bioseqalign 0.0.1
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.
- data/ext/bioseqalign/FitAlign.cpp +48 -0
- data/ext/bioseqalign/FitAlign.cpp~ +42 -0
- data/ext/bioseqalign/FitAlign.hpp +22 -0
- data/ext/bioseqalign/FitAlign.hpp~ +20 -0
- data/ext/bioseqalign/GlobalAlign.cpp +45 -0
- data/ext/bioseqalign/GlobalAlign.cpp~ +53 -0
- data/ext/bioseqalign/GlobalAlign.hpp +20 -0
- data/ext/bioseqalign/GlobalAlign.hpp~ +53 -0
- data/ext/bioseqalign/LocalAlign.cpp +53 -0
- data/ext/bioseqalign/LocalAlign.cpp~ +1 -0
- data/ext/bioseqalign/LocalAlign.hpp +21 -0
- data/ext/bioseqalign/LocalAlign.hpp~ +1 -0
- data/ext/bioseqalign/Makefile +251 -0
- data/ext/bioseqalign/PairwiseAlign.cpp +33 -0
- data/ext/bioseqalign/PairwiseAlign.cpp~ +23 -0
- data/ext/bioseqalign/PairwiseAlign.hpp +54 -0
- data/ext/bioseqalign/PairwiseAlign.hpp~ +54 -0
- data/ext/bioseqalign/PrefixSuffixAlign.cpp +52 -0
- data/ext/bioseqalign/PrefixSuffixAlign.cpp~ +42 -0
- data/ext/bioseqalign/PrefixSuffixAlign.hpp +30 -0
- data/ext/bioseqalign/PrefixSuffixAlign.hpp~ +20 -0
- data/ext/bioseqalign/extconf.rb +2 -0
- data/ext/bioseqalign/extconf.rb~ +2 -0
- data/ext/bioseqalign/fitalgntest.cpp +49 -0
- data/ext/bioseqalign/fitalgntest.cpp~ +37 -0
- data/ext/bioseqalign/runTest.rb +17 -0
- data/ext/bioseqalign/runTest.rb~ +8 -0
- data/lib/bioseqalign.rb +151 -0
- metadata +91 -0
data/lib/bioseqalign.rb
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require 'bioseqalign/SeqAlign'
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class BioSeqAlign
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#
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# fit seq2 into seq1, returns the score
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#
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def self.fitAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = FitAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignScore
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end
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#
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# fit seq2 into seq1, returns alignment
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#
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# example:
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# [input]:: seq1 = <tt>AAAAAAAAGCTGAAAAAAAA</tt>
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#
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# seq2 = <tt>GCTG</tt>
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#
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# [output]:: <tt>["AAAAAAAAGCTGAAAAAAAA", "--------GCTG--------"]</tt>
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#
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# result of fitting alignment
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#
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# seq1: <tt>AAAAAAAAGCTGAAAAAAAA</tt>
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#
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# seq2: <tt>--------GCTG--------</tt>
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#
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def self.fitAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = FitAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignment
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end
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#
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# prefix-suffix alignment, returns score. Prefix of seq2 aligned with
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# suffix of seq1
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#
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def self.prefixSuffixAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = PrefixSuffixAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignScore
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end
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#
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# prefix-suffix alignment, returns alignment. Prefix of seq2 aligned with
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# suffix of seq1
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#
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# example:
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#
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# [input]:: seq1 = <tt>GGGGGGGGAAAAA</tt>
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#
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# seq2 = <tt>AAAAAACTGATAC</tt>
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#
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# [output]:: <tt>["GGGGGGGGAAAAA--------", "--------AAAAAACTGATAC"]</tt>
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#
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# result of prefix-suffix alignment
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#
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# seq1: <tt>GGGGGGGGAAAAA--------</tt>
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#
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# seq2: <tt>--------AAAAAACTGATAC</tt>
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#
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def self.prefixSuffixAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = PrefixSuffixAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignment
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end
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#
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# local alignment of seq1 and seq2, returns score.
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#
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def self.localAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = LocalAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignScore
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end
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#
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# local alignment of seq1 and seq2, returns alignment.
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#
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# example:
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#
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# [input]:: seq1 = <tt>CTGAGTCGATAA</tt>
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#
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# seq2 = <tt>GGGGTCGATTTT</tt>
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#
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# [output]:: <tt>["GTCGAT", "GTCGAT"]</tt>
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#
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# result of local alignment
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#
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# seq1: <tt>GTCGAT</tt>
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#
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# seq2: <tt>GTCGAT</tt>
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#
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def self.localAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = LocalAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignment
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end
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#
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# global alignment of seq1 and seq2, returns score.
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#
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def self.globalAlignScore(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = GlobalAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignScore
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end
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#
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# global alignment of seq1 and seq2, returns alignment.
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#
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# example:
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#
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# [input]:: seq1 = <tt>CTGAGTCGATAA</tt>
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#
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# seq2 = <tt>GGGGTCGATTTT</tt>
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#
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# [output]:: <tt>["CTGAGTCGA-TA", "AGGGGTCGATTT"]</tt>
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#
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# result of global alignment
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#
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# seq1: <tt>CTGAGTCGA-TA</tt>
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#
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# seq2: <tt>AGGGGTCGATTT</tt>
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#
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def self.globalAlignStr(seq1, seq2, match=1, mismatch=-1, indel=-1)
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fa = GlobalAlign.new(seq1, seq2)
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fa.setMatchScore(match)
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fa.setMismatchScore(mismatch)
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fa.setIndelScore(indel)
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fa.run
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fa.getAlignment
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end
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end
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metadata
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--- !ruby/object:Gem::Specification
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name: bioseqalign
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version: !ruby/object:Gem::Version
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version: 0.0.1
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prerelease:
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platform: ruby
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authors:
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- Stefano R.B.
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-06-04 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rice
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requirement: !ruby/object:Gem::Requirement
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none: false
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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: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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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: A simple gem to perform fast pairwise sequence alignment using seqan
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email: stefano.rb@gmail.com
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executables: []
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extensions:
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- ext/bioseqalign/extconf.rb
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extra_rdoc_files: []
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files:
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- lib/bioseqalign.rb
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- ext/bioseqalign/FitAlign.hpp
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- ext/bioseqalign/extconf.rb
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- ext/bioseqalign/PrefixSuffixAlign.hpp~
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- ext/bioseqalign/GlobalAlign.hpp
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- ext/bioseqalign/PrefixSuffixAlign.hpp
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- ext/bioseqalign/LocalAlign.cpp~
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- ext/bioseqalign/PrefixSuffixAlign.cpp~
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- ext/bioseqalign/runTest.rb
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- ext/bioseqalign/PrefixSuffixAlign.cpp
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- ext/bioseqalign/LocalAlign.hpp
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- ext/bioseqalign/GlobalAlign.hpp~
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- ext/bioseqalign/PairwiseAlign.cpp
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- ext/bioseqalign/runTest.rb~
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- ext/bioseqalign/FitAlign.cpp~
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- ext/bioseqalign/LocalAlign.cpp
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- ext/bioseqalign/Makefile
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- ext/bioseqalign/fitalgntest.cpp~
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- ext/bioseqalign/PairwiseAlign.hpp
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- ext/bioseqalign/PairwiseAlign.cpp~
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- ext/bioseqalign/LocalAlign.hpp~
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- ext/bioseqalign/GlobalAlign.cpp~
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- ext/bioseqalign/PairwiseAlign.hpp~
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- ext/bioseqalign/extconf.rb~
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- ext/bioseqalign/FitAlign.hpp~
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- ext/bioseqalign/fitalgntest.cpp
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- ext/bioseqalign/GlobalAlign.cpp
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- ext/bioseqalign/FitAlign.cpp
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homepage: http://rubygems.org/gems/bioseqalign
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licenses:
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- MIT
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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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- ext
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required_ruby_version: !ruby/object:Gem::Requirement
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none: false
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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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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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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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requirements: []
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rubyforge_project:
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rubygems_version: 1.8.23
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signing_key:
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specification_version: 3
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summary: Pairwise sequence alignment using seqan
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test_files: []
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