libssw 0.0.0.pre

checksums.yaml

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+SHA256:
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+  data.tar.gz: af7af5c499367ad64f4914bd1c4efce747966170d181960fa20b2c419745666b
+SHA512:
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data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2021 kojix2
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# ruby-libssw
+
+[libssw](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library) - fast SIMD parallelized implementation of the Smith-Waterman algorithm - for Ruby
+
+## Installation
+
+```ssh
+gem install libssw
+```
+
+## Usage
+
+```ruby
+require 'libssw'
+SSW = LibSSW
+```
+
+## Development
+
+```sh
+git clone --recurse-submodules https://github.com/kojix2/ruby-libssw
+bundle exec rake libssw:compile
+bundle exec rake test
+```
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/kojix2/ruby-libssw.
+
+## License
+
+* [MIT License](https://opensource.org/licenses/MIT).

data/exe/rbssw

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+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+require 'libssw'

data/lib/libssw.rb

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+# frozen_string_literal: true
+
+require 'forwardable'
+require_relative 'libssw/version'
+
+module LibSSW
+  class Error < StandardError; end
+
+  class << self
+    attr_accessor :ffi_lib
+  end
+
+  lib_name = case RbConfig::CONFIG['host_os']
+             when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
+               'libssw.dll'   # unconfirmed
+             when /darwin|mac os/
+               'libssw.dylib' # unconfirmed
+             else
+               'libssw.so'
+             end
+
+  self.ffi_lib = if ENV['LIBSSWDIR'] && !ENV['LIBSSWDIR'].empty?
+                   File.expand_path(lib_name, ENV['LIBUIDIR'])
+                 else
+                   File.expand_path("../vendor/#{lib_name}", __dir__)
+                 end
+
+  autoload :FFI, 'libssw/ffi'
+
+  extend Forwardable
+  Align   = FFI::Align
+  Profile = FFI::Profile
+  def_delegators :FFI,
+                 :ssw_init,
+                 :init_destroy,
+                 :align_destroy,
+                 :mark_mismatch
+end

data/lib/libssw/BLOSUM50.rb

@@ -0,0 +1,29 @@
+module LibSSW
+  BLOSUM50 = [
+	  #  A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+   	 5, -2, -1, -2, -1, -1, -1,  0, -2, -1, -2, -1, -1, -3, -1,  1,  0, -3, -2,  0, -2, -1, -1, -5,	# A
+    -2,  7, -1, -2, -4,  1,  0, -3,  0, -4, -3,  3, -2, -3, -3, -1, -1, -3, -1, -3, -1,  0, -1, -5,	# R
+    -1, -1,  7,  2, -2,  0,  0,  0,  1, -3, -4,  0, -2, -4, -2,  1,  0, -4, -2, -3,  5,  0, -1, -5,	# N
+    -2, -2,  2,  8, -4,  0,  2, -1, -1, -4, -4, -1, -4, -5, -1,  0, -1, -5, -3, -4,  6,  1, -1, -5,	# D
+    -1, -4, -2, -4, 13, -3, -3, -3, -3, -2, -2, -3, -2, -2, -4, -1, -1, -5, -3, -1, -3, -3, -1, -5,	# C
+    -1,  1,  0,  0, -3,  7,  2, -2,  1, -3, -2,  2,  0, -4, -1,  0, -1, -1, -1, -3,  0,  4, -1, -5,	# Q
+    -1,  0,  0,  2, -3,  2,  6, -3,  0, -4, -3,  1, -2, -3, -1, -1, -1, -3, -2, -3,  1,  5, -1, -5,	# E
+     0, -3,  0, -1, -3, -2, -3,  8, -2, -4, -4, -2, -3, -4, -2,  0, -2, -3, -3, -4, -1, -2, -1, -5,	# G
+    -2,  0,  1, -1, -3,  1,  0, -2, 10, -4, -3,  0, -1, -1, -2, -1, -2, -3,  2, -4,  0,  0, -1, -5,	# H
+    -1, -4, -3, -4, -2, -3, -4, -4, -4,  5,  2, -3,  2,  0, -3, -3, -1, -3, -1,  4, -4, -3, -1, -5,	# I
+    -2, -3, -4, -4, -2, -2, -3, -4, -3,  2,  5, -3,  3,  1, -4, -3, -1, -2, -1,  1, -4, -3, -1, -5,	# L
+    -1,  3,  0, -1, -3,  2,  1, -2,  0, -3, -3,  6, -2, -4, -1,  0, -1, -3, -2, -3,  0,  1, -1, -5,	# K
+    -1, -2, -2, -4, -2,  0, -2, -3, -1,  2,  3, -2,  7,  0, -3, -2, -1, -1,  0,  1, -3, -1, -1, -5,	# M
+    -3, -3, -4, -5, -2, -4, -3, -4, -1,  0,  1, -4,  0,  8, -4, -3, -2,  1,  4, -1, -4, -4, -1, -5,	# F
+    -1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -4, -1, -3, -4, 10, -1, -1, -4, -3, -3, -2, -1, -1, -5,	# P
+   	 1, -1,  1,  0, -1,  0, -1,  0, -1, -3, -3,  0, -2, -3, -1,  5,  2, -4, -2, -2,  0,  0, -1, -5,	# S
+     0, -1,  0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1,  2,  5, -3, -2,  0,  0, -1, -1, -5, 	# T
+    -3, -3, -4, -5, -5, -1, -3, -3, -3, -3, -2, -3, -1,  1, -4, -4, -3, 15,  2, -3, -5, -2, -1, -5, 	# W
+    -2, -1, -2, -3, -3, -1, -2, -3,  2, -1, -1, -2,  0,  4, -3, -2, -2,  2,  8, -1, -3, -2, -1, -5, 	# Y
+     0, -3, -3, -4, -1, -3, -3, -4, -4,  4,  1, -3,  1, -1, -3, -2,  0, -3, -1,  5, -3, -3, -1, -5, 	# V
+    -2, -1,  5,  6, -3,  0,  1, -1,  0, -4, -4,  0, -3, -4, -2,  0,  0, -5, -3, -3,  6,  1, -1, -5, 	# B
+    -1,  0,  0,  1, -3,  4,  5, -2,  0, -3, -3,  1, -1, -4, -1,  0, -1, -2, -2, -3,  1,  5, -1, -5, 	# Z
+    -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -5, 	# X
+    -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5,  1 	# *
+    ]
+end

data/lib/libssw/ffi.rb

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+# frozen_string_literal: true
+
+require 'fiddle/import'
+
+module LibSSW
+  module FFI
+    extend Fiddle::Importer
+
+    begin
+      dlload LibSSW.ffi_lib
+    rescue LoadError => e
+      raise LoadError, "Could not find libssw shared library. \n#{e}"
+    end
+
+    class << self
+      attr_reader :func_map
+
+      def try_extern(signature, *opts)
+        extern(signature, *opts)
+      rescue StandardError => e
+        warn "#{e.class.name}: #{e.message}"
+      end
+
+      def ffi_methods
+        @ffi_methods ||= func_map.each_key.to_a
+      end
+    end
+
+    Align = struct [
+      'uint16_t score1',
+      'uint16_t score2',
+      'int32_t ref_begin1',
+      'int32_t ref_end1',
+      'int32_t	read_begin1',
+      'int32_t read_end1',
+      'int32_t ref_end2',
+      'uint32_t* cigar',
+      'int32_t cigarLen'
+    ]
+
+    Profile = struct [
+      'int32_t* byte', # __m128i* profile_byte;	// 0: none
+      'int32_t* word', # __m128i* profile_word;	// 0: none
+      'const int8_t* read',
+      'const int8_t* mat',
+      'int32_t readLen',
+      'int32_t n',
+      'uint8_t bias'
+    ]
+
+    # s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size)
+    try_extern 's_profile* ssw_init (const int8_t* read, int32_t readLen, const int8_t* mat, int32_t n, int8_t score_size)'
+
+    try_extern 'void init_destroy (s_profile* p)'
+
+    try_extern 's_align* ssw_align ('   \
+               'const s_profile* prof,' \
+               'const int8_t* ref,'     \
+               'int32_t refLen,'        \
+               'uint8_t weight_gapO,'   \
+               'uint8_t weight_gapE,'   \
+               'uint8_t flag,'          \
+               'uint16_t filters,'      \
+               'int32_t filterd,'       \
+               'int32_t maskLen)'
+
+    try_extern 'void align_destroy (s_align* a)'
+
+    try_extern 'int32_t mark_mismatch (' \
+               'int32_t ref_begin1,'     \
+               'int32_t read_begin1,'    \
+               'int32_t read_end1,'      \
+               'const int8_t* ref,'      \
+               'const int8_t* read,'     \
+               'int32_t readLen,'        \
+               'uint32_t** cigar,'       \
+               'int32_t* cigarLen)'
+  end
+end

data/lib/libssw/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module LibSSW
+  VERSION = '0.0.0.pre'
+end

metadata

@@ -0,0 +1,121 @@
+--- !ruby/object:Gem::Specification
+name: libssw
+version: !ruby/object:Gem::Version
+  version: 0.0.0.pre
+platform: ruby
+authors:
+- kojix2
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2021-01-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: fiddle
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.7
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.7
+- !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: 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: rubocop
+  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: Ruby bindings for libssw
+email:
+- 2xijok@gmail.com
+executables:
+- rbssw
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- exe/rbssw
+- lib/libssw.rb
+- lib/libssw/BLOSUM50.rb
+- lib/libssw/ffi.rb
+- lib/libssw/version.rb
+homepage: https://github.com/kojix2/ruby-libssw
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2.5'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">"
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubygems_version: 3.2.3
+signing_key: 
+specification_version: 4
+summary: Ruby bindings for libssw
+test_files: []