minimap2 0.2.22.0 → 0.2.23.0
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- checksums.yaml +4 -4
- data/README.md +1 -1
- data/lib/minimap2/ffi/constants.rb +17 -14
- data/lib/minimap2/ffi.rb +1 -2
- data/lib/minimap2/version.rb +2 -2
- data/lib/minimap2.rb +0 -3
- data/vendor/libminimap2.so +0 -0
- metadata +6 -77
- data/lib/minimap2/ffi_helper.rb +0 -53
checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: b22ce0b5ca5e9cb117ba31802303053571c40d0893065298f8585f00dfdcb653
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data.tar.gz: b76275c1b624ddbd12dc4bd1185f77ef16656fb113df4d668b1b651cd67ed1d1
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: a7a8ec0bbf34a82bf827293038a46210665a7c903e15fe3b2dbcfe71e88125ae82cca9b6649efefa1208e109538961c2a124517dc258ae2de8de8ff7aba10030
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data.tar.gz: 9807c04d8cabd3b548a780c12266d6b0f4e3cfd4aae539e4d289541d64bff1e07ffebd9765fb6d0e33fb317030eb8142c950e21658b72be752b08aa90982be08
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data/README.md
CHANGED
@@ -83,7 +83,7 @@ pp hits[0]
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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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86
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-
Note: `Aligner#map` has been changed to `
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+
Note: `Aligner#map` has been changed to `align`, because `map` means iterator in Ruby.
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```markdown
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* Minimap2 module
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@@ -101,6 +101,7 @@ module Minimap2
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101
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:min_cnt, :int, # min number of minimizers on each chain
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102
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:min_chain_score, :int, # min chaining score
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:chain_gap_scale, :float,
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+
:chain_skip_scale, :float,
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:rmq_size_cap, :int,
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:rmq_inner_dist, :int,
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:rmq_rescue_size, :int,
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@@ -132,6 +133,7 @@ module Minimap2
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:pe_ori, :int,
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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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136
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+
:q_occ_frac, :float,
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:min_mid_occ, :int32_t,
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136
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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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@@ -188,7 +190,7 @@ module Minimap2
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:n_ambi_trans_strand, :uint32,
|
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:n_cigar, :uint32
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-
|
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+
bit_field :n_ambi_trans_strand,
|
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:n_ambi, 30, # number of ambiguous bases
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:trans_strand, 2 # transcript strand: 0 for unknown, 1 for +, 2 for -
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@@ -220,19 +222,20 @@ module Minimap2
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:div, :float,
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:p, Extra.ptr
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-
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:mapq,
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:split,
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:rev,
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:inv,
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-
:sam_pri,
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:proper_frag,
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:pe_thru,
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:seg_split,
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:seg_id,
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:split_inv,
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:is_alt,
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-
:
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bit_field :fields,
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:mapq, 8,
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:split, 2,
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:rev, 1,
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:inv, 1,
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:sam_pri, 1,
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:proper_frag, 1,
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:pe_thru, 1,
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:seg_split, 1,
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:seg_id, 8,
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:split_inv, 1,
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:is_alt, 1,
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:strand_retained, 1,
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:dummy, 5
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end
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# memory buffer for thread-local storage during mapping
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data/lib/minimap2/ffi.rb
CHANGED
data/lib/minimap2/version.rb
CHANGED
data/lib/minimap2.rb
CHANGED
data/vendor/libminimap2.so
CHANGED
Binary file
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
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.
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version: 0.2.23.0
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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-
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date: 2021-11-19 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: ffi
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@@ -25,90 +25,20 @@ dependencies:
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name:
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name: ffi-bitfield
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: irb
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: minitest
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
|
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
|
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name: rubocop
|
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: tty-command
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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description:
|
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description: Ruby bindings to the Minimap2 aligner.
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email:
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- 2xijok@gmail.com
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executables: []
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@@ -124,7 +54,6 @@ files:
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- lib/minimap2/ffi/constants.rb
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- lib/minimap2/ffi/functions.rb
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- lib/minimap2/ffi/mappy.rb
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- lib/minimap2/ffi_helper.rb
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- lib/minimap2/version.rb
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- vendor/libminimap2.so
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homepage: https://github.com/kojix2/ruby-minimap2
|
@@ -146,7 +75,7 @@ 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: 3.2.
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rubygems_version: 3.2.26
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signing_key:
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specification_version: 4
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summary: minimap2
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data/lib/minimap2/ffi_helper.rb
DELETED
@@ -1,53 +0,0 @@
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# frozen_string_literal: true
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require 'ffi'
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-
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module FFI
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class BitStruct < Struct
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class << self
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# def union_layout(*args)
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# Class.new(FFI::Union) { layout(*args) }
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# end
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# def struct_layout(*args)
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# Class.new(FFI::Struct) { layout(*args) }
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# end
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-
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module BitFieldsModule
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def [](name)
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bit_fields = self.class.bit_fields_map
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parent, start, width = bit_fields[name]
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if parent
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(super(parent) >> start) & ((1 << width) - 1)
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else
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super(name)
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end
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end
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end
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private_constant :BitFieldsModule
|
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-
|
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attr_reader :bit_fields_map
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-
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def bitfields(*args)
|
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unless instance_variable_defined?(:@bit_fields)
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@bit_fields_map = {}
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prepend BitFieldsModule
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end
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-
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parent = args.shift
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labels = []
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widths = []
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args.each_slice(2) do |l, w|
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labels << l
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widths << w
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-
end
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starts = widths.inject([0]) do |result, w|
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result << (result.last + w)
|
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-
end
|
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-
labels.zip(starts, widths).each do |l, s, w|
|
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@bit_fields_map[l] = [parent, s, w]
|
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-
end
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end
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end
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end
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end
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