasses BGZF blocking, so must be used with care in
-    # specialised circumstances only.
-    attach_function \
-      :bgzf_raw_read,
-      [BGZF, :pointer, :size_t],
-      :ssize_t
-
-    # Write _length_ bytes directly to the underlying stream without
-    # compressing.  Bypasses BGZF blocking, so must be used with care
-    # in specialised circumstances only.
-    attach_function \
-      :bgzf_raw_write,
-      [BGZF, :pointer, :size_t],
-      :ssize_t
-
-    # Write the data in the buffer to the file.
-    attach_function \
-      :bgzf_flush,
-      [BGZF],
-      :int
-
-    # Return a virtual file pointer to the current location in the file.
-    def self.bgzf_tell(fp)
-      (fp[:block_address] << 16) | (fp[:block_offset] & 0xFFFF)
-    end
-
-    # Set the file to read from the location specified by _pos_.
-    attach_function \
-      :bgzf_seek,
-      [BGZF, :int64, :int],
-      :int64
-
-    # Check if the BGZF end-of-file (EOF) marker is present
-    attach_function \
-      :bgzf_check_EOF,
-      [BGZF],
-      :int
-
-    # Return the file's compression format
-    attach_function \
-      :bgzf_compression,
-      [BGZF],
-      :int
-
-    # Check if a file is in the BGZF format
-    attach_function \
-      :bgzf_is_bgzf,
-      [:string],
-      :int
-
-    # Set the cache size. Only effective when compiled with -DBGZF_CACHE.
-    attach_function \
-      :bgzf_set_cache_size,
-      [BGZF, :int],
-      :void
-
-    # Flush the file if the remaining buffer size is smaller than _size_
-    attach_function \
-      :bgzf_flush_try,
-      [BGZF, :ssize_t],
-      :int
-
-    # Read one byte from a BGZF file. It is faster than bgzf_read()
-    attach_function \
-      :bgzf_getc,
-      [BGZF],
-      :int
-
-    # Read one line from a BGZF file. It is faster than bgzf_getc()
-    attach_function \
-      :bgzf_getline,
-      [BGZF, :int, KString],
-      :int
-
-    # Read the next BGZF block.
-    attach_function \
-      :bgzf_read_block,
-      [BGZF],
-      :int
-
-    # Enable multi-threading (when compiled with -DBGZF_MT) via a shared
-    # thread pool.
-    attach_function \
-      :bgzf_thread_pool,
-      [BGZF, :pointer, :int],
-      :int
-
-    # Enable multi-threading (only effective when the library was compiled
-    # with -DBGZF_MT)
-    attach_function \
-      :bgzf_mt,
-      [BGZF, :int, :int],
-      :int
-
-    # Compress a single BGZF block.
-    attach_function \
-      :bgzf_compress,
-      %i[pointer pointer pointer size_t int],
-      :int
-
-    # Position BGZF at the uncompressed offset
-    attach_function \
-      :bgzf_useek,
-      [BGZF, :off_t, :int],
-      :int
-
-    # Position in uncompressed BGZF
-    attach_function \
-      :bgzf_utell,
-      [BGZF],
-      :off_t
-
-    # Tell BGZF to build index while compressing.
-    attach_function \
-      :bgzf_index_build_init,
-      [BGZF],
-      :int
-
-    # Load BGZF index
-    attach_function \
-      :bgzf_index_load,
-      [BGZF, :string, :string],
-      :int
-
-    # Load BGZF index from an hFILE
-    attach_function \
-      :bgzf_index_load_hfile,
-      [BGZF, HFile, :string],
-      :int
-
-    # Save BGZF index
-    attach_function \
-      :bgzf_index_dump,
-      [BGZF, :string, :string],
-      :int
-
-    # Write a BGZF index to an hFILE
-    attach_function \
-      :bgzf_index_dump_hfile,
-      [BGZF, HFile, :string],
-      :int
-  end
-end