minimap2 0.2.22.0 → 0.2.23.0

checksums.yaml

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

@@ -83,7 +83,7 @@ pp hits[0]
 
 API is based on [Mappy](https://github.com/lh3/minimap2/tree/master/python), the official Python binding for Minimap2. 
 
-Note: `Aligner#map` has been changed to `aligne`, because `map` means iterator in Ruby.
+Note: `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
 
 ```markdown
 * Minimap2 module

data/lib/minimap2/ffi/constants.rb

@@ -101,6 +101,7 @@ module Minimap2
         :min_cnt,              :int,     # min number of minimizers on each chain
         :min_chain_score,      :int,     # min chaining score
         :chain_gap_scale,      :float,
+        :chain_skip_scale,     :float,
         :rmq_size_cap,         :int,
         :rmq_inner_dist,       :int,
         :rmq_rescue_size,      :int,
@@ -132,6 +133,7 @@ module Minimap2
         :pe_ori,               :int,
         :pe_bonus,             :int,
         :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
+        :q_occ_frac,           :float,
         :min_mid_occ,          :int32_t,
         :mid_occ,              :int32_t, # ignore seeds with occurrences above this threshold
         :max_occ,              :int32_t,
@@ -188,7 +190,7 @@ module Minimap2
         :n_ambi_trans_strand, :uint32,
         :n_cigar,             :uint32
 
-      bitfields :n_ambi_trans_strand,
+      bit_field :n_ambi_trans_strand,
                 :n_ambi, 30,      # number of ambiguous bases
                 :trans_strand, 2  # transcript strand: 0 for unknown, 1 for +, 2 for -
 
@@ -220,19 +222,20 @@ module Minimap2
         :div,    :float,
         :p,      Extra.ptr
 
-      bitfields :fields,
-                :mapq,        8,
-                :split,       2,
-                :rev,         1,
-                :inv,         1,
-                :sam_pri,     1,
-                :proper_frag, 1,
-                :pe_thru,     1,
-                :seg_split,   1,
-                :seg_id,      8,
-                :split_inv,   1,
-                :is_alt,      1,
-                :dummy,       6
+      bit_field :fields,
+                :mapq,            8,
+                :split,           2,
+                :rev,             1,
+                :inv,             1,
+                :sam_pri,         1,
+                :proper_frag,     1,
+                :pe_thru,         1,
+                :seg_split,       1,
+                :seg_id,          8,
+                :split_inv,       1,
+                :is_alt,          1,
+                :strand_retained, 1,
+                :dummy,           5
     end
 
     # memory buffer for thread-local storage during mapping

data/lib/minimap2/ffi.rb

@@ -1,8 +1,7 @@
 # frozen_string_literal: true
 
 # bit fields
-require_relative 'ffi_helper'
-
+require 'ffi/bit_struct'
 module Minimap2
   # Native APIs
   module FFI

data/lib/minimap2/version.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
 module Minimap2
-  # Minimap2-2.22 (r1101)
-  VERSION = '0.2.22.0'
+  # Minimap2-2.23 (r1111)
+  VERSION = '0.2.23.0'
 end

data/lib/minimap2.rb

@@ -3,9 +3,6 @@
 # dependencies
 require 'ffi'
 
-# bit fields
-require_relative 'minimap2/ffi_helper'
-
 # modules
 require_relative 'minimap2/aligner'
 require_relative 'minimap2/alignment'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.22.0
+  version: 0.2.23.0
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-08-08 00:00:00.000000000 Z
+date: 2021-11-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -25,90 +25,20 @@ 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: []
@@ -124,7 +54,6 @@ 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
@@ -146,7 +75,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.22
+rubygems_version: 3.2.26
 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