minimap2 0.2.22.0 → 0.2.24.1

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.22.0
+  version: 0.2.24.1
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-08-08 00:00:00.000000000 Z
+date: 2021-12-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -25,98 +25,118 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: bundler
+  name: ffi-bitfield
   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: 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'
-- !ruby/object:Gem::Dependency
-  name: tty-command
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: minimap2
+description: Ruby bindings to the Minimap2 aligner.
 email:
 - 2xijok@gmail.com
 executables: []
-extensions: []
+extensions:
+- ext/Rakefile
 extra_rdoc_files: []
 files:
 - LICENSE.txt
 - README.md
+- ext/Rakefile
+- ext/cmappy/cmappy.c
+- ext/cmappy/cmappy.h
+- ext/minimap2.patch
+- ext/minimap2/FAQ.md
+- ext/minimap2/LICENSE.txt
+- ext/minimap2/MANIFEST.in
+- ext/minimap2/Makefile
+- ext/minimap2/Makefile.simde
+- ext/minimap2/NEWS.md
+- ext/minimap2/README.md
+- ext/minimap2/align.c
+- ext/minimap2/bseq.c
+- ext/minimap2/bseq.h
+- ext/minimap2/code_of_conduct.md
+- ext/minimap2/cookbook.md
+- ext/minimap2/esterr.c
+- ext/minimap2/example.c
+- ext/minimap2/format.c
+- ext/minimap2/hit.c
+- ext/minimap2/index.c
+- ext/minimap2/kalloc.c
+- ext/minimap2/kalloc.h
+- ext/minimap2/kdq.h
+- ext/minimap2/ketopt.h
+- ext/minimap2/khash.h
+- ext/minimap2/krmq.h
+- ext/minimap2/kseq.h
+- ext/minimap2/ksort.h
+- ext/minimap2/ksw2.h
+- ext/minimap2/ksw2_dispatch.c
+- ext/minimap2/ksw2_extd2_sse.c
+- ext/minimap2/ksw2_exts2_sse.c
+- ext/minimap2/ksw2_extz2_sse.c
+- ext/minimap2/ksw2_ll_sse.c
+- ext/minimap2/kthread.c
+- ext/minimap2/kthread.h
+- ext/minimap2/kvec.h
+- ext/minimap2/lchain.c
+- ext/minimap2/main.c
+- ext/minimap2/map.c
+- ext/minimap2/minimap.h
+- ext/minimap2/minimap2.1
+- ext/minimap2/misc.c
+- ext/minimap2/misc/README.md
+- ext/minimap2/misc/mmphase.js
+- ext/minimap2/misc/paftools.js
+- ext/minimap2/mmpriv.h
+- ext/minimap2/options.c
+- ext/minimap2/pe.c
+- ext/minimap2/python/README.rst
+- ext/minimap2/python/cmappy.h
+- ext/minimap2/python/cmappy.pxd
+- ext/minimap2/python/mappy.pyx
+- ext/minimap2/python/minimap2.py
+- ext/minimap2/sdust.c
+- ext/minimap2/sdust.h
+- ext/minimap2/seed.c
+- ext/minimap2/setup.py
+- ext/minimap2/sketch.c
+- ext/minimap2/splitidx.c
+- ext/minimap2/sse2neon/emmintrin.h
+- ext/minimap2/test/MT-human.fa
+- ext/minimap2/test/MT-orang.fa
+- ext/minimap2/test/q-inv.fa
+- ext/minimap2/test/q2.fa
+- ext/minimap2/test/t-inv.fa
+- ext/minimap2/test/t2.fa
+- ext/minimap2/tex/Makefile
+- ext/minimap2/tex/bioinfo.cls
+- ext/minimap2/tex/blasr-mc.eval
+- ext/minimap2/tex/bowtie2-s3.sam.eval
+- ext/minimap2/tex/bwa-s3.sam.eval
+- ext/minimap2/tex/bwa.eval
+- ext/minimap2/tex/eval2roc.pl
+- ext/minimap2/tex/graphmap.eval
+- ext/minimap2/tex/hs38-simu.sh
+- ext/minimap2/tex/minialign.eval
+- ext/minimap2/tex/minimap2.bib
+- ext/minimap2/tex/minimap2.tex
+- ext/minimap2/tex/mm2-s3.sam.eval
+- ext/minimap2/tex/mm2-update.tex
+- ext/minimap2/tex/mm2.approx.eval
+- ext/minimap2/tex/mm2.eval
+- ext/minimap2/tex/natbib.bst
+- ext/minimap2/tex/natbib.sty
+- ext/minimap2/tex/ngmlr.eval
+- ext/minimap2/tex/roc.gp
+- ext/minimap2/tex/snap-s3.sam.eval
 - lib/minimap2.rb
 - lib/minimap2/aligner.rb
 - lib/minimap2/alignment.rb
@@ -124,9 +144,7 @@ files:
 - lib/minimap2/ffi/constants.rb
 - lib/minimap2/ffi/functions.rb
 - lib/minimap2/ffi/mappy.rb
-- lib/minimap2/ffi_helper.rb
 - lib/minimap2/version.rb
-- vendor/libminimap2.so
 homepage: https://github.com/kojix2/ruby-minimap2
 licenses:
 - MIT
@@ -146,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.22
+rubygems_version: 3.3.3
 signing_key: 
 specification_version: 4
 summary: minimap2

data/lib/minimap2/ffi_helper.rb

@@ -1,53 +0,0 @@
-# frozen_string_literal: true
-
-require 'ffi'
-
-module FFI
-  class BitStruct < Struct
-    class << self
-      # def union_layout(*args)
-      #   Class.new(FFI::Union) { layout(*args) }
-      # end
-
-      # def struct_layout(*args)
-      #   Class.new(FFI::Struct) { layout(*args) }
-      # end
-
-      module BitFieldsModule
-        def [](name)
-          bit_fields = self.class.bit_fields_map
-          parent, start, width = bit_fields[name]
-          if parent
-            (super(parent) >> start) & ((1 << width) - 1)
-          else
-            super(name)
-          end
-        end
-      end
-      private_constant :BitFieldsModule
-
-      attr_reader :bit_fields_map
-
-      def bitfields(*args)
-        unless instance_variable_defined?(:@bit_fields)
-          @bit_fields_map = {}
-          prepend BitFieldsModule
-        end
-
-        parent = args.shift
-        labels = []
-        widths = []
-        args.each_slice(2) do |l, w|
-          labels << l
-          widths << w
-        end
-        starts = widths.inject([0]) do |result, w|
-          result << (result.last + w)
-        end
-        labels.zip(starts, widths).each do |l, s, w|
-          @bit_fields_map[l] = [parent, s, w]
-        end
-      end
-    end
-  end
-end