bio-velvet_underground 0.0.1

data/lib/bio-velvet_underground.rb

@@ -0,0 +1,12 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-velvet_underground/velvet_underground.rb'
+

data/lib/bio-velvet_underground/external/VERSION

@@ -0,0 +1 @@
+1

data/lib/bio-velvet_underground/velvet_underground.rb

@@ -0,0 +1,72 @@
+require 'ffi'
+require 'pry'
+
+module Bio
+  module Velvet
+    class Underground
+      extend FFI::Library
+      ffi_lib File.join(File.dirname(__FILE__),'external','libvelvet.so.1.0')
+
+      class BinarySequenceStore
+        # Parse a CnyUnifiedSeq file in so that sequences can be accessed
+        def initialize(cny_unified_seq_file)
+          readset_pointer = Bio::Velvet::Underground.importCnyReadSet cny_unified_seq_file
+          @readset = Bio::Velvet::Underground::ReadSet.new(readset_pointer)
+        end
+
+        # Return a sequence from the store given its read ID.
+        def [](sequence_id)
+          if sequence_id==0 or sequence_id > @readset[:readCount]
+            raise "Invalid sequence_id #{sequence_id}"
+          end
+
+          pointer = Bio::Velvet::Underground.getTightStringInArray(
+            @readset[:tSequences], sequence_id-1
+            )
+          Bio::Velvet::Underground.readTightString pointer
+        end
+
+        # Number of sequences in this store
+        def length
+          @readset[:readCount]
+        end
+      end
+
+      private
+      # struct readSet_st {
+      #  char **sequences;
+      #  TightString *tSequences;
+      #  char **labels;
+      #  char *tSeqMem;
+      #  Quality **confidenceScores;
+      #  Probability **kmerProbabilities;
+      #  IDnum *mateReads;
+      #  Category *categories;
+      #  unsigned char *secondInPair;
+      #  IDnum readCount;
+      # };
+      class ReadSet < FFI::Struct
+        layout :sequences, :pointer, # char **sequences;
+        :tSequences, :pointer, # TightString *tSequences;
+        :labels, :pointer, # char **labels;
+        :tSeqMem, :pointer, # char *tSeqMem; #TODO: they don't really mean char* here - meant as an unsigned short?
+        :confidenceScores, :pointer, # Quality **confidenceScores;
+        :kmerProbabilities, :pointer, # Probability **kmerProbabilities;
+        :mateReads, :pointer, # IDnum *mateReads;
+        :categories, :pointer, # Category *categories;
+        :secondInPair, :pointer, # unsigned char *secondInPair;
+        :readCount, :int32 # IDnum readCount;
+      end
+
+      # ReadSet *importCnyReadSet(char *filename);
+      attach_function :importCnyReadSet, [:string], :pointer
+
+      # char *readTightString(TightString * tString); #tightString.h
+      attach_function :readTightString, [:pointer], :string
+
+      # TightString *getTightStringInArray(TightString * tString,
+      #			   IDnum	 position);
+      attach_function :getTightStringInArray, [:pointer, :int32], :pointer
+    end
+  end
+end

data/spec/binary_sequence_store_spec.rb

@@ -0,0 +1,27 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "binary sequence store" do
+  it "should be able to load sequences" do
+    path = File.join TEST_DATA_DIR, '1', 'CnyUnifiedSeq'
+    seqs = Bio::Velvet::Underground::BinarySequenceStore.new path
+    seqs[1].should == 'CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGA'
+    seqs[77].should == 'CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT'
+  end
+
+  it "should be #length" do
+    path = File.join TEST_DATA_DIR, '1', 'CnyUnifiedSeq'
+    seqs = Bio::Velvet::Underground::BinarySequenceStore.new path
+    seqs.length.should == 77
+  end
+
+  it 'should respect array boundaries' do
+    path = File.join TEST_DATA_DIR, '1', 'CnyUnifiedSeq'
+    seqs = Bio::Velvet::Underground::BinarySequenceStore.new path
+    expect {
+      seqs[0]
+      }.to raise_error
+    expect {
+      seqs[78]
+      }.to raise_error
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,31 @@
+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+require 'rspec'
+require 'bio-velvet_underground'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+TEST_DATA_DIR=File.join File.dirname(__FILE__),'data'
+
+RSpec.configure do |config|
+
+end

metadata

@@ -0,0 +1,456 @@
+--- !ruby/object:Gem::Specification
+name: bio-velvet_underground
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ben Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-03-31 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.9'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+description: Bindings to some internals of the velvet assembler.
+email: donttrustben@gmail.com
+executables: []
+extensions:
+- ext/mkrf_conf.rb
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".gitmodules"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- ext/bioruby.patch
+- ext/mkrf_conf.rb
+- ext/src/Makefile
+- ext/src/src/allocArray.c
+- ext/src/src/allocArray.h
+- ext/src/src/autoOpen.c
+- ext/src/src/autoOpen.h
+- ext/src/src/binarySequences.c
+- ext/src/src/binarySequences.h
+- ext/src/src/concatenatedGraph.c
+- ext/src/src/concatenatedGraph.h
+- ext/src/src/concatenatedPreGraph.c
+- ext/src/src/concatenatedPreGraph.h
+- ext/src/src/correctedGraph.c
+- ext/src/src/correctedGraph.h
+- ext/src/src/dfib.c
+- ext/src/src/dfib.h
+- ext/src/src/dfibHeap.c
+- ext/src/src/dfibHeap.h
+- ext/src/src/dfibpriv.h
+- ext/src/src/fib.c
+- ext/src/src/fib.h
+- ext/src/src/fibHeap.c
+- ext/src/src/fibHeap.h
+- ext/src/src/fibpriv.h
+- ext/src/src/globals.h
+- ext/src/src/graph.c
+- ext/src/src/graph.h
+- ext/src/src/graphReConstruction.c
+- ext/src/src/graphReConstruction.h
+- ext/src/src/graphStats.c
+- ext/src/src/graphStats.h
+- ext/src/src/kmer.c
+- ext/src/src/kmer.h
+- ext/src/src/kmerOccurenceTable.c
+- ext/src/src/kmerOccurenceTable.h
+- ext/src/src/kseq.h
+- ext/src/src/locallyCorrectedGraph.c
+- ext/src/src/locallyCorrectedGraph.h
+- ext/src/src/passageMarker.c
+- ext/src/src/passageMarker.h
+- ext/src/src/preGraph.c
+- ext/src/src/preGraph.h
+- ext/src/src/preGraphConstruction.c
+- ext/src/src/preGraphConstruction.h
+- ext/src/src/readCoherentGraph.c
+- ext/src/src/readCoherentGraph.h
+- ext/src/src/readSet.c
+- ext/src/src/readSet.h
+- ext/src/src/recycleBin.c
+- ext/src/src/recycleBin.h
+- ext/src/src/roadMap.c
+- ext/src/src/roadMap.h
+- ext/src/src/run.c
+- ext/src/src/run.h
+- ext/src/src/run2.c
+- ext/src/src/scaffold.c
+- ext/src/src/scaffold.h
+- ext/src/src/shortReadPairs.c
+- ext/src/src/shortReadPairs.h
+- ext/src/src/splay.c
+- ext/src/src/splay.h
+- ext/src/src/splayTable.c
+- ext/src/src/splayTable.h
+- ext/src/src/tightString.c
+- ext/src/src/tightString.h
+- ext/src/src/utility.c
+- ext/src/src/utility.h
+- ext/src/third-party/zlib-1.2.3/ChangeLog
+- ext/src/third-party/zlib-1.2.3/FAQ
+- ext/src/third-party/zlib-1.2.3/INDEX
+- ext/src/third-party/zlib-1.2.3/Makefile
+- ext/src/third-party/zlib-1.2.3/Makefile.in
+- ext/src/third-party/zlib-1.2.3/README
+- ext/src/third-party/zlib-1.2.3/adler32.c
+- ext/src/third-party/zlib-1.2.3/algorithm.txt
+- ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup
+- ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas
+- ext/src/third-party/zlib-1.2.3/as400/bndsrc
+- ext/src/third-party/zlib-1.2.3/as400/compile.clp
+- ext/src/third-party/zlib-1.2.3/as400/readme.txt
+- ext/src/third-party/zlib-1.2.3/as400/zlib.inc
+- ext/src/third-party/zlib-1.2.3/compress.c
+- ext/src/third-party/zlib-1.2.3/configure
+- ext/src/third-party/zlib-1.2.3/contrib/README.contrib
+- ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb
+- ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb
+- ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb
+- ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt
+- ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb
+- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb
+- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads
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+- ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S
+- ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile
+- ext/src/third-party/zlib-1.2.3/contrib/blast/README
+- ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c
+- ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h
+- ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk
+- ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt
+- ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas
+- ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas
+- ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt
+- ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build
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+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt
+- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt
+- ext/src/third-party/zlib-1.2.3/contrib/infback9/README
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+- ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h
+- ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h
+- ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h
+- ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c
+- ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h
+- ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c
+- ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S
+- ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp
+- ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp
+- ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h
+- ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h
+- ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp
+- ext/src/third-party/zlib-1.2.3/contrib/iostream3/README
+- ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO
+- ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc
+- ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc
+- ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h
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+- ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat
+- ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt
+- ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip
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+- ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c
+- ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h
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+- ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h
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+- ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h
+- ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw
+- ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c
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+- ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln
+- ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj
+- ext/src/third-party/zlib-1.2.3/crc32.c
+- ext/src/third-party/zlib-1.2.3/crc32.h
+- ext/src/third-party/zlib-1.2.3/deflate.c
+- ext/src/third-party/zlib-1.2.3/deflate.h
+- ext/src/third-party/zlib-1.2.3/example.c
+- ext/src/third-party/zlib-1.2.3/examples/README.examples
+- ext/src/third-party/zlib-1.2.3/examples/fitblk.c
+- ext/src/third-party/zlib-1.2.3/examples/gun.c
+- ext/src/third-party/zlib-1.2.3/examples/gzappend.c
+- ext/src/third-party/zlib-1.2.3/examples/gzjoin.c
+- ext/src/third-party/zlib-1.2.3/examples/gzlog.c
+- ext/src/third-party/zlib-1.2.3/examples/gzlog.h
+- ext/src/third-party/zlib-1.2.3/examples/zlib_how.html
+- ext/src/third-party/zlib-1.2.3/examples/zpipe.c
+- ext/src/third-party/zlib-1.2.3/examples/zran.c
+- ext/src/third-party/zlib-1.2.3/gzio.c
+- ext/src/third-party/zlib-1.2.3/infback.c
+- ext/src/third-party/zlib-1.2.3/inffast.c
+- ext/src/third-party/zlib-1.2.3/inffast.h
+- ext/src/third-party/zlib-1.2.3/inffixed.h
+- ext/src/third-party/zlib-1.2.3/inflate.c
+- ext/src/third-party/zlib-1.2.3/inflate.h
+- ext/src/third-party/zlib-1.2.3/inftrees.c
+- ext/src/third-party/zlib-1.2.3/inftrees.h
+- ext/src/third-party/zlib-1.2.3/make_vms.com
+- ext/src/third-party/zlib-1.2.3/minigzip.c
+- ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor
+- ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2
+- ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx
+- ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc
+- ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc
+- ext/src/third-party/zlib-1.2.3/old/Makefile.riscos
+- ext/src/third-party/zlib-1.2.3/old/README
+- ext/src/third-party/zlib-1.2.3/old/descrip.mms
+- ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2
+- ext/src/third-party/zlib-1.2.3/old/os2/zlib.def
+- ext/src/third-party/zlib-1.2.3/old/visual-basic.txt
+- ext/src/third-party/zlib-1.2.3/old/zlib.html
+- ext/src/third-party/zlib-1.2.3/projects/README.projects
+- ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt
+- ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp
+- ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp
+- ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp
+- ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw
+- ext/src/third-party/zlib-1.2.3/qnx/package.qpg
+- ext/src/third-party/zlib-1.2.3/trees.c
+- ext/src/third-party/zlib-1.2.3/trees.h
+- ext/src/third-party/zlib-1.2.3/uncompr.c
+- ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt
+- ext/src/third-party/zlib-1.2.3/win32/Makefile.bor
+- ext/src/third-party/zlib-1.2.3/win32/Makefile.emx
+- ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc
+- ext/src/third-party/zlib-1.2.3/win32/Makefile.msc
+- ext/src/third-party/zlib-1.2.3/win32/VisualC.txt
+- ext/src/third-party/zlib-1.2.3/win32/zlib.def
+- ext/src/third-party/zlib-1.2.3/win32/zlib1.rc
+- ext/src/third-party/zlib-1.2.3/zconf.h
+- ext/src/third-party/zlib-1.2.3/zconf.in.h
+- ext/src/third-party/zlib-1.2.3/zlib.3
+- ext/src/third-party/zlib-1.2.3/zlib.h
+- ext/src/third-party/zlib-1.2.3/zutil.c
+- ext/src/third-party/zlib-1.2.3/zutil.h
+- lib/bio-velvet_underground.rb
+- lib/bio-velvet_underground/external/VERSION
+- lib/bio-velvet_underground/velvet_underground.rb
+- spec/binary_sequence_store_spec.rb
+- spec/data/1/CnyUnifiedSeq
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-velvet_underground
+licenses:
+- GPL
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Bindings to some internals of the velvet assembler
+test_files: []