bio-bwa 0.2.0

data/test/data/testdata.long.fa

@@ -0,0 +1,175 @@
+>NM_204276
+GCGCCGCGGGAGCGCGCAGTTCGGTGTGGCTGTGCCGTGCCCGCGGGGAGCCCCGCGCTT
+GGGGCGATGCTGCGGTCCCGGAGCGCTCCCGGGGGCCGGAGGGAGGTTTGCCAACAAGTG
+TTCCAGTGAGATAAAAAAATGGCTTACAAATCTGGGAAAAGACCTACTTTCTTTGAAGTA
+TTTAAGGCGCATTGTAGCGATTCAGACTTGGGGCCTGTAAGTCTTGACTGGTTTGAAGAG
+CTCAGCTCAGAAGCACCTCCGTATGAGCCTAAGTTGTTAGGAGAACCTGAGGGTCCCATT
+GGATGGTTTGATCAAACTTTTAAAACTCCAAAGGCAAAATCTTCTACGGACAGCCAGTTG
+GCATCAACTCCACTGATTTTTAAAGAACAGAATACAATGCCGCCTTTTTCTTCTCCTGGA
+AAAGAATTGGATCAGAAAAAAATGGAAACAAGCAGAGAGAATTTGCTAAGTCCAAGTATG
+GCAGGAAGAAAGACAGATCAAGAAAATCAAATACTCGCTTCTCCTCATGGTATCTGCCAC
+AACTACACTGCTGCTAGTCCAGCTATTGTAAGGAATCCTTGCAGAACACCACAGGGAAGT
+AATATACCTGGACCATATGGAAGCTTGTTTTGCACACCAAAATTCTTGGAGATCCCAACT
+CCGAAACGGATTTCTGAAAGTCTGGGAGCAGAAGTGGATCCAGAAATGTCCTGGACAAGT
+TCTTTAGCTACTCCTCCTACACTTGGTGTGACAGTGATAATAGCTAGAGAGAATGATTCT
+ATTTCTGGAGCAAAGCAGCAGGATGAAAGAGCTGAGATAGTTTTGCACAACTTTTTATCT
+GAAGATGATGGATATACTGCAAAGAATGATACAAGTCTGCTGTCCATACCAGAGACGGTA
+AAACTAAATGCTAGAGATGACATAAAAGATCTTGAGTCAGAAGTGTTAGATGGTTTATTT
+GGTGAGACAAATAGCTTTGAGGATTCATTCAACTTGCCTGCTGAATCCAGTGGAATTCTG
+TTGTCGCCACGTGCTCTGGATGCAATAGAGAAATGTGAAATAAAAATAGATGAAGCACAA
+GAAAAGAGTGATGTTCTTTCAGAGCAACATAGGAGAAGAAAGTCTACCATTTCACAGGAG
+GTGAAAGCTGCTAACTGGACTGAAAAAAGCTGCTGTGTTGAAGTGAAGGATTCTATAATC
+CAGAACACCAATGAAGATATCATGGATAGTAAAGACAACTGCTTACTAGGGCGTGAAAAG
+GAATTGGAGTATCTTAGGATTGCAGGAAACTTGCAAGATAATAGAACACAGAAATCATCT
+GTGAATGAGAAGCTTGTGAAAGATGTGCTGTCTTCATCAAGCCAGTGGTCTCAGCTGAAC
+TTGTCTGGTCTTGATGTAACTCATCTGGAAATGTCTATATGTAGCTCTCCACAGTCTGAC
+TCATGTAGAGAGAAAGGTTTAGAAGAGAAGTCAGTACTGATGACCAAGGATGATGCTGTA
+GAAACATCTTTACTGAATACTTCAGGCTTGAGAAATGCACAGGAGCTCTCAAGTGCCAGT
+TTGTCAGAAAATGGCAGTGATACGAAAATATCTAAAAACAACCCAATGTCAGAAATAACT
+CCAGTAAAACCTGTGTGTGCAAGTCCGAAGTTGGTAAAAGGATATGCACATGAGGAGGTT
+TCCGGAATGAGCTTTTTAAACTGTAGTTCTTTTTTAATTGAAAGTACAAATGTCATGGAG
+TATTCTGTAGTCTACAACAGCACTTTTTCCACGCATTTAAAAGCAACTTCGCAATCTGTG
+GTAACTGATGTTCTTTCTCACCCTCTTATATGTAGTGCTGCATCTCCAGATAATTGCAGT
+GACCTACATTTAAGAAATAGTGAAAAAACTCTTAGGAAATCTAACTTTAAAAGCCTAAAT
+ATGTTATCCAGATTGAGGAAGAAATCCAAGAGATTTATTTATACAATAAATAATACTTTA
+GTGTATCAGGAAGAAAATGTGCAGAAAGAAGTAACCTCTGAATCACCTGATAATCCTGTA
+TTAACACATTTGGAATCTGATTTACATGAATTTAAAGATTGTCAGGTGGCCACAGATGGT
+AACCAAGACTGCTTGCTTTCGGCTGAGAGGCAATCAAATATCAAAGAAAATAATTTAAAC
+ACTCTTACCATAAAGGTAGATATAATGGATAACTCATCTGATAATTCTGTCAACAATAGG
+CTGAAACAAGAGCTGAGTGAGTCAGGGAAAAATGCAAGAGAGTATCAACCTGCTACCTCA
+TTTAAATGCTTAAAAGCTTCTCATACTGAGAGTGAAGACACAACAGATTGTTTAAACAGT
+GGAAGAATTTCAAATATAAAACATAAGGTACTAACTTCGGCATACCTAATGGCAAGAAGG
+CATTCCAGATTGTTTCCTGAAGACTGTTGCTTAAGGAAAGGCAAGAATGATACATATACC
+GTTTCTAATGTGAACAGTCGAGCTGCTGTACCTCGGAGCCCTAAAGGACAGCCTCCACAG
+TCCTCTCCTAGTTGTAGTGATTGCTTGATTGATATGCGCCATGGCACTGCGTTTGTGACA
+AACAGCAAGTTCAATAATACTTTGAGTCACATCAAGTTTGGCATGAACAGAGTCAGTAGT
+AACTCTTGCAATAAAATATCGGCTGATAAAAGACGTGCTTCAGATCAGTTGTCAGTAGCT
+GAATGTAGGGAAATAGTTGCACCTTTGGGAATAAACTGCTTAGAAAACAATAGTACTAGC
+TTAAAACAACGGGGAAAAGAAGATGTAGATGAAAATCAAGAAACACTCTCTATTAAAAGC
+AGTGAAAACCCTCAAGCAGCTGCTTGGAATAACGAATCTATAGAGGTTGCTGAAGAATTC
+TTGGATTGTATAGATAATTCTTTGAATGAAGTAGTTTCTGAAGAAGATAGACAAGTAGCA
+CCTGTGTATTTCAACACAAAGCCAATTGAAAGCCTAGAACATAAAGGGAAATCATCAGGA
+GATCTTAACGCATGCAGTTCAAGTTTGAGCTTTGGTGGCTTCCAGACTGCTTCCAATAAG
+CAGATTAAATTCTCAGAAAGCAGCATAGCGAAAGGCAAAATGCTGTTCAAAGATATTGAA
+AATGAATTCTTTGAAGCCTCTTCCATGGAAAGAGTCAGAAATTTTTCAAATCGAGTTCAA
+AAGGAGAATATATTTTCCTCAGATTTGGAAAGCAAAACAGGCAGTACTTCATCTGGTTTG
+CAGACAAGGTGTATGCAATATATTCCACGTAAAGTTGATTTATGTAAAAACTCGCCTAGA
+AATCAACTATCTGTGCAAGAACCAAATCAGTCTTTGACAGCAAGCCAAGAAGCTGAAATT
+GCTGAACTTTCTAATATCTTGGAAGAAACGGGTAGCCAGTTTGAATTCACACAATTTAGA
+AAGCAAAGTAACATGATACAAAGTCACATTCAGCAGTTTGGAGCAACGAATGTGGAAAAT
+GCTTCTGAAGCAGGGGAAGATACTAATTTCTATAGCACTCTTAAATCTGAAAATCATGTA
+ATAAATGACGAGTATTGCAGTAAGttgaaaaatgaaaatgaatgtaaaatggtagaatat
+gaaaaagaagacacagtggtttttcataaaaataaaagaaaaGTTACTTTTACTAACTTG
+GACAGAAATGAAAGTAGAATATCCAGCCATGAGAGCTGTCCGGTACCTTTACGGGACAGC
+TTTTCTAATTTTGTAGGATTTACTTCAGCTGGAGGTAAAAAAATAAATATTTGTAAGGCA
+GCTTTGACCAGATCTGCAGAGCTTTTCAAGGACTTGGATGATGATAACTTTTTGTTTAAA
+TCTTCTGGAACTAATACCAGATGCTGCAATTCAGATGGGCATGTATCTTCTAACTGGAAT
+TTTCTCAGATGCCAGACAAAAGAAGATGAAGGAGGAATACTTTGTGTTCCAAACATAAAA
+AGCGTAGGTCCCATTTCCCACCATTCAGAGAAAAAATATGCAGAAAATATTAGTTCACCA
+TGTAAGGAAAATACAGAAAACTGGACAGAAATATTAAGTGATAATGTTGATTTCAGTTGT
+ACTAATGGTGGATATTCTGCCTCTGGAATGAGAAACAGTCCGTCATCCTTTAAAAAACCT
+CACCAGAACTGTAAAAATTCTGATCAGTTTCTGAATCAAGGAAACAGCGAAGTTGAAGGT
+TGTTTGCAAGAAGACACTTCATATCTGATTTGTCTAGGAGATAATATTACTAGTGCAGAA
+GAACATGATTTAAATGTTTCAGATGAAATGGAAAACCTGTCCCCTAATCAGAAAGAAGAC
+AGAAAGCAGGAAGATGAGCATTTGCTGCTAAACCGTCAAGCTGCAGACACTGATGCTGTA
+TCCATTTCTGATTCATCGTTCCGTAGTTCTCTACGTGATCTCAACGTACAATGTGGGGAA
+AGAGATACAGATGTTTCAGAGAAATCTAGTAAACAAAAGACAAATAGTGTCAGTGTGGAA
+GGAGAAGACTCCACCTATAAGAACCTGTTTGTGAGTGAAAGTGAGATTAAAATAGGCTCT
+AACCAACGTCATCAAGTACCTTCCGAGCAAGAGATGGATGTTGACAAAAACAAAGTTAAG
+GGAACTTATCTGACTGGTTTCTGTACTGCTAGTGGCAAGAAAATAACAATTGCTGATGGA
+TTTTTGGCTAAAGCTGAAGAGTTTTTTTCAGAAAATAATGTTGATTTAGGAAAAGATGAT
+AATGATTGTTTTGAGGACTGCTTAAGAAAATGTAATAAAAGCTATGTTAAAGACCGTGAC
+TTATGTATGGACAGTACTGCTCATTGTGATGCAGATGTACTTAATTTTAAAGATAAGCTT
+ATTCCTCAAGAACCTGGGGACCGACTAAAGCAGACAATAGAGGAGAGTCCCATTATACAA
+GCTGTTAATCATGACAGCATTAAAGTGGGTGCATTTATTAATGTGGATGAAGATTGTGAA
+AGAAATTTGGCAGCTCCATGTGCAAATAAGGAAGCTTATGTCAGACCTGGAAAGTCAGAA
+GTAGAATCTCTTCCTGTACATGGGAACAATTCTTTAAGTAGAACTCTTTTGCTTGAAGAC
+AGAAAACAGTTTGCAGAGAGAGATGTGGAATACTCAGCAACAAAGAGGGATAATTCAGAA
+AGCAAACCTGACTCTTCTCTGAAGTGTGCTACATCTCTGCATTTAACAAAGGTGTCGAGT
+CACCTTGCAGATAATTCTGTGCCTGGTGGTATTATTCAGACTGTATCTGCTGAGGATAGT
+TGCAAGTCTAATCAGTCCTTCCTCTTACCTCGTGGTAGTGTTCCAAGAAGTACCTCACCT
+TATCTGAACTGCGGCAATAAGGAGATTGACTTAAAACGTTTAAATGAACCTTGTTCCAAT
+ACAGACAGTTTCACAAATACTGTAGATAATGCTCACCAAGAACAGTCTGAATTTGATCTT
+CCTGAAGATGAAACTAATTTAACCTGCTTACAGGAAACATCACTTAATGCTGAAAGTCAA
+AAGAGTGATCTGAAACAAGTGTTCAGTACAGCAAAAGGTAAAGCAGTCTCTGTTTCAGAA
+AGTGCATTAGCAAGCATCAGACAAATGTTTCAAACAGACTGTGATGCATCTGTAAAATCT
+GAAATTGAGACTAAATCAGGAACTAATCAAACAGCAATTGCTGGAAGTTCATCTTTCAGC
+ATTCATGCTGGGGGTCCTGGTTTTGCTACATTTTTAGATACTAGAAAAAGTGAGATGAAT
+GTGGCTGCACCTCATTTTATTAATGGAAATGGGAATCTTATTGAAAACAATCACCAAGGC
+GCAAACATGTTTGCAGATGCAGATTCTGTTCCAGGTTTTCAGATGCAATGCTTTGAGCAG
+AAGAGTAAGCTTTTAGGACACTTTCCTGTGCCAGATAAGCAGATGGAGCAGTCAGGTCCT
+TCAGGCAACCTTGGGTTTTTCAGTACGGCAAGTGGGAAGCCTGTGCAACTATCAGAAGAG
+TCGCTAAAGAAAGCTAGACAGCTCTTTTCTGAAATGGAAGGTAGCCATTCATCAGGGCTA
+CAAGATGCACATTTGCTTGAAGACGTTGAGAAATCCACAAACCATGGTGAAGTATTTCCT
+AGAGAAATGCAGCTACTGCTGCCAAGAGGGAAGGAGAATGCCAGCACGGATAAGATTTCA
+AGTCCTGCTTTGGGGTTCAGCACTGCAAGTGGAAAGCAAGTGACCATCTCTGAAAGTGCC
+TATCAGAAAGCAAAGGCAATTTTAAAGGAAGCAGATGGCTTTTTAAGCAGTGAGCTTGGT
+GTTACAAATGAACTTTGTGAAATTAAAGAGAGTGGTCAACATGCAGAATATTTAACTGGT
+AAAGTAATTTCAGAATCCAAAACTGAAAAAAGCTGCAGTGAGGAGCTTGACTTGAAAAGC
+ATTCACCCTGAAAAAATGAAGTCTTTGCCAAGCACTCACCGTGTCAAAATTACTGAGTAT
+GTACCACATAGTAAGAGAAACAGCCAGTCAGCACCATTTAAAAATAGCTTTGAGCAAGAA
+GAGACCAGATTTTTCAGAAAAGGAGAGCTGAATCTGGGGATAAAAGCAGAGTCTGAATCA
+GATTTATGCAGTGCTACATCTAAAGCAGAAATAAACATTTTCCAAACTCCAAAAGACTAC
+TTGAAAACAGAGGCTGTAGAAAGTGCAAAAGCCTTTATGGAAGATGATCTTTCGGATTCT
+GGAGTCCAGGTCAAGTCTGCACAGTCCTTTGGCAAAATGTCAGATAACTTTCAAAACAAG
+CCCTTTGGGAAGAGACACTTGGATGAAAAAGACTCACATGGAGAACCTCCAATTAAAAGA
+CAGCTACTGCTTGAATTTGAGAAGATGAAGATTCCCCCCAAATCTGTGAAACCTTTGAAA
+AGCACTCCTGATGGCATTTTCAAAGACAGAAGAAAATTTATGTACCACGTCCCTTTAAAA
+CCAGTAACTTGTCGACCTTTGGGGACTACTAAGGAACGACAAGAAGTCAGGAACCCTACA
+CTTACTCTTCCTGATCAAGACTTGAAAGGATTTAAATCTATACCTGCCGTTTTTCAGCAC
+TGTGCCCTACGGCAGTCTTCAAGTGGTGCTTCAGGGCTTTTTACTCCACATAAGGCCGTG
+GCCAAGGATAGCGAGGAAACAAGAAGTTTGTGCAAGTCAGGCAAAGCTGTTAAAACTTTT
+GTTCCACCCTTCAAAACCAAGCTGACACTTTCTACAGGTGAACAAGGCGGCAGCAAGAGA
+TGTCACTCACCAATCAGAAACAGTGTGATGGAGGAGAGGGAATTAAATCAAATCCCAGTT
+GAACAAAATAGTGCTGAAGCTCGGGATCACCAGTCCTGCATCCTGCATGCAGCGGTCACT
+GACATAGAAAATGACAATTTAGTTACAAGCAACATGATGGCAAATCTCCACTGTGCTAGA
+GATCTACAGGAAATGAGAATTAAAAAGAAATATAGGCAAAATATTAGCCCACAGCCAGGC
+AGCCTTTATGTCACTAAAACATCTGCAAGAAATAGAATCTCTTTGAAAACTGCAGTTGAA
+GAGGAAACACCCAGTTTTCATTCTACAGAAAAGCTTTACACATACGGAGTTTCAAAACAT
+TGCATACAAGTTAACAGCACAAATGCAGAATCATTTCAGTTTCTCATTGAAGAATTTTTC
+AGTAAGGAGTATTTATTAGCAGGAAATGGGATACAACTTGCTGATGGAGGATGGCTGATA
+CCTACAGATGAGGGAAAGGCTGGAAAAAAGGAATTTTACAGGGCTCTCTGCGATACTCCT
+GGTGTGGATCCCAAGCTAATAACAGAGGCCTGGGTTTACAATCATTATAGGTGGATTGTA
+TGGAAACTGGCAGCCATGGAAGTGTGTTTTCCACATAAATTTGCTAACAGATGCTTGACA
+CCAGAAACAGTACTGTTGCAGTTGAAATATAGGTATGACTTGGAAATCGATAAAAGTAAA
+CGATCAGCAATCAAAAAAATAACAGAGAGAGATGATGCAGCAGGTAAAACACTTGTGCTG
+TGTGTTTCTAAAGTCCTATCACTGAACACTGCTGTATCTCCTAGTAATAGTAATAACAAC
+ACGGAAGGTGAAAAAGCAGCAGCAATAATTGAAGTTACTGATGGCTGGTATGGGATTAGA
+GCTCTTTTGGATCCACCTCTCAAAGCTTTCTTACATAGAAGAAGGCTGACTGTTGGTCAG
+AAGATCATAGTGCATGGAGCAGAACTTATTGGCTCTCCAAATGGATGTACGCCACTGGAA
+GCCCCAGATTCCCTTATGCTAAAGATTGCAGCAAACAGCACGCGATGCGCACGGTGGTAC
+ACAAAGCTGGGATTTCATCGGGACCCCAGACCTTTCCCTTTGCCTCTGTCATCACTTTAC
+AGTGAGGGTGGTACAGTGGGCTGCATTGATGTGGTTGTCCAAAGAACTTATCCTATTCAG
+TGGATGGAAAAGACATCAGCTGGCTCATATGTGTTTCGTAACAGCCGAGCTGAAGAAAGG
+GAAGCTGCCAAGCATGCGGAGGATCAACAAAAGAAACTGGAAGCTCTATTTGCAAAAATT
+CAAGCAGAATTTGAAAAGCACGAAGAGAGAAATTGCAGAAGAGCACCAAGGTCACGCATA
+GTCACAAGGCAGCAAATCCATAATTTGCAAGATGGTGCAGAACTTTATGAAGCAATTCAG
+AATGCAGCTGATCCCAGTTATATGGAGGGATATCTCAGTGAAGATCAGTTAAAAGCTCTG
+AATGCTCACAAGCAGCTGATGAACGATAAAAAACAAACTCGGATACGGGAAGAATTCAAG
+AAGGCTGTCGAGTCTGCAGAACAGGAAAAACATGGTTTTTCCAAAAGGGATGTGTCTACT
+GTATGGAAATTATTTGTGATAGACTATAGAAAGCAAGAAAAACATAGAGGAGTGATCCTG
+AGTATCTGGCGTCCACTGCTGGATGTGTGTTCACTGCTGAAGGAAGGCAGTCGGTACAGA
+ATCTGCCAGCTGTCAACATCGCAGTCCAAAGGAAGATCAGACTCAACTAACGTACAGTTA
+TCAGCAACAAAGAAAACTCGGTATCTACAACTATCAGTCTCACAGAAGATGCTGCAGCAG
+AttttttttCCAAGAAAGGCTCTCAAATTCACCAGCCTGTTGGATCCTTCTTATCAGCCA
+CCATGTGCCGAAGTTGATGTAGTTGGAGTTGTAATATCCATTAGCAGGACAGGATTCTCT
+AACATGGTTTATTTATCTGATGAAAGCTATAATCTTGTGGCAATAAAAATCTGGGCAGAT
+CTCCGGCATTTTGCTATCGAAGATATCGTTGTCCGCTGTTCGTTCATTGCTGCAAGCAAC
+CTTCAGTGGCAGTCTGAATTCAGATCAGAAATTCCTGTGCTGTTGGCCGGAGATCTTTCT
+GCATTCTCAGCTAGCCCAAAGGAAAACCATCTTCAAGAGAAGTTTAATGAACTGCGAAGG
+ATGATAGAGAATGTGGACTCCTTTTGCTCTGATGCAGAAAGTAAATTGATGAATTTGCTA
+CAAAGAAATTGCTCACTTACACCCATTTTACCTAAGAGATGTGGTTTGGAATGCTCTTCT
+CCTTCCTGCAACTCAGGCCTTTATGCAGAAGATAGAAGTTCGATCTCTTCCAAAATTGAA
+ACGAAGCATCCAAGCCCCTTGTCAGCTAGCACACCAAATACAAAGCTTTTCCCACAAGGC
+TCAGCAATAACGCCTTCATCTGCTGTAAGTAGTGAGAACCATCCCAGAAACAGCAAAAAG
+AGAAAAGCAGTGGACTTCCTCAGCTGCATACCTGCCCCTCCACCACTGACACCGCTCTGT
+TCCATCATTTCTCCATCTTTAAAAAAGGCATTTCAGCCTCCGCGACGTTTGGGCTCACAG
+CATAGCAAGTTATCAAAAGAAACAAACCCAAACGCTGGTTGTGTCACCCCCAGTAGAAGA
+CTGAGAGAAGCTGTCCAGCTTCCTGATAATGACCTGGTTGCTGATGAAGAACTTGCAATG
+ATTAATACACAAGCACTCATAAATACTGTACCGGAAGAAAAGAAGATGGATTATGTAAAT
+GAAGACAGTACAAGGGCTACTAACTTATCTGGTGATACAAGAGCTACTAATTTATCTCGT
+GATATGAGGGCTCCTAATTTATCTGGTGATCTTTCATCCAAAAATAGTTCCAGATCTGCT
+AAGGAAGCAAACAGTTCATTGAAAAGCAGTTCTGAAGGAGCTGATGCTCTCCAGAAGGAC
+ACAGAGGAACCTGAGGGTTCGTTATCAATCCGCAGAGTGCTGCAAAGGCGCAAATCCCGC
+AAATGCTACTAGATGCACATGTACAGTACTGTGTATATTTCAAATTTAAATGTTTTTACT
+TTGTACATTAAAGCCTGATTGTAATAAAGTTACATTACAAAATTCAT

data/test/data/testdata.short.fa

@@ -0,0 +1,2 @@
+>short
+GCTTCTGAAGCAGGGGAAGATACTAATTTCTATAGCACTCTTAAATCTGAAAATCATGTA

data/test/helper.rb

@@ -0,0 +1,18 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-bwa'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-bwa_basic.rb

@@ -0,0 +1,62 @@
+
+$:<<"."
+require 'test/helper'
+require 'digest/md5'
+
+class TestBioBwa < Test::Unit::TestCase
+  
+  def setup
+    @testdata = File.join("test","data","testdata")
+  end
+  
+  def test_1bwa_fa2pac
+    Bio::BWA.fa2pac(:file_in => "#{@testdata}.fa",:prefix => @testdata)
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
+    assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5)
+  end
+
+  
+  def test_2pac2bwt
+    out = "#{@testdata}.bwt"
+    Bio::BWA.pac2bwt(:file_in => "#{@testdata}.pac",:file_out => out)
+    md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
+    assert_equal("3c5e20c123ed8ab961287933e9734e70",md5)
+  end
+  
+  def test_4bwtupdate
+    out = File.join("test","data","testdata.bwt")
+    FileUtils.cp out,"#{@testdata}.updated.bwt"
+    Bio::BWA.bwtupdate(:file_in => "#{@testdata}.updated.bwt")
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.updated.bwt","rb") {|f| f.read})
+    assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5)
+    FileUtils.rm(out)
+  end
+  
+  def test_3pac_rev
+    out = File.join("test","data","out.rev.pac")
+    Bio::BWA.pac_rev(:file_in => "#{@testdata}.pac",:file_out => out)
+    md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
+    assert_equal("879cd21435a314f672c7de6d13977d69",md5)
+    FileUtils.rm(out)
+  end
+  
+  def test_5bwt2sa
+    out = File.join("test","data","out.sa")
+    bwt = File.join("test","data","testdata.updated.bwt")
+    Bio::BWA.bwt2sa(:file_in => bwt,:file_out => out)
+    md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
+    assert_equal("948d0ebf6176f61de3ecdc8c085ae88a",md5)
+    FileUtils.rm(out)
+    FileUtils.rm(bwt)
+    FileUtils.rm("#{@testdata}.pac")
+    FileUtils.rm("#{@testdata}.amb")
+    FileUtils.rm("#{@testdata}.ann")
+  end
+  
+  def test_no_method
+    assert_raise NoMethodError do
+      Bio::BWA.fake_method("some_file")
+    end
+  end
+
+end

data/test/test_bio-bwa_make_index.rb

@@ -0,0 +1,42 @@
+
+$:<<"."
+require 'test/helper'
+require 'digest/md5'
+
+class TestBwaIndex < Test::Unit::TestCase
+  
+  def setup
+    @testdata = File.join("test","data","testdata")
+  end
+
+  def test_make_index_colorspace
+    out = File.join("test","data","out")
+    Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{out}", :c => true)
+    md5_rbwt = Digest::MD5::hexdigest(File.open("#{out}.rbwt","rb") {|f| f.read})
+    md5_rpac = Digest::MD5::hexdigest(File.open("#{out}.rpac","rb") {|f| f.read})
+    md5_bwt = Digest::MD5::hexdigest(File.open("#{out}.bwt","rb") {|f| f.read})
+    md5_pac = Digest::MD5::hexdigest(File.open("#{out}.pac","rb") {|f| f.read})
+    md5_sa = Digest::MD5::hexdigest(File.open("#{out}.sa","rb") {|f| f.read})
+    assert_equal("6d6fd723604377dc5d6ad6c0f4f1cdf6",md5_rbwt)
+    assert_equal("64838ba5ad44f662266853ebc9451191",md5_rpac)
+    assert_equal("12fb7007102154f4bc428ea01a99a6ea",md5_bwt)
+    assert_equal("8cb0c5f86a5b927c233e3d5268f01f6a",md5_pac)
+    assert_equal("95711a0e5c06419017a02c73d12b99a2",md5_sa)
+    FileUtils.rm Dir.glob(out+".*")
+  end
+  
+  def test_make_index
+    Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{@testdata}")
+    md5_bwt = Digest::MD5::hexdigest(File.open("#{@testdata}.bwt","rb") {|f| f.read})
+    md5_pac = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
+    assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5_bwt)
+    assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5_pac)
+  end
+  
+  def test_errors
+    assert_raise ArgumentError do
+      Bio::BWA.make_index(:a => 'is',:prefix => "foo", :c => true)
+    end
+  end
+  
+end

data/test/test_bio-bwa_run_aln.rb

@@ -0,0 +1,49 @@
+$:<<"."
+require 'test/helper'
+require 'digest/md5'
+
+class TestBioBwa < Test::Unit::TestCase
+  
+  def setup
+    @testdata = File.join("test","data","testdata")
+  end
+  
+  def test_short_read_alignment
+    assert_nothing_raised do
+      Bio::BWA.short_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa",:file_out=>"#{@testdata}.sai")
+    end
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sai","rb") {|f| f.read})
+    assert_equal("56793f4473805683a7d494808c19f79e",md5)
+  end
+  
+  def test_long_read_alignment
+    assert_nothing_raised do
+      Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw")
+    end
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.bwasw","rb") {|f| f.read})
+    assert_equal("f569b0dfa7482d468bc68eb8151fb117",md5)
+    FileUtils.rm("#{@testdata}.bwasw")
+  end
+  
+  def test_simple_SW
+    if RUBY_PLATFORM != 'java' then # the method redirect STDOUT to a file and this test does not pass in JRuby
+      assert_nothing_raised do
+        Bio::BWA.simple_SW(:long_seq=>"#{@testdata}.long.fa",:short_seq=>"#{@testdata}.short.fa",:f => true,:file_out => "#{@testdata}.stdsw")
+      end
+      md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.stdsw","rb") {|f| f.read})
+      assert_equal("cedb41d4ba3581111fbcefec6063dc86",md5)
+      FileUtils.rm("#{@testdata}.stdsw")
+    end
+  end
+  
+  def test_errors
+    assert_raise ArgumentError do
+      Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_out=>"#{@testdata}.fa")
+    end
+    
+    assert_raise ArgumentError do
+      Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw", :unknown_parameter => "foo")
+    end
+  end
+  
+end

data/test/test_bio-bwa_sam_conversion.rb

@@ -0,0 +1,49 @@
+$:<<"."
+require 'test/helper'
+require 'digest/md5'
+
+class TestBioBwa < Test::Unit::TestCase
+  
+  def setup
+    @testdata = File.join("test","data","testdata")
+  end
+  
+  def test_sai_to_sam_single
+    assert_nothing_raised do 
+      Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
+    end
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sam","rb") {|f| f.read})
+    assert_equal("5c523ae7bf18656190fa0bcd8944bd14",md5)
+    FileUtils.rm("#{@testdata}.sam") 
+  end
+  
+  def test_sai_to_sam_paired
+    assert_nothing_raised do 
+      Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>["#{@testdata}.sai","#{@testdata}.sai"],:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
+    end
+    md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sampe","rb") {|f| f.read})
+    assert_equal("8c3847bade0a19e5de77c274355fe154",md5)
+    FileUtils.rm("#{@testdata}.sampe")
+  end
+  
+  def test_zomg_cleanup
+    assert_nothing_raised do
+      list = Dir.glob("#{@testdata}.*")
+      list.delete("#{@testdata}.fa")
+      list.delete("#{@testdata}.long.fa")
+      list.delete("#{@testdata}.short.fa")
+      list.each {|l| FileUtils.rm(l)}
+    end
+  end
+  
+  def test_errors
+    assert_raise ArgumentError do
+      Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
+    end
+    
+    assert_raise ArgumentError do
+      Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
+    end
+  end
+  
+end

metadata

@@ -0,0 +1,218 @@
+--- !ruby/object:Gem::Specification 
+name: bio-bwa
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.2.0
+platform: ruby
+authors: 
+- Francesco Strozzi
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-03-22 00:00:00 +01:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: ffi
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.0.5
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+description: Ruby binding for BWA mapping software, built using Ruby-FFI library
+email: francesco.strozzi@gmail.com
+executables: []
+
+extensions: 
+- ext/mkrf_conf.rb
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-bwa.gemspec
+- doc/Bio.html
+- doc/Bio/BWA.html
+- doc/Bio/BWA/Library.html
+- doc/_index.html
+- doc/class_list.html
+- doc/css/common.css
+- doc/css/full_list.css
+- doc/css/style.css
+- doc/file.LICENSE.html
+- doc/file.README.html
+- doc/file_list.html
+- doc/frames.html
+- doc/index.html
+- doc/js/app.js
+- doc/js/full_list.js
+- doc/js/jquery.js
+- doc/method_list.html
+- doc/top-level-namespace.html
+- ext/COPYING
+- ext/ChangeLog
+- ext/NEWS
+- ext/README
+- ext/bamlite.c
+- ext/bamlite.h
+- ext/bntseq.c
+- ext/bntseq.h
+- ext/bwa.1
+- ext/bwape.c
+- ext/bwase.c
+- ext/bwase.h
+- ext/bwaseqio.c
+- ext/bwt.c
+- ext/bwt.h
+- ext/bwt_gen/Makefile
+- ext/bwt_gen/QSufSort.c
+- ext/bwt_gen/QSufSort.h
+- ext/bwt_gen/bwt_gen.c
+- ext/bwt_gen/bwt_gen.h
+- ext/bwt_lite.c
+- ext/bwt_lite.h
+- ext/bwtaln.c
+- ext/bwtaln.h
+- ext/bwtgap.c
+- ext/bwtgap.h
+- ext/bwtindex.c
+- ext/bwtio.c
+- ext/bwtmisc.c
+- ext/bwtsw2.h
+- ext/bwtsw2_aux.c
+- ext/bwtsw2_chain.c
+- ext/bwtsw2_core.c
+- ext/bwtsw2_main.c
+- ext/cs2nt.c
+- ext/is.c
+- ext/khash.h
+- ext/kseq.h
+- ext/ksort.h
+- ext/kstring.c
+- ext/kstring.h
+- ext/kvec.h
+- ext/main.c
+- ext/main.h
+- ext/mkrf_conf.rb
+- ext/qualfa2fq.pl
+- ext/simple_dp.c
+- ext/simpletest.c
+- ext/solid2fastq.pl
+- ext/stdaln.c
+- ext/stdaln.h
+- ext/utils.c
+- ext/utils.h
+- lib/bio-bwa.rb
+- lib/bio/bwa.rb
+- lib/bio/bwa/library.rb
+- test/data/testdata.fa
+- test/data/testdata.long.fa
+- test/data/testdata.short.fa
+- test/helper.rb
+- test/test_bio-bwa_basic.rb
+- test/test_bio-bwa_make_index.rb
+- test/test_bio-bwa_run_aln.rb
+- test/test_bio-bwa_sam_conversion.rb
+has_rdoc: true
+homepage: http://github.com/fstrozzi/bioruby-bwa
+licenses: 
+- MIT/GPLv3
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -1510626449413692226
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.6.2
+signing_key: 
+specification_version: 3
+summary: Ruby binding for BWA mapping software
+test_files: 
+- test/helper.rb
+- test/test_bio-bwa_basic.rb
+- test/test_bio-bwa_make_index.rb
+- test/test_bio-bwa_run_aln.rb
+- test/test_bio-bwa_sam_conversion.rb