bioseqalign 0.0.1 → 0.0.2
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- data/ext/bioseqalign/fitalgntest.cpp +11 -5
- data/ext/bioseqalign/runTest.rb +20 -2
- data/lib/bioseqalign.rb +13 -11
- metadata +3 -3
@@ -13,7 +13,9 @@ extern "C"
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13
13
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//void Init_FitAlign()
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14
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void Init_SeqAlign()
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{
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16
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-
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16
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+
Module rb_cModule = define_module("SeqAlign");
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17
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+
//Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class<PairwiseAlign>("PairwiseAlign")
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18
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+
Data_Type<PairwiseAlign> rb_cPairwiseAlign = define_class_under<PairwiseAlign>(rb_cModule,"PairwiseAlign")
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.define_constructor(Constructor<PairwiseAlign>())
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.define_constructor(Constructor<PairwiseAlign,std::string,std::string>())
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//.define_constructor(Constructor<PairwiseAlign,std::string,std::string,int,int,int>())
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@@ -25,23 +27,27 @@ void Init_SeqAlign()
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25
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.define_method("setMatchScore", &PairwiseAlign::setMatchScore)
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.define_method("setMismatchScore", &PairwiseAlign::setMismatchScore)
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.define_method("setIndelScore", &PairwiseAlign::setIndelScore);
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28
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-
Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
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30
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+
//Data_Type<FitAlign> rb_cFitAlign = define_class<FitAlign,PairwiseAlign>("FitAlign")
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31
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+
Data_Type<FitAlign> rb_cFitAlign = define_class_under<FitAlign,PairwiseAlign>(rb_cModule,"FitAlign")
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.define_constructor(Constructor<FitAlign>())
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.define_constructor(Constructor<FitAlign,std::string,std::string>())
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//.define_constructor(Constructor<FitAlign,std::string,std::string,int,int,int>())
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.define_method("run", &FitAlign::run)
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.define_method("getAlignment", &FitAlign::getAlignment);
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34
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-
Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
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37
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+
//Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class<PrefixSuffixAlign,PairwiseAlign>("PrefixSuffixAlign")
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+
Data_Type<PrefixSuffixAlign> rb_cPrefixSuffixAlign = define_class_under<PrefixSuffixAlign,PairwiseAlign>(rb_cModule, "PrefixSuffixAlign")
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.define_constructor(Constructor<PrefixSuffixAlign>())
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.define_constructor(Constructor<PrefixSuffixAlign,std::string,std::string>())
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.define_method("run", &PrefixSuffixAlign::run)
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.define_method("getAlignment", &PrefixSuffixAlign::getAlignment);
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-
Data_Type<LocalAlign> rb_cLocalAlign = define_class<LocalAlign,PairwiseAlign>("LocalAlign")
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43
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+
//Data_Type<LocalAlign> rb_cLocalAlign = define_class<LocalAlign,PairwiseAlign>("LocalAlign")
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+
Data_Type<LocalAlign> rb_cLocalAlign = define_class_under<LocalAlign,PairwiseAlign>(rb_cModule,"LocalAlign")
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.define_constructor(Constructor<LocalAlign>())
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.define_constructor(Constructor<LocalAlign,std::string,std::string>())
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.define_method("run", &LocalAlign::run)
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.define_method("getAlignment", &LocalAlign::getAlignment);
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-
Data_Type<GlobalAlign> rb_cGlobalAlign = define_class<GlobalAlign,PairwiseAlign>("GlobalAlign")
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+
//Data_Type<GlobalAlign> rb_cGlobalAlign = define_class<GlobalAlign,PairwiseAlign>("GlobalAlign")
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Data_Type<GlobalAlign> rb_cGlobalAlign = define_class_under<GlobalAlign,PairwiseAlign>(rb_cModule,"GlobalAlign")
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.define_constructor(Constructor<GlobalAlign>())
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.define_constructor(Constructor<GlobalAlign,std::string,std::string>())
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.define_method("run", &GlobalAlign::run)
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data/ext/bioseqalign/runTest.rb
CHANGED
@@ -1,5 +1,23 @@
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1
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-
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2
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-
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1
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require './SeqAlign'
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+
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+
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module BSA
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+
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include SeqAlign
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7
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+
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end
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9
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+
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fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
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fa.run
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puts fa.getAlignScore
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+
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#fa = SeqAlign::FitAlign.new("AAAACCCAAA", "CCC")
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#puts fa
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#fa = BSA::FitAlign.new("AAAACCCAAA", "CCC")
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+
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+
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Process.exit(0)
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+
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require './SeqAlign'
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sa = PairwiseAlign.new("TCGA", "TCGA")
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data/lib/bioseqalign.rb
CHANGED
@@ -1,10 +1,13 @@
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require 'bioseqalign/SeqAlign'
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2
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-
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module BioSeqAlign
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+
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include SeqAlign
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+
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#
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# fit seq2 into seq1, returns the score
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#
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-
def
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def BioSeqAlign.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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@@ -28,7 +31,7 @@ class BioSeqAlign
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#
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# seq2: <tt>--------GCTG--------</tt>
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#
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-
def
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def BioSeqAlign.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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@@ -40,7 +43,7 @@ class BioSeqAlign
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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
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def BioSeqAlign.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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@@ -66,7 +69,7 @@ class BioSeqAlign
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#
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# seq2: <tt>--------AAAAAACTGATAC</tt>
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#
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-
def
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def BioSeqAlign.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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@@ -77,7 +80,7 @@ class BioSeqAlign
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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
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def BioSeqAlign.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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@@ -102,7 +105,7 @@ class BioSeqAlign
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#
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# seq2: <tt>GTCGAT</tt>
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#
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-
def
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def BioSeqAlign.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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@@ -113,7 +116,7 @@ class BioSeqAlign
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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
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def BioSeqAlign.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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@@ -138,7 +141,7 @@ class BioSeqAlign
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#
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# seq2: <tt>AGGGGTCGATTT</tt>
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#
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-
def
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def BioSeqAlign.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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@@ -146,6 +149,5 @@ class BioSeqAlign
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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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-
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+
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end
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metadata
CHANGED
@@ -1,7 +1,7 @@
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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.
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version: 0.0.2
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5
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prerelease:
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platform: ruby
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authors:
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2014-06
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+
date: 2014-08-06 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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@@ -62,7 +62,7 @@ files:
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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:
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+
homepage: https://github.com/stefrb/bioseqalign
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licenses:
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- MIT
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post_install_message:
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