minimap2 0.2.24.0 → 0.2.24.2

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Files changed (7) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +7 -2
  3. data/ext/Rakefile +4 -2
  4. data/lib/minimap2/ffi/constants.rb +29 -29
  5. data/lib/minimap2/ffi/mappy.rb +10 -10
  6. data/lib/minimap2/version.rb +1 -1
  7. metadata +3 -3
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data/README.md CHANGED
@@ -2,8 +2,9 @@
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  [![Gem Version](https://img.shields.io/gem/v/minimap2?color=brightgreen)](https://rubygems.org/gems/minimap2)
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  [![CI](https://github.com/kojix2/ruby-minimap2/workflows/CI/badge.svg)](https://github.com/kojix2/ruby-minimap2/actions)
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+ [![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/minimap2)
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+ [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://kojix2.github.io/ruby-minimap2/)
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  [![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
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- [![Docs Latest](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/minimap2)
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  [![DOI](https://zenodo.org/badge/325711305.svg)](https://zenodo.org/badge/latestdoi/325711305)
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  :dna: [minimap2](https://github.com/lh3/minimap2) - the long-read mapper - for [Ruby](https://github.com/ruby/ruby)
@@ -107,7 +108,7 @@ pp hits
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  * API is based on [Mappy](https://github.com/lh3/minimap2/tree/master/python), the official Python binding for Minimap2.
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  * `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
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- * See [RubyDoc](https://rubydoc.info/gems/minimap2/) for details.
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+ * See [documentation](https://kojix2.github.io/ruby-minimap2/) for details.
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  <details>
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  <summary><b>C Structures and Functions</b></summary>
@@ -174,6 +175,10 @@ ruby-minimap2 is a library under development and there are many points to be imp
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  Please feel free to report [bugs](https://github.com/kojix2/ruby-minimap2/issues) and [pull requests](https://github.com/kojix2/ruby-minimap2/pulls)!
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+ Do you need commit rights to my repository?
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+ Do you want to get admin rights and take over the project?
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+ If so, please feel free to contact me @kojix2.
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+
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  ## License
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  [MIT License](https://opensource.org/licenses/MIT).
data/ext/Rakefile CHANGED
@@ -23,9 +23,11 @@ namespace :minimap2 do
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  when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
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  sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
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  when /darwin|mac os/
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- sh "clang -dynamiclib -undefined dynamic_lookup -o #{target_fname} *.o"
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+ sh "clang -dynamiclib -undefined dynamic_lookup -o #{target_fname} *.o -lm -lz -lpthread"
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+ sh "otool -L #{target_fname}"
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  else
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- sh "cc -shared -o #{target_fname} -lm -lz -lpthread *.o"
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+ sh "cc *.o -shared -o #{target_fname} -lm -lz -lpthread"
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+ sh "ldd -r #{target_fname}"
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  end
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  sh "rm cmappy.h cmappy.c"
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  sh "git apply -R ../minimap2.patch"
data/lib/minimap2/ffi/constants.rb CHANGED
@@ -135,9 +135,9 @@ module Minimap2
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  :pe_bonus, :int,
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  :mid_occ_frac, :float, # only used by mm_mapopt_update(); see below
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  :q_occ_frac, :float,
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- :min_mid_occ, :int32_t,
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- :mid_occ, :int32_t, # ignore seeds with occurrences above this threshold
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- :max_occ, :int32_t,
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+ :min_mid_occ, :int32,
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+ :mid_occ, :int32, # ignore seeds with occurrences above this threshold
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+ :max_occ, :int32,
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  :mini_batch_size, :int64_t, # size of a batch of query bases to process in parallel
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  :max_sw_mat, :int64_t,
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  :cap_kalloc, :int64_t,
@@ -149,19 +149,19 @@ module Minimap2
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  layout \
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  :name, :string, # name of the db sequence
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  :offset, :uint64_t, # offset in mm_idx_t::S
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- :len, :uint32_t, # length
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- :is_alt, :uint32_t
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+ :len, :uint32, # length
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+ :is_alt, :uint32
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  end
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  class Idx < ::FFI::Struct
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  layout \
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- :b, :int32_t,
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- :w, :int32_t,
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- :k, :int32_t,
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- :flag, :int32_t,
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- :n_seq, :uint32_t, # number of reference sequences
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- :index, :int32_t,
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- :n_alt, :int32_t,
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+ :b, :int32,
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+ :w, :int32,
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+ :k, :int32,
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+ :flag, :int32,
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+ :n_seq, :uint32, # number of reference sequences
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+ :index, :int32,
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+ :n_alt, :int32,
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  :seq, IdxSeq.ptr, # sequence name, length and offset
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  :S, :pointer, # 4-bit packed sequence
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  :B, :pointer, # index (hidden)
@@ -203,23 +203,23 @@ module Minimap2
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  class Reg1 < ::FFI::BitStruct
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  layout \
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- :id, :int32_t, # ID for internal uses (see also parent below)
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- :cnt, :int32_t, # number of minimizers; if on the reverse strand
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- :rid, :int32_t, # reference index; if this is an alignment from inversion rescue
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- :score, :int32_t, # DP alignment score
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- :qs, :int32_t, # query start
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- :qe, :int32_t, # query end
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- :rs, :int32_t, # reference start
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- :re, :int32_t, # reference end
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- :parent, :int32_t, # parent==id if primary
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- :subsc, :int32_t, # best alternate mapping score
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- :as, :int32_t, # offset in the a[] array (for internal uses only)
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- :mlen, :int32_t, # seeded exact match length
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- :blen, :int32_t, # seeded alignment block length
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- :n_sub, :int32_t, # number of suboptimal mappings
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- :score0, :int32_t, # initial chaining score (before chain merging/spliting)
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- :fields, :uint32_t,
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- :hash, :uint32_t,
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+ :id, :int32, # ID for internal uses (see also parent below)
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+ :cnt, :int32, # number of minimizers; if on the reverse strand
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+ :rid, :int32, # reference index; if this is an alignment from inversion rescue
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+ :score, :int32, # DP alignment score
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+ :qs, :int32, # query start
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+ :qe, :int32, # query end
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+ :rs, :int32, # reference start
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+ :re, :int32, # reference end
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+ :parent, :int32, # parent==id if primary
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+ :subsc, :int32, # best alternate mapping score
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+ :as, :int32, # offset in the a[] array (for internal uses only)
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+ :mlen, :int32, # seeded exact match length
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+ :blen, :int32, # seeded alignment block length
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+ :n_sub, :int32, # number of suboptimal mappings
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+ :score0, :int32, # initial chaining score (before chain merging/spliting)
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+ :fields, :uint32,
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+ :hash, :uint32,
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  :div, :float,
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  :p, Extra.ptr
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data/lib/minimap2/ffi/mappy.rb CHANGED
@@ -7,20 +7,20 @@ module Minimap2
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  class Hit < ::FFI::Struct
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  layout \
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  :ctg, :string,
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- :ctg_start, :int32_t,
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- :ctg_end, :int32_t,
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- :qry_start, :int32_t,
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- :qry_end, :int32_t,
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- :blen, :int32_t,
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- :mlen, :int32_t,
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- :NM, :int32_t,
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- :ctg_len, :int32_t,
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+ :ctg_start, :int32,
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+ :ctg_end, :int32,
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+ :qry_start, :int32,
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+ :qry_end, :int32,
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+ :blen, :int32,
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+ :mlen, :int32,
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+ :NM, :int32,
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+ :ctg_len, :int32,
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  :mapq, :uint8_t,
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  :is_primary, :uint8_t,
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  :strand, :int8_t,
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  :trans_strand, :int8_t,
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- :seg_id, :int32_t,
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- :n_cigar32, :int32_t,
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+ :seg_id, :int32,
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+ :n_cigar32, :int32,
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  :cigar32, :pointer
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  end
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data/lib/minimap2/version.rb CHANGED
@@ -2,5 +2,5 @@
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  module Minimap2
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  # Minimap2-2.23 (r1111)
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- VERSION = "0.2.24.0"
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+ VERSION = "0.2.24.2"
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
1
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  --- !ruby/object:Gem::Specification
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  name: minimap2
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  version: !ruby/object:Gem::Version
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- version: 0.2.24.0
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+ version: 0.2.24.2
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  platform: ruby
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  authors:
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  - kojix2
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2021-12-27 00:00:00.000000000 Z
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+ date: 2022-11-09 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: ffi
@@ -164,7 +164,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubygems_version: 3.3.3
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+ rubygems_version: 3.3.7
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  signing_key:
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  specification_version: 4
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  summary: minimap2