minimap2 0.0.3 → 0.0.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +12 -3
- data/lib/minimap2/ffi/constants.rb +5 -4
- data/lib/minimap2/version.rb +1 -1
- metadata +3 -3
checksums.yaml
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@@ -1,7 +1,7 @@
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c5ef413b53423059804163320f8d5cd9ca0366fa7473603b06a857c109b99395
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data.tar.gz: 64cdc52d1961e793f9dc0a966c9f63f357aa3992c4cf8f3341d1cd64c0eea01a
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metadata.gz:
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metadata.gz: cf3a7c4294279f7a79a6f931f50c243f72b17658a69f4e6eec13e8584b61d503a6da164be3b01ca81cb52679d893efd903ac41387ec418f43c016e392d027ed4
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data.tar.gz: 4cac45c87e639ec4b698990e80e9a64aad902a368f44e35223a31ce162eeafa46137b06faa99b345f8e57a99cce4b9e39bb2959dd29d8a5c09d746439431df21
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data/README.md
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@@ -35,14 +35,23 @@ Ruby-minimap2 is tested on Ubuntu and macOS.
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```ruby
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require "minimap2"
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```
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create aligner
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```ruby
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aligner = Minimap2::Aligner.new("minimap2/test/MT-human.fa")
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```
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retrieve a subsequence from the index
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-
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```ruby
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seq = aligner.seq("MT_human", 100, 200)
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```
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mapping
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```ruby
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hits = aligner.align(seq)
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pp hits[0].to_h
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# {:ctg => "MT_human",
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@@ -77,6 +77,7 @@ module Minimap2
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:sdust_thres, :int, # score threshold for SDUST; 0 to disable
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:max_qlen, :int, # max query length
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:bw, :int, # bandwidth
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:bw_long, :int,
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:max_gap, :int, # break a chain if there are no minimizers in a max_gap window
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:max_gap_ref, :int,
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:max_frag_len, :int,
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@@ -85,14 +86,14 @@ module Minimap2
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:min_cnt, :int, # min number of minimizers on each chain
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:min_chain_score, :int, # min chaining score
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:chain_gap_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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:rmq_rescue_ratio, :float,
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:mask_level, :float,
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:mask_len, :int,
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:pri_ratio, :float,
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:best_n, :int, # top best_n chains are subjected to DP alignment
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:max_join_long, :int,
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:max_join_short, :int,
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:min_join_flank_sc, :int,
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:min_join_flank_ratio, :float,
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:alt_drop, :float,
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:a, :int, # matching score
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:b, :int, # mismatch
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data/lib/minimap2/version.rb
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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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: 0.0.
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version: 0.0.4
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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: 2021-05-27 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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@@ -131,7 +131,7 @@ 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: 3.2.15
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signing_key:
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specification_version: 4
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summary: minimap2
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