--- !ruby/object:Gem::Specification
name: finishm
version: !ruby/object:Gem::Version
  version: 0.0.4
platform: ruby
authors:
- Ben J. Woodcroft
autorequire: 
bindir: bin
cert_chain: []
date: 2015-08-30 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bio-ipcress
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
- !ruby/object:Gem::Dependency
  name: bio-logger
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.0'
- !ruby/object:Gem::Dependency
  name: bio
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.4.3
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.4'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.4.3
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.4'
- !ruby/object:Gem::Dependency
  name: progressbar
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.21'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.21'
- !ruby/object:Gem::Dependency
  name: bio-samtools
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.6'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.6'
- !ruby/object:Gem::Dependency
  name: ruby-graphviz
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.9
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.9
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.0'
- !ruby/object:Gem::Dependency
  name: ds
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.4
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.4
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
- !ruby/object:Gem::Dependency
  name: hopcsv
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.4.3
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.4'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.4.3
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.4'
- !ruby/object:Gem::Dependency
  name: bio-velvet
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.6'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.6'
- !ruby/object:Gem::Dependency
  name: bio-velvet_underground
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.3'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.3'
- !ruby/object:Gem::Dependency
  name: ruby-progressbar
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.4.2
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.4'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.4.2
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.4'
- !ruby/object:Gem::Dependency
  name: yargraph
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.4
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.4
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.0'
- !ruby/object:Gem::Dependency
  name: pry
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.10'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.10'
- !ruby/object:Gem::Dependency
  name: rspec
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.8.0
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.8'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.8.0
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.8'
- !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: rdoc
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '3.12'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '3.12'
- !ruby/object:Gem::Dependency
  name: bundler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.6.2
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.6'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.6.2
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.6'
- !ruby/object:Gem::Dependency
  name: jeweler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.0.1
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 2.0.1
    - - "~>"
      - !ruby/object:Gem::Version
        version: '2.0'
- !ruby/object:Gem::Dependency
  name: bio-commandeer
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.1'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '0.1'
description: De-novo assemblies generally only provide draft genomes. FinishM is aimed
  at improving these draft assemblies.
email: donttrustben near gmail.com
executables:
- finishm
extensions:
- ext/mkrf_conf.rb
extra_rdoc_files:
- LICENSE.txt
- README.md
files:
- ".document"
- ".gitmodules"
- ".rspec"
- Gemfile
- LICENSE.txt
- README.md
- Rakefile
- VERSION
- bin/finishm
- 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/graphStructures.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/probe_node_finder.c
- ext/src/src/probe_node_finder.h
- ext/src/src/readCoherentGraph.c
- ext/src/src/readCoherentGraph.h
- ext/src/src/readSet.c
- ext/src/src/readSet.h
- ext/src/src/readToNode.c
- ext/src/src/readToNode.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/runReadToNode.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/adler32.o
- 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/compress.o
- 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
- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb
- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads
- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb
- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads
- ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr
- ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586
- ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S
- ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686
- 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
- ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm
- 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
- ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c
- 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
- ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj
- ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm
- ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj
- 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
- ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile
- ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h
- ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h
- ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h
- ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h
- ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h
- ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c
- ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h
- ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas
- ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt
- ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak
- ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas
- ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile
- ext/src/third-party/zlib-1.2.3/contrib/puff/README
- ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c
- 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
- ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt
- ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile
- ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc
- ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c
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- ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor
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- ext/src/third-party/zlib-1.2.3/old/README
- ext/src/third-party/zlib-1.2.3/old/descrip.mms
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- ext/src/third-party/zlib-1.2.3/old/os2/zlib.def
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- ext/src/third-party/zlib-1.2.3/qnx/package.qpg
- ext/src/third-party/zlib-1.2.3/trees.c
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- ext/src/third-party/zlib-1.2.3/uncompr.c
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- ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt
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- ext/src/third-party/zlib-1.2.3/zutil.h
- ext/src/third-party/zlib-1.2.3/zutil.o
- finishm.gemspec
- lib/assembly/a_b_visualiser.rb
- lib/assembly/acyclic_connection_finder.rb
- lib/assembly/all_orfs.rb
- lib/assembly/bad_format_writer.rb
- lib/assembly/bam_probe_read_selector.rb
- lib/assembly/bubbly_assembler.rb
- lib/assembly/c_probe_node_finder.rb
- lib/assembly/connection_interpreter.rb
- lib/assembly/contig_printer.rb
- lib/assembly/coverage_based_graph_filter.rb
- lib/assembly/depth_first_search.rb
- lib/assembly/dijkstra.rb
- lib/assembly/fluffer.rb
- lib/assembly/graph_explorer.rb
- lib/assembly/graph_generator.rb
- lib/assembly/height_finder.rb
- lib/assembly/hybrid_velvet_graph.rb
- lib/assembly/input_genome.rb
- lib/assembly/kmer_coverage_based_path_filter.rb
- lib/assembly/node_finder.rb
- lib/assembly/oriented_node_trail.rb
- lib/assembly/paired_end_assembler.rb
- lib/assembly/paired_end_neighbour_finder.rb
- lib/assembly/probed_graph.rb
- lib/assembly/read_input.rb
- lib/assembly/read_to_node.rb
- lib/assembly/scaffold_breaker.rb
- lib/assembly/sequence_hasher.rb
- lib/assembly/single_coherent_paths_between_nodes.rb
- lib/assembly/single_coherent_wanderer.rb
- lib/assembly/single_ended_assembler.rb
- lib/assembly/velvet_c_binding.rb
- lib/assembly/velvet_graph_sequence_extractor.rb
- lib/external/VERSION
- lib/finishm/assemble.rb
- lib/finishm/explore.rb
- lib/finishm/finisher.rb
- lib/finishm/fluff.rb
- lib/finishm/gapfiller.rb
- lib/finishm/orfs_finder.rb
- lib/finishm/path_counter.rb
- lib/finishm/primers.rb
- lib/finishm/primers_check.rb
- lib/finishm/roundup.rb
- lib/finishm/sequence.rb
- lib/finishm/visualise.rb
- lib/finishm/wander.rb
- lib/kmer_abundance_pattern.rb
- lib/kmer_multi_abundance_file.rb
- lib/oligo_designer.rb
- lib/priner.rb
- spec/acyclic_connection_finder_spec.rb
- spec/all_orfs_spec.rb
- spec/assemble_spec.rb
- spec/bubbly_assembler_spec.rb
- spec/c_node_finder_spec.rb
- spec/connection_interpreter_spec.rb
- spec/contig_printer_spec.rb
- spec/coverage_based_graph_filter_spec.rb
- spec/data/6_3e4e5e6e.1vANME.bam
- spec/data/6_3e4e5e6e.1vANME.bam.bai
- spec/data/acyclic_connection_finder/1/probes.fa
- spec/data/acyclic_connection_finder/1/random1.fa
- spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz
- spec/data/acyclic_connection_finder/1/random2.fa
- spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz
- spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa
- spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa
- spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz
- spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31
- spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31
- spec/data/assembly_visualiser/Graph
- spec/data/assembly_visualiser/start_kmers1
- spec/data/bands.csv
- spec/data/c_probe_node_finder/1/CnyUnifiedSeq
- spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names
- spec/data/c_probe_node_finder/1/Graph2
- spec/data/c_probe_node_finder/1/LastGraph
- spec/data/c_probe_node_finder/1/Log
- spec/data/c_probe_node_finder/1/PreGraph
- spec/data/c_probe_node_finder/1/Roadmaps
- spec/data/c_probe_node_finder/1/contigs.fa
- spec/data/c_probe_node_finder/1/stats.txt
- spec/data/contig_printer/1/HOWTO_RECREATE
- spec/data/contig_printer/1/contigs.fa
- spec/data/contig_printer/1/seq.fa
- spec/data/contig_printer/1/seq.fa.svg
- spec/data/contig_printer/1/seq.fa.velvet/Graph2
- spec/data/contig_printer/1/seq.fa.velvet/LastGraph
- spec/data/contig_printer/1/seq.fa.velvet/Log
- spec/data/contig_printer/1/seq.fa.velvet/PreGraph
- spec/data/contig_printer/1/seq.fa.velvet/Roadmaps
- spec/data/contig_printer/1/seq.fa.velvet/Sequences
- spec/data/contig_printer/1/seq.fa.velvet/contigs.fa
- spec/data/contig_printer/1/seq.fa.velvet/stats.txt
- spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam
- spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai
- spec/data/contig_printer/1/seq.node12.fa
- spec/data/contig_printer/1/seq1_1to550.fa
- spec/data/contig_printer/1/seq2_1to550.fa
- spec/data/contig_printer/1/seq2_1to550.fa.fai
- spec/data/explore/1/2seqs.sammy.fa
- spec/data/explore/1/HOWTO_RECREATE.txt
- spec/data/explore/1/a.fa
- spec/data/explore/1/seq1_and_a.fa
- spec/data/explore/1/seq2.fa
- spec/data/fluff/1/2seqs.sammy.fa
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- spec/data/fluff/1/seq1.fa
- spec/data/fluff/1/seq2.fa
- spec/data/gapfilling/1/reads.fa
- spec/data/gapfilling/1/trail_with_Ns.fa
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- spec/data/gapfilling/6/to_gapfill.fa
- spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv
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- spec/data/kmers_count2.csv
- spec/data/out
- spec/data/positive_latching_pair.fa
- spec/data/primers.csv
- spec/data/read_selection_by_kmer/blacklist1.txt
- spec/data/read_selection_by_kmer/input.fasta
- spec/data/read_selection_by_kmer/whitelist1.txt
- spec/data/read_selection_by_kmer/whitelist2.txt
- spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt
- spec/data/read_to_node/1_a_graph/LastGraph
- spec/data/read_to_node/1_a_graph/ReadToNode.bin
- spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt
- spec/data/read_to_node/2_no_read256_or_259/LastGraph
- spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin
- spec/data/read_to_node/3_no_last_read/LastGraph
- spec/data/read_to_node/3_no_last_read/ReadToNode.bin
- spec/data/t/details.txt
- spec/data/t/details.txt.srt
- spec/data/t/location.txt
- spec/data/t/location.txt.srt
- spec/data/tweak/1_gap_then_unscaffolded/answer.fa
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- spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa
- spec/data/tweak/2_second_genome/answer2.fa
- spec/data/tweak/2_second_genome/reads.fa.gz
- spec/data/tweak/3_variant/answer.fa
- spec/data/tweak/3_variant/lesser_answer.fa
- spec/data/tweak/3_variant/reads.fa.gz
- spec/data/tweak/3_variant/with_gaps.fa
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- spec/data/velvet_test_trails/Assem/LastGraph
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- spec/data/velvet_test_trails/Assem/stats.txt
- spec/data/velvet_test_trails/node_fwds.fa
- spec/data/velvet_test_trails/node_seqs.fa
- spec/data/velvet_test_trails/nodes_fwd_rev.fa
- spec/data/velvet_test_trails/read1.fa
- spec/data/velvet_test_trails/reads.fa
- spec/data/velvet_test_trails_reverse/Assem/LastGraph
- spec/data/velvet_test_trails_reverse/Assem/a.svg
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- spec/data/visualise/2_paired_end/rand2.fa
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- spec/data/wander/1/random1.fa
- spec/data/wander/1/random1.sammy.fa
- spec/depth_first_search_spec.rb
- spec/dijkstra_spec.rb
- spec/explore_spec.rb
- spec/fluffer_spec.rb
- spec/gapfiller_spec.rb
- spec/graph_explorer_spec.rb
- spec/graph_generator_spec.rb
- spec/height_finder_spec.rb
- spec/kmer_abundance_pattern_spec.rb
- spec/kmer_coverage_based_path_filter_spec.rb
- spec/kmer_profile_finder_spec.rb
- spec/kmers_count_tabulate_spec.rb
- spec/oriented_node_trail_spec.rb
- spec/paired_end_neighbours_spec.rb
- spec/paths_between_nodes_spec.rb
- spec/priner_spec.rb
- spec/read_input_spec.rb
- spec/read_selection_by_kmer_spec.rb
- spec/read_to_node_spec.rb
- spec/roundup_spec.rb
- spec/scaffold_breaker_spec.rb
- spec/sequence_spec.rb
- spec/single_coherent_paths_between_nodes_spec.rb
- spec/single_coherent_wanderer_spec.rb
- spec/single_ended_assembler_spec.rb
- spec/spec_helper.rb
- spec/velvet_graph_sequence_extractor_spec.rb
- spec/visualise_spec.rb
- spec/wander_spec.rb
- spec/watch_for_changes.sh
- validation/fasta_compare.rb
- validation/gapfill_simulate_perfect.rb
homepage: http://github.com/wwood/finishm
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: Genome improvement and finishing with or without further sequencing effort
test_files: []