minimap2 0.2.26.1 → 0.2.28.0
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 +16 -16
- data/ext/Rakefile +1 -3
- data/ext/minimap2/NEWS.md +68 -1
- data/ext/minimap2/README.md +8 -5
- data/ext/minimap2/align.c +19 -5
- data/ext/minimap2/cookbook.md +2 -2
- data/ext/minimap2/format.c +83 -17
- data/ext/minimap2/index.c +1 -0
- data/ext/minimap2/lchain.c +5 -5
- data/ext/minimap2/main.c +14 -6
- data/ext/minimap2/minimap.h +4 -1
- data/ext/minimap2/minimap2.1 +60 -11
- data/ext/minimap2/misc/paftools.js +88 -36
- data/ext/minimap2/mmpriv.h +1 -2
- data/ext/minimap2/options.c +25 -7
- data/ext/minimap2/python/README.rst +3 -1
- data/ext/minimap2/python/cmappy.pxd +1 -0
- data/ext/minimap2/python/mappy.pyx +4 -2
- data/ext/minimap2/python/minimap2.py +5 -3
- data/ext/minimap2/seed.c +2 -1
- data/ext/minimap2/setup.py +1 -1
- data/lib/minimap2/aligner.rb +6 -3
- data/lib/minimap2/alignment.rb +2 -1
- data/lib/minimap2/ffi/constants.rb +5 -1
- data/lib/minimap2/ffi/functions.rb +16 -3
- data/lib/minimap2/ffi.rb +1 -0
- data/lib/minimap2/version.rb +1 -1
- data/lib/minimap2.rb +2 -2
- metadata +6 -6
data/lib/minimap2/version.rb
CHANGED
data/lib/minimap2.rb
CHANGED
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@@ -37,7 +37,7 @@ module Minimap2
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# @example Get minimap2 version
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# Minimap2.execute('--version')
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-
def
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+
def execute(*rb_argv)
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str_ptrs = []
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# First argument is the program name.
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str_ptrs << ::FFI::MemoryPointer.from_string("minimap2")
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@@ -76,7 +76,7 @@ module Minimap2
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# @param [String] file_path
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# @param [Boolean] comment If True, the comment will be read.
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# @yield [name, seq, qual, comment]
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# @return [Enumerator] enum
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# @return [Enumerator] enum Return Enumerator if not block given.
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# Note: You can BioRuby instead of this method.
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def fastx_read(file_path, comment: false, &block)
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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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: 0.2.28.0
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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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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2024-03-29 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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@@ -150,7 +150,7 @@ homepage: https://github.com/kojix2/ruby-minimap2
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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@@ -165,8 +165,8 @@ 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.
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signing_key:
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rubygems_version: 3.5.3
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signing_key:
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specification_version: 4
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summary: minimap2
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test_files: []
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