RubyGems - finishm - Versions diffs - 0.0.1 - Mend

finishm 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.

Files changed (554) hide show

checksums.yaml +7 -0
data/.document +5 -0
data/.gitmodules +3 -0
data/.rspec +1 -0
data/Gemfile +31 -0
data/LICENSE.txt +20 -0
data/README.md +59 -0
data/Rakefile +51 -0
data/VERSION +1 -0
data/bin/assembly_visualiser +106 -0
data/bin/check_primer_combinations.rb +73 -0
data/bin/contig_joiner.rb +244 -0
data/bin/contigs_against_assembly.rb +153 -0
data/bin/finishm +143 -0
data/bin/finishm_assembler +55 -0
data/bin/finishm_gap_closer.rb +241 -0
data/bin/kmer_abundance_file_tool.rb +49 -0
data/bin/kmer_pattern_to_assembly.rb +377 -0
data/bin/kmer_profile_finder.rb +92 -0
data/bin/kmers_count_parse.d +52 -0
data/bin/kmers_count_tabulate.d +123 -0
data/bin/kmers_count_tabulate.rb +84 -0
data/bin/pcr_result_parser.rb +108 -0
data/bin/primer_finder.rb +119 -0
data/bin/read_selection_by_kmer.d +174 -0
data/bin/scaffold_by_pattern.rb +119 -0
data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
data/bin/scaffold_end_coverages.rb +69 -0
data/bin/trail_validator.rb +84 -0
data/ext/mkrf_conf.rb +56 -0
data/ext/src/Makefile +140 -0
data/ext/src/src/allocArray.c +305 -0
data/ext/src/src/allocArray.h +86 -0
data/ext/src/src/autoOpen.c +107 -0
data/ext/src/src/autoOpen.h +18 -0
data/ext/src/src/binarySequences.c +813 -0
data/ext/src/src/binarySequences.h +125 -0
data/ext/src/src/concatenatedGraph.c +233 -0
data/ext/src/src/concatenatedGraph.h +30 -0
data/ext/src/src/concatenatedPreGraph.c +262 -0
data/ext/src/src/concatenatedPreGraph.h +29 -0
data/ext/src/src/correctedGraph.c +2643 -0
data/ext/src/src/correctedGraph.h +32 -0
data/ext/src/src/dfib.c +509 -0
data/ext/src/src/dfib.h +69 -0
data/ext/src/src/dfibHeap.c +89 -0
data/ext/src/src/dfibHeap.h +39 -0
data/ext/src/src/dfibpriv.h +105 -0
data/ext/src/src/fib.c +628 -0
data/ext/src/src/fib.h +78 -0
data/ext/src/src/fibHeap.c +79 -0
data/ext/src/src/fibHeap.h +41 -0
data/ext/src/src/fibpriv.h +110 -0
data/ext/src/src/globals.h +154 -0
data/ext/src/src/graph.c +3932 -0
data/ext/src/src/graph.h +233 -0
data/ext/src/src/graphReConstruction.c +1472 -0
data/ext/src/src/graphReConstruction.h +30 -0
data/ext/src/src/graphStats.c +2167 -0
data/ext/src/src/graphStats.h +72 -0
data/ext/src/src/graphStructures.h +52 -0
data/ext/src/src/kmer.c +652 -0
data/ext/src/src/kmer.h +73 -0
data/ext/src/src/kmerOccurenceTable.c +236 -0
data/ext/src/src/kmerOccurenceTable.h +44 -0
data/ext/src/src/kseq.h +223 -0
data/ext/src/src/locallyCorrectedGraph.c +557 -0
data/ext/src/src/locallyCorrectedGraph.h +40 -0
data/ext/src/src/passageMarker.c +677 -0
data/ext/src/src/passageMarker.h +137 -0
data/ext/src/src/preGraph.c +1717 -0
data/ext/src/src/preGraph.h +106 -0
data/ext/src/src/preGraphConstruction.c +990 -0
data/ext/src/src/preGraphConstruction.h +26 -0
data/ext/src/src/probe_node_finder.c +84 -0
data/ext/src/src/probe_node_finder.h +6 -0
data/ext/src/src/readCoherentGraph.c +557 -0
data/ext/src/src/readCoherentGraph.h +30 -0
data/ext/src/src/readSet.c +1734 -0
data/ext/src/src/readSet.h +67 -0
data/ext/src/src/readToNode.c +218 -0
data/ext/src/src/readToNode.h +35 -0
data/ext/src/src/recycleBin.c +199 -0
data/ext/src/src/recycleBin.h +58 -0
data/ext/src/src/roadMap.c +342 -0
data/ext/src/src/roadMap.h +65 -0
data/ext/src/src/run.c +318 -0
data/ext/src/src/run.h +52 -0
data/ext/src/src/run2.c +744 -0
data/ext/src/src/runReadToNode.c +29 -0
data/ext/src/src/scaffold.c +1876 -0
data/ext/src/src/scaffold.h +64 -0
data/ext/src/src/shortReadPairs.c +1243 -0
data/ext/src/src/shortReadPairs.h +32 -0
data/ext/src/src/splay.c +259 -0
data/ext/src/src/splay.h +43 -0
data/ext/src/src/splayTable.c +1315 -0
data/ext/src/src/splayTable.h +31 -0
data/ext/src/src/tightString.c +362 -0
data/ext/src/src/tightString.h +82 -0
data/ext/src/src/utility.c +199 -0
data/ext/src/src/utility.h +98 -0
data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
data/ext/src/third-party/zlib-1.2.3/README +125 -0
data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
data/ext/src/third-party/zlib-1.2.3/configure +459 -0
data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
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data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
data/ext/src/third-party/zlib-1.2.3/example +0 -0
data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
data/ext/src/third-party/zlib-1.2.3/gzio.o +0 -0
data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
data/ext/src/third-party/zlib-1.2.3/infback.o +0 -0
data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
data/ext/src/third-party/zlib-1.2.3/inffast.o +0 -0
data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
data/ext/src/third-party/zlib-1.2.3/inflate.o +0 -0
data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
data/ext/src/third-party/zlib-1.2.3/inftrees.o +0 -0
data/ext/src/third-party/zlib-1.2.3/libz.a +0 -0
data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
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data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
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data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
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data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
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data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
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data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
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data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
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data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
data/lib/assembly/a_b_visualiser.rb +169 -0
data/lib/assembly/acyclic_connection_finder.rb +81 -0
data/lib/assembly/all_orfs.rb +615 -0
data/lib/assembly/bad_format_writer.rb +46 -0
data/lib/assembly/bam_probe_read_selector.rb +48 -0
data/lib/assembly/bubbly_assembler.rb +842 -0
data/lib/assembly/c_probe_node_finder.rb +38 -0
data/lib/assembly/connection_interpreter.rb +350 -0
data/lib/assembly/contig_printer.rb +400 -0
data/lib/assembly/coverage_based_graph_filter.rb +68 -0
data/lib/assembly/depth_first_search.rb +63 -0
data/lib/assembly/dijkstra.rb +216 -0
data/lib/assembly/fluffer.rb +253 -0
data/lib/assembly/graph_explorer.rb +85 -0
data/lib/assembly/graph_generator.rb +315 -0
data/lib/assembly/height_finder.rb +355 -0
data/lib/assembly/hybrid_velvet_graph.rb +70 -0
data/lib/assembly/input_genome.rb +182 -0
data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
data/lib/assembly/node_finder.rb +171 -0
data/lib/assembly/oriented_node_trail.rb +507 -0
data/lib/assembly/paired_end_assembler.rb +53 -0
data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
data/lib/assembly/probed_graph.rb +105 -0
data/lib/assembly/read_input.rb +79 -0
data/lib/assembly/read_to_node.rb +37 -0
data/lib/assembly/scaffold_breaker.rb +126 -0
data/lib/assembly/sequence_hasher.rb +71 -0
data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
data/lib/assembly/single_coherent_wanderer.rb +261 -0
data/lib/assembly/single_ended_assembler.rb +441 -0
data/lib/assembly/velvet_c_binding.rb +54 -0
data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
data/lib/external/VERSION +1 -0
data/lib/finishm/assemble.rb +224 -0
data/lib/finishm/explore.rb +217 -0
data/lib/finishm/finisher.rb +303 -0
data/lib/finishm/fluff.rb +122 -0
data/lib/finishm/gapfiller.rb +325 -0
data/lib/finishm/orfs_finder.rb +88 -0
data/lib/finishm/path_counter.rb +90 -0
data/lib/finishm/primers.rb +425 -0
data/lib/finishm/primers_check.rb +176 -0
data/lib/finishm/roundup.rb +344 -0
data/lib/finishm/sequence.rb +142 -0
data/lib/finishm/visualise.rb +430 -0
data/lib/finishm/wander.rb +270 -0
data/lib/kmer_abundance_pattern.rb +79 -0
data/lib/kmer_multi_abundance_file.rb +48 -0
data/lib/oligo_designer.rb +88 -0
data/lib/priner.rb +66 -0
data/spec/acyclic_connection_finder_spec.rb +551 -0
data/spec/all_orfs_spec.rb +443 -0
data/spec/assemble_spec.rb +186 -0
data/spec/bubbly_assembler_spec.rb +707 -0
data/spec/c_node_finder_spec.rb +58 -0
data/spec/connection_interpreter_spec.rb +284 -0
data/spec/contig_printer_spec.rb +291 -0
data/spec/coverage_based_graph_filter_spec.rb +102 -0
data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
data/spec/data/assembly_visualiser/Graph +46 -0
data/spec/data/assembly_visualiser/start_kmers1 +2 -0
data/spec/data/bands.csv +1 -0
data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
data/spec/data/c_probe_node_finder/1/Log +756 -0
data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
data/spec/data/contig_printer/1/contigs.fa +4 -0
data/spec/data/contig_printer/1/seq.fa +2408 -0
data/spec/data/contig_printer/1/seq.fa.svg +153 -0
data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
data/spec/data/contig_printer/1/seq.node12.fa +4 -0
data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
data/spec/data/explore/1/a.fa +2 -0
data/spec/data/explore/1/seq1_and_a.fa +3 -0
data/spec/data/explore/1/seq2.fa +2 -0
data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
data/spec/data/fluff/1/seq1.fa +2 -0
data/spec/data/fluff/1/seq2.fa +2 -0
data/spec/data/gapfilling/1/reads.fa +171 -0
data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
data/spec/data/gapfilling/2/reference.fa +2 -0
data/spec/data/gapfilling/2/reference_part1.fa +4 -0
data/spec/data/gapfilling/2/reference_part2.fa +4 -0
data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
data/spec/data/gapfilling/2/with_gaps.fa +4 -0
data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
data/spec/data/gapfilling/3/reads.fa.gz +0 -0
data/spec/data/gapfilling/3/reference_part1.fa +4 -0
data/spec/data/gapfilling/3/reference_part2.fa +4 -0
data/spec/data/gapfilling/3/with_gaps.fa +4 -0
data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
data/spec/data/gapfilling/4/reads.fa.gz +0 -0
data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
data/spec/data/gapfilling/5/answer.fna +2 -0
data/spec/data/gapfilling/5/gappy.fna +2 -0
data/spec/data/gapfilling/5/reads.fa +17961 -0
data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
data/spec/data/gapfilling/6/random1.fa +28 -0
data/spec/data/gapfilling/6/random2.fa +28 -0
data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
data/spec/data/kmers_count1.csv +2 -0
data/spec/data/kmers_count2.csv +3 -0
data/spec/data/out +3 -0
data/spec/data/positive_latching_pair.fa +2 -0
data/spec/data/primers.csv +4 -0
data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
data/spec/data/read_selection_by_kmer/input.fasta +6 -0
data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
data/spec/data/t/details.txt +5 -0
data/spec/data/t/details.txt.srt +5 -0
data/spec/data/t/location.txt +3 -0
data/spec/data/t/location.txt.srt +3 -0
data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
data/spec/data/tweak/3_variant/answer.fa +2 -0
data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
data/spec/data/velvet_test_trails/Assem/Graph +17 -0
data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
data/spec/data/velvet_test_trails/Assem/Log +35 -0
data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
data/spec/data/velvet_test_trails/read1.fa +2 -0
data/spec/data/velvet_test_trails/reads.fa +50 -0
data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
data/spec/data/visualise/1/LastGraph +6695 -0
data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
data/spec/data/wander/1/random1.fa +2 -0
data/spec/data/wander/1/random1.sammy.fa +804 -0
data/spec/depth_first_search_spec.rb +190 -0
data/spec/dijkstra_spec.rb +143 -0
data/spec/explore_spec.rb +29 -0
data/spec/fluffer_spec.rb +155 -0
data/spec/gapfiller_spec.rb +107 -0
data/spec/graph_explorer_spec.rb +475 -0
data/spec/graph_generator_spec.rb +99 -0
data/spec/height_finder_spec.rb +306 -0
data/spec/kmer_abundance_pattern_spec.rb +56 -0
data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
data/spec/kmer_profile_finder_spec.rb +38 -0
data/spec/kmers_count_tabulate_spec.rb +120 -0
data/spec/oriented_node_trail_spec.rb +221 -0
data/spec/paired_end_neighbours_spec.rb +126 -0
data/spec/paths_between_nodes_spec.rb +349 -0
data/spec/priner_spec.rb +7 -0
data/spec/read_input_spec.rb +23 -0
data/spec/read_selection_by_kmer_spec.rb +166 -0
data/spec/read_to_node_spec.rb +35 -0
data/spec/roundup_spec.rb +366 -0
data/spec/scaffold_breaker_spec.rb +144 -0
data/spec/sequence_spec.rb +43 -0
data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
data/spec/single_coherent_wanderer_spec.rb +120 -0
data/spec/single_ended_assembler_spec.rb +398 -0
data/spec/spec_helper.rb +310 -0
data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
data/spec/visualise_spec.rb +105 -0
data/spec/wander_spec.rb +119 -0
data/spec/watch_for_changes.sh +16 -0
data/validation/fasta_compare.rb +72 -0
data/validation/gapfill_simulate_perfect.rb +108 -0
metadata +899 -0

data/spec/coverage_based_graph_filter_spec.rb ADDED

@@ -0,0 +1,102 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+#Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
+describe "coverage based graph filter" do
+  it 'should filter nodes by coverage' do
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
+    graph.nodes.length.should == 4
+    cutoffer = Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter.new
+    deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 0)
+    deleted_nodes.length.should == 0
+    deleted_arcs.length.should == 0
+    graph.nodes.length.should == 4
+    deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 3.5)
+    deleted_nodes.length.should == 2
+    deleted_arcs.length.should == 4
+    graph.nodes.length.should == 2
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
+    deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10)
+    deleted_nodes.length.should == 4
+    deleted_arcs.length.should == 4
+    graph.nodes.length.should == 0
+  end
+  it 'should respect whitelisted sequences' do
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
+    graph.nodes.length.should == 4
+    cutoffer = Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter.new
+    deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10, :whitelisted_sequences => [1])
+    deleted_nodes.length.should == 1
+    graph.nodes.length.should == 3
+    graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
+    deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10, :whitelisted_sequences => [1,2])
+    deleted_nodes.length.should == 0
+    deleted_arcs.length.should == 0
+    graph.nodes.length.should == 4
+  end
+  it 'should filter by connectivity' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [3,4]
+    ])
+    filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
+    graph.nodes.length.should == 4
+    filter.remove_unconnected_nodes(graph,[graph.nodes[1]])
+    graph.nodes.length.should == 2
+    graph.arcs.length.should == 1
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3],
+      [3,4]
+    ])
+    filter.remove_unconnected_nodes(graph,[graph.nodes[1]])
+    graph.nodes.length.should == 4
+  end
+  it 'should filter by leashed connectivity' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [3,4]
+    ])
+    filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
+    graph.nodes.length.should == 4
+    filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 5)
+    graph.nodes.length.should == 2 #or 1.meh.
+    graph.arcs.length.should == 1
+  end
+  it 'should filter by leashed connectivity 2 nodes' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3],
+      [3,4]
+    ])
+    graph.nodes.length.should == 4
+    filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
+    filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 15)
+    graph.nodes.length.should == 3#or 2.meh.
+  end
+  it 'should filter by fake leashed connectivity' do
+    graph = GraphTesting.emit([
+      [1,2],
+      [2,3],
+      [3,4]
+    ])
+    graph.nodes.length.should == 4
+    filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
+    filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 9999)
+    graph.nodes.length.should == 4
+  end
+end

data/spec/data/6_3e4e5e6e.1vANME.bam ADDED

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data/spec/data/6_3e4e5e6e.1vANME.bam.bai ADDED

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data/spec/data/acyclic_connection_finder/1/probes.fa ADDED

@@ -0,0 +1,5 @@
+>probe_fwd
+GCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCA
+>probe_rev_revcom
+ACTGGAGTCGGCGCGATCGCGGCGGTTAGTAGGCTCTTGAGTACCCATGCTTCCTCAGCTCTATGATGAACCCAGTGCCTGGGCGCCCATT

data/spec/data/acyclic_connection_finder/1/random1.fa ADDED

	@@ -0,0 +1,2 @@
1	+ >random_sequence_length_1000
2	+ GGCAGAGCGGTAACCGACAGGCGTAATTGAAGCACCAAGCAAAGCTTAATGGCATGTGAAGCACCCCCGGTTCGTGAACAGAACCTTCGGGCGTTGGTATTCACCTTGGCACCTATACCTAGACACAGACTACGCGTTTTGAACGATTAGTATCCGCGACTTTCAGTGCCTTCTACAGGACGCAAGCTGACAGGCATACTCTACCCAAATTATGCGCGATCCCCTATCTGTACGGAGACGGGTGACCTCGTAACCTGCTATGAGAATCATCAAGAATCTGTCGGGTTAGCGACCACAACGGCCGATAGTGTTGCGATATCGGCCTAACCACGCGACTAATCGCCTACCACGACCGGTCACGACGAGACCTGCAGGTCGACATGAAGACGATGTTGTAAGGCGTAAAACTCCGACTGTGGCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCAAATGGGCGCCCAGGCACTGGGTTCATCATAGAGCTGAGGAAGCATGGGTACTCAAGAGCCTACTAACCGCCGCGATCGCGCCGACTCCAGTGCCTGTAGTTCTTCATAATAAAATAACACGTCACTTGCTCCATGTACGCGCTACGTTTGACGTTGCTAGACGGATACCAACGCCCCGGGCGATAAATGTTCCGTGGTCGCTTCTGGTAGGATGCAATTGACGATTTTCCACATGGGCTCGTATGTCCCACCGCCCTCTGGTCGAACATGCGAGCGTACACTGTCATATCCCCACTAGCGGAGCAACCGACGGACCAAACGTCTGTCGTCTGGATATGTAAGCTAACATAACTCCAATCTGATTGGCGTGCTATATATTCGAGCGAAGCCTTTTGTGTTCTCACTGGAAAGAGTGGCATTTCTGCCGCTGGAAGATTAAGATTTTAGCCTGAGGTGGCACAGTCTCTATGATTGAGGGGAAATTACGGTGTGTCC

data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz ADDED

Binary file

data/spec/data/acyclic_connection_finder/1/random2.fa ADDED

	@@ -0,0 +1,2 @@
1	+ >random_sequence_length_1000
2	+ GGCAGAGCGGTAACCGACAGGCGTAATTGAAGCACCAAGCAAAGCTTAATGGCATGTGAAGCACCCCCGGTTCGTGAACAGAACCTTCGGGCGTTGGTATTCACCTTGGCACCTATACCTAGACACAGACTACGCGTTTTGAACGATTAGTATCCGCGACTTTCAGTGCCTTCTACAGGACGCAAGCTGACAGGCATACTCTACCCAAATTATGCGCGATCCCCTATCTGTACGGAGACGGGTGACCTCGTAACCTGCTATGAGAATCATCAAGAATCTGTCGGGTTAGCGACCACAACGGCCGATAGTGTTGCGATATCGGCCTAACCACGCGACTAATCGCCTACCACGACCGGTCACGACGAGACCTGCAGGTCGACATGAAGACGATGTTGTAAGGCGTAAAACTCCGACTGTGGCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATGGGCGCCCAGGCACTGGGTTCATCATAGAGCTGAGGAAGCATGGGTACTCAAGAGCCTACTAACCGCCGCGATCGCGCCGACTCCAGTGCCTGTAGTTCTTCATAATAAAATAACACGTCACTTGCTCCATGTACGCGCTACGTTTGACGTTGCTAGACGGATACCAACGCCCCGGGCGATAAATGTTCCGTGGTCGCTTCTGGTAGGATGCAATTGACGATTTTCCACATGGGCTCGTATGTCCCACCGCCCTCTGGTCGAACATGCGAGCGTACACTGTCATATCCCCACTAGCGGAGCAACCGACGGACCAAACGTCTGTCGTCTGGATATGTAAGCTAACATAACTCCAATCTGATTGGCGTGCTATATATTCGAGCGAAGCCTTTTGTGTTCTCACTGGAAAGAGTGGCATTTCTGCCGCTGGAAGATTAAGATTTTAGCCTGAGGTGGCACAGTCTCTATGATTGAGGGGAAATTACGGTGTGTCC

data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz ADDED

Binary file

data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa ADDED

@@ -0,0 +1,39 @@
+>random_sequence_length_3000
+TTGTAATGAGGGATCTCATAGGGCTCTTGGTAGTCACGATTCCCTCGGTTATAGTTGCAGGAGACGGGGGTTAACCGTAA
+ACAAGACTCGCTTATCGCTACGACCTGCACAACTAAGCTTCGGCTGCAGCCCACCGACTGTAGAATCCGGCCCAGTCTGC
+CTATGTATGGCAGCATCTTATCGGTATGACACGCCAACAATCTCCTGTACAAGAGATTATCAAGCAATCAATGAAGCATC
+CACTCTTGTCTGTCGGGATGTATATGCGCGACCGTGTTAGCCTTGCGTGGTGGCATGAAACCATCGAATAGCACCACCTA
+GTGCGGTGGACCTGTCCGCTCGACTACCGGCCGGTTAAGACAGCAAAGTGCACCTGACGGAATTATTACGCTGTCTACAC
+GAACAAGTCTACCCCCATAATTATTGCTGGTATAACCGCTCGCTATAATTCGCGTCTGCTTTAAGGTACGGTCGGTCAAA
+TGGGCGTTATCTTGATTTTTCCATATCCATCTCTCAGATCGAGCCGATACGAATGAATAATTATGCCGACCAGTTCATTA
+ATTGAACCTTCCCAGAGCTTCCTTCAAAATCATTCTGAGACGGATGTTGCGCCCATGACTCCGGGGGGTTGGGTACTTGG
+ATGATTCCCACGACCCCAGAGAGTCCTGACATTACGTCTCGGGTTCACAGCGAGCCAAATGGGGGCAGTCTGGTCCCGTG
+ACGACCACCGATTGATTGAGACAATGAGCGTCACAACTACCAGTCAACTCGTCTGGCATAGTTACTCATCGCCACACGAT
+GCTTGTCTGTTGAGTCTTGGGCCATAAATTGCTCGAGGGGGCGCTCTGCCAAAGAGAGCATGCTACTGCACGTATCTCTT
+AACTATCGTACCCGATACTGATGTTGCGTCGGTTCGTGCAGACTATTACCGGAGCGAGCTGCCATACAGTGCGGTGATCT
+GAAGGAGCGCCCACGCTGCTCAACCCCACCGCTATCTTTCAAGCATGCCGTGACAAATGCGAAGGCCGGACACTGCATTG
+GGATAATATTTCGTACTGGCGACATATGACTACACAGCTAAAGGGGGCGACAGTTGTGATATATACCCAAATGATCTGTT
+TCCCTCTTACCTTCATTACGGCCTTATCGCAGTGCTAATCCTCTGGTCTTTTACGTAAGTATGCGTAATCGGCGTTATCC
+CGGCAGAACTCGATCCGGGCTGAGAGAATGATTCCAGGTACAGGATTAGAAGCCATTTGGGAAGAGAAGCGCAGGGCTAG
+CACGATAATGATGTAAGAAAGAACCACTAACGTTGTATTTGACCACTGTCAACGTATAGGCAGCGAGGATCACTGTTTCA
+GACCGATTTACATTCGTTAGCCGAACCGAATGCTCAGGTCGGAACTGGGTCCAGATGAACCACAATTCCGCGCTGGTAAG
+GAAGTCCGTTCTTCATCCAGAGGTCCACGCCAAAGCAGTCATTATCGGGTGGGTAGTCTCCATCGTAAGCTAAGTTAAAG
+ATGCAAGGTGCTTCAAGTACCTGCTCCCAGGCTAGTTTACAACTCTGGGGATAGTGTTTTACCGAGGAGGCATGCCCTAG
+GTTGTGGACCATGATCGGCCCCCCCTCCCTACTGCGTTACTTTACGGCGAATGGGACACCGTAGTTTTTTGCTATAGCTA
+ATCCGCAGTTCTCCCGTACGGTATACACGCGATAGCTCCGTATTAAGATCCGTGCGTTGCCACAGTACCCCGCAGGCGAC
+CTACCATCCCATACCGTCCTTCGAAGATACGTAAGATCGAGCGTGAGTTTTTTTTAATGTTGCTTACTAACTTAACACGT
+CGGAGGGATGCTGTGTGACGGGGGGCACAATAAATCAACCTCCGAAGCAAGACGCACCATTACCAGTGTCGCCGGGATGC
+ACGTTACAACCTTTTCTATTTCTACAGACTGTGGGTATACATCCGTAAATTAATTAATCAGTATTCTGATTTAGGAAACG
+TGGATCCCCTTCAAAAGTGGCAGGTATGATGGGTCCTATGCGCGTTATAAATGTAAGTTCTATGTTGCCATTAAAAGCTC
+GCCAGAGACACGATACGGCGAGGACGGTTAGATGGCGTGCACCTTATGGCATCTGCGCGCAAACGGTAGAGGCAAGGAGT
+TCCTATATCCCAAAAACTATTCGGGTTTTGCCTATTGCTGAGACTTACATCTCGGCTGTGATCCTCAGCTGTCAGAGGAG
+TAGTGTGGCGCATTTCGTCACCTGCCCGCTGGTTAATAGAGACTCGGTCAGGTAGGAATGTTATGTTCCGGCAAATCACC
+CACAAATTATACGGTGCTTAATTACTTTTTGTCGAAGGCCATCTTTCATGGGCCTGCGTTACTCAAATAAATGCGACTAG
+GAGCCTCTGTACCCCGGGGGCTATCGTCAACCAACTACTGATTCAATCGTACGGCAACAGCCTTAAGAGGGTCAGGCCAA
+TTCCGGGGCCCCTAGAAGTTGAACAAATGCCGGCATGTGATAATGTTTAATGTAGTCGCCACACCAAGAACGATTTAATT
+GGACGGCCGAAATAAGAAGTTCAACATGTTTGCCGGTGGCGCAGGAGTCTTAGTTAGAGTTAGCGAGTGGGCTCGGTAAT
+AGGTGTACGTCCCTGTAGCTAATTTCGAGACTAACTTCCTATTCCCTGTCGCCTTGATTGATGTGGTCTCAGCAACGAGT
+CTTAGCTAGGGTTACCGTTTGTTGGTCTGGAATCAGGTAGGAGACGTATACAAACGGATAGTTTCACCGGAGCGCTCTCC
+TGGAGCTGCTCGCGCGCACTAACTGAAATGGCGTTTGGACTGCGATGGAAGAGGAGCCGCGCTTAGGGCCTGCTCCGAAA
+TGCTTCAGATCATCCACGTTCTACGGCGGACGCCGTCCTAACTTAGGTCAGGGAGTCCCGTACCGATACTACTCTAAAGC
+CGGGAGTGAAGTCTAGGTACTTAAGAGCTCACGCGGGTCA

data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa ADDED

@@ -0,0 +1,39 @@
+>random_sequence_length_3000
+TTGTAATGAGGGATCTCATAGGGCTCTTGGTAGTCACGATTCCCTCGGTTATAGTTGCAGGAGACGGGGGTTAACCGTAA
+ACAAGACTCGCTTATCGCTACGACCTGCACAACTAAGCTTCGGCTGCAGCCCACCGACTGTAGAATCCGGCCCAGTCTGC
+CTATGTATGGCAGCATCTTATCGGTATGACACGCCAACAATCTCCTGTACAAGAGATTATCAAGCAATCAATGAAGCATC
+CACTCTTGTCTGTCGGGATGTATATGCGCGACCGTGTTAGCCTTGCGTGGTGGCATGAAACCATCGAATAGCACCACCTA
+GTGCGGTGGACCTGTCCGCTCGACTACCGGCCGGTTAAGACAGCAAAGTGCACCTGACGGAATTATTACGCTGTCTACAC
+GAACAAGTCTACCCCCATAATTATTGCTGGTATAACCGCTCGCTATAATTCGCGTCTGCTTTAAGGTACGGTCGGTCAAA
+TGGGCGTTATCTTGATTTTTCCATATCCATCTCTCAGATCGAGCCGATACGAATGAATAATTATGCCGACCAGTTCATTA
+ATTGAACCTTCCCAGAGCTTCCTTCAAAATCATTCTGAGACGGATGTTGCGCCCATGACTCCGGGGGGTTGGGTACTTGG
+ATGATTCCCACGACCCCAGAGAGTCCTGACATTACGTCTCGGGTTCACAGCGAGCCAAATGGGGGCAGTCTGGTCCCGTG
+ACGACCACCGATTGATTGAGACAATGAGCGTCACAACTACCAGTCAACTCGTCTGGCATAGTTACTCATCGCCACACGAT
+GCTTGTCTGTTGAGTCTTGGGCCATAAATTGCTCGAGGGGGCGCTCTGCCAAAGAGAGCATGCTACTGCACGTATCTCTT
+AACTATCGTACCCGATACTGATGTTGCGTCGGTTCGTGCAGACTATTACCGGAGCGAGCTGCCATACAGTGCGGTGATCT
+GAAGGAGCGCCCACGCTGCTCAACCCCACCGCTATCTTTCAAGCATGCCGTGACAAATGCGAAGGCCGGACACTGCATTG
+GGATAATATTTCGTACTGGCGACATATGACTACACAGCTAAAGGGGGCGACAGTTGTGATATATACCCAAATGATCTGTT
+TCCCTCTTACCTTCATTACGGCCTTATCGCAGTGCTAATCCTCTGGTCTTTTACGTAAGTATGCGTAATCGGCGTTATCC
+CGGCAGAACTCGATCCGGGCTGAGAGAATGATTCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCAGGTACAGGATTAGAAGCCATTTGGGAAGAGAAGCGCAGGGCTAG
+CACGATAATGATGTAAGAAAGAACCACTAACGTTGTATTTGACCACTGTCAACGTATAGGCAGCGAGGATCACTGTTTCA
+GACCGATTTACATTCGTTAGCCGAACCGAATGCTCAGGTCGGAACTGGGTCCAGATGAACCACAATTCCGCGCTGGTAAG
+GAAGTCCGTTCTTCATCCAGAGGTCCACGCCAAAGCAGTCATTATCGGGTGGGTAGTCTCCATCGTAAGCTAAGTTAAAG
+ATGCAAGGTGCTTCAAGTACCTGCTCCCAGGCTAGTTTACAACTCTGGGGATAGTGTTTTACCGAGGAGGCATGCCCTAG
+GTTGTGGACCATGATCGGCCCCCCCTCCCTACTGCGTTACTTTACGGCGAATGGGACACCGTAGTTTTTTGCTATAGCTA
+ATCCGCAGTTCTCCCGTACGGTATACACGCGATAGCTCCGTATTAAGATCCGTGCGTTGCCACAGTACCCCGCAGGCGAC
+CTACCATCCCATACCGTCCTTCGAAGATACGTAAGATCGAGCGTGAGTTTTTTTTAATGTTGCTTACTAACTTAACACGT
+CGGAGGGATGCTGTGTGACGGGGGGCACAATAAATCAACCTCCGAAGCAAGACGCACCATTACCAGTGTCGCCGGGATGC
+ACGTTACAACCTTTTCTATTTCTACAGACTGTGGGTATACATCCGTAAATTAATTAATCAGTATTCTGATTTAGGAAACG
+TGGATCCCCTTCAAAAGTGGCAGGTATGATGGGTCCTATGCGCGTTATAAATGTAAGTTCTATGTTGCCATTAAAAGCTC
+GCCAGAGACACGATACGGCGAGGACGGTTAGATGGCGTGCACCTTATGGCATCTGCGCGCAAACGGTAGAGGCAAGGAGT
+TCCTATATCCCAAAAACTATTCGGGTTTTGCCTATTGCTGAGACTTACATCTCGGCTGTGATCCTCAGCTGTCAGAGGAG
+TAGTGTGGCGCATTTCGTCACCTGCCCGCTGGTTAATAGAGACTCGGTCAGGTAGGAATGTTATGTTCCGGCAAATCACC
+CACAAATTATACGGTGCTTAATTACTTTTTGTCGAAGGCCATCTTTCATGGGCCTGCGTTACTCAAATAAATGCGACTAG
+GAGCCTCTGTACCCCGGGGGCTATCGTCAACCAACTACTGATTCAATCGTACGGCAACAGCCTTAAGAGGGTCAGGCCAA
+TTCCGGGGCCCCTAGAAGTTGAACAAATGCCGGCATGTGATAATGTTTAATGTAGTCGCCACACCAAGAACGATTTAATT
+GGACGGCCGAAATAAGAAGTTCAACATGTTTGCCGGTGGCGCAGGAGTCTTAGTTAGAGTTAGCGAGTGGGCTCGGTAAT
+AGGTGTACGTCCCTGTAGCTAATTTCGAGACTAACTTCCTATTCCCTGTCGCCTTGATTGATGTGGTCTCAGCAACGAGT
+CTTAGCTAGGGTTACCGTTTGTTGGTCTGGAATCAGGTAGGAGACGTATACAAACGGATAGTTTCACCGGAGCGCTCTCC
+TGGAGCTGCTCGCGCGCACTAACTGAAATGGCGTTTGGACTGCGATGGAAGAGGAGCCGCGCTTAGGGCCTGCTCCGAAA
+TGCTTCAGATCATCCACGTTCTACGGCGGACGCCGTCCTAACTTAGGTCAGGGAGTCCCGTACCGATACTACTCTAAAGC
+CGGGAGTGAAGTCTAGGTACTTAAGAGCTCACGCGGGTCA

data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz ADDED

Binary file

data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 ADDED

@@ -0,0 +1,220 @@
+TTTCGGATAGGCTCTAAGAATGAAGATAATA
+AAATCTGATTCAGGCGACGGATGCCTAGATT
+GGATAACGTTCAGAGCTTCTGGACTTTTCGG
+TCGTCCTGATTGTCCTGCATTCAGTGCCGGT
+TAATAAAATCTGATTCAGGCGACGGATGCCT
+ACCATCCGCCCTGGTGTGATCCCCTACGCTA
+CAAGAAGCCCCGGGAGGGATTTGAACCCTCG
+TTTGAACCCTCGACCTCGTCCTGATTGTCCT
+ACGTTCAGAGCTTCTGGACTTTTCGGATAGG
+ACCCTCGACCTCGTCCTGATTGTCCTGCATT
+AGAGATACTTGACCATCCGCCCTGGTGTGAT
+TTACACTTCGCATGTGCATGGATAACGTTCA
+ATAAAATCTGATTCAGGCGACGGATGCCTAG
+CTTCGCATGTGCATGGATAACGTTCAGAGCT
+GATTCAGGCGACGGATGCCTAGATTAGCATT
+TCTGGACTTTTCGGATAGGCTCTAAGAATGA
+TTTTCGGATAGGCTCTAAGAATGAAGATAAT
+CAGAGCTTCTGGACTTTTCGGATAGGCTCTA
+ATGAAGATAATAAAATCTGATTCAGGCGACG
+ATAGGCTCTAAGAATGAAGATAATAAAATCT
+GAGATACTTGACCATCCGCCCTGGTGTGATC
+AGAAGCCCCGGGAGGGATTTGAACCCTCGAC
+CGGATGCCTAGATTAGCATTAGAGATACTTG
+ACTTTTCGGATAGGCTCTAAGAATGAAGATA
+GCATTAGAGATACTTGACCATCCGCCCTGGT
+GCTAACTTGGCTAATAAATTTCAAGAAGCCC
+TTCGGATAGGCTCTAAGAATGAAGATAATAA
+CTGGTGTGATCCCCTACGCTAACTTGGCTAA
+AGAGCTTCTGGACTTTTCGGATAGGCTCTAA
+TAGGCTCTAAGAATGAAGATAATAAAATCTG
+CATGTGCATGGATAACGTTCAGAGCTTCTGG
+GCTAATAAATTTCAAGAAGCCCCGGGAGGGA
+ATCCCCTACGCTAACTTGGCTAATAAATTTC
+CGCCCTGGTGTGATCCCCTACGCTAACTTGG
+CCCTACGCTAACTTGGCTAATAAATTTCAAG
+AACTTGGCTAATAAATTTCAAGAAGCCCCGG
+CCTCGTCCTGATTGTCCTGCATTCAGTGCCG
+TGAAGATAATAAAATCTGATTCAGGCGACGG
+AAGCCCCGGGAGGGATTTGAACCCTCGACCT
+CTGGACTTTTCGGATAGGCTCTAAGAATGAA
+ACTTGACCATCCGCCCTGGTGTGATCCCCTA
+GATGCCTAGATTAGCATTAGAGATACTTGAC
+ATCTGATTCAGGCGACGGATGCCTAGATTAG
+TAAATTTCAAGAAGCCCCGGGAGGGATTTGA
+GTTCAGAGCTTCTGGACTTTTCGGATAGGCT
+TCCTGATTGTCCTGCATTCAGTGCCGGTTAC
+TCTGATTCAGGCGACGGATGCCTAGATTAGC
+CTTGGCTAATAAATTTCAAGAAGCCCCGGGA
+GGCTAATAAATTTCAAGAAGCCCCGGGAGGG
+CCTACGCTAACTTGGCTAATAAATTTCAAGA
+AAGAAGCCCCGGGAGGGATTTGAACCCTCGA
+CTTGACCATCCGCCCTGGTGTGATCCCCTAC
+GTCCTGATTGTCCTGCATTCAGTGCCGGTTA
+GATAACGTTCAGAGCTTCTGGACTTTTCGGA
+GGATGCCTAGATTAGCATTAGAGATACTTGA
+ATAACGTTCAGAGCTTCTGGACTTTTCGGAT
+ATGTGCATGGATAACGTTCAGAGCTTCTGGA
+TTTCAAGAAGCCCCGGGAGGGATTTGAACCC
+CATTAGAGATACTTGACCATCCGCCCTGGTG
+TTAGCATTAGAGATACTTGACCATCCGCCCT
+ATTGTCCTGCATTCAGTGCCGGTTACCAAGG
+CTCGACCTCGTCCTGATTGTCCTGCATTCAG
+CCCTGGTGTGATCCCCTACGCTAACTTGGCT
+GATTTGAACCCTCGACCTCGTCCTGATTGTC
+AGGCTCTAAGAATGAAGATAATAAAATCTGA
+TTGACCATCCGCCCTGGTGTGATCCCCTACG
+CTAACTTGGCTAATAAATTTCAAGAAGCCCC
+ACACTTCGCATGTGCATGGATAACGTTCAGA
+CCTCGACCTCGTCCTGATTGTCCTGCATTCA
+TACGCTAACTTGGCTAATAAATTTCAAGAAG
+CTGATTCAGGCGACGGATGCCTAGATTAGCA
+AGGCGACGGATGCCTAGATTAGCATTAGAGA
+ACGCTAACTTGGCTAATAAATTTCAAGAAGC
+GAAGATAATAAAATCTGATTCAGGCGACGGA
+TCAAGAAGCCCCGGGAGGGATTTGAACCCTC
+GACGGATGCCTAGATTAGCATTAGAGATACT
+GGACTTTTCGGATAGGCTCTAAGAATGAAGA
+CCGGGAGGGATTTGAACCCTCGACCTCGTCC
+TCTAAGAATGAAGATAATAAAATCTGATTCA
+TGCCTAGATTAGCATTAGAGATACTTGACCA
+GGTGTGATCCCCTACGCTAACTTGGCTAATA
+ATCCGCCCTGGTGTGATCCCCTACGCTAACT
+TAACTTGGCTAATAAATTTCAAGAAGCCCCG
+CGACGGATGCCTAGATTAGCATTAGAGATAC
+TTCTGGACTTTTCGGATAGGCTCTAAGAATG
+AGCCCCGGGAGGGATTTGAACCCTCGACCTC
+CCTGCATTCAGTGCCGGTTACCAAGGACGCG
+AGCATTAGAGATACTTGACCATCCGCCCTGG
+AATTTCAAGAAGCCCCGGGAGGGATTTGAAC
+GGATAGGCTCTAAGAATGAAGATAATAAAAT
+GACTTTTCGGATAGGCTCTAAGAATGAAGAT
+GATCCCCTACGCTAACTTGGCTAATAAATTT
+GTGATCCCCTACGCTAACTTGGCTAATAAAT
+CGCTAACTTGGCTAATAAATTTCAAGAAGCC
+GAATGAAGATAATAAAATCTGATTCAGGCGA
+GATAGGCTCTAAGAATGAAGATAATAAAATC
+CTACGCTAACTTGGCTAATAAATTTCAAGAA
+CCCTCGACCTCGTCCTGATTGTCCTGCATTC
+CACTTCGCATGTGCATGGATAACGTTCAGAG
+TTCAGGCGACGGATGCCTAGATTAGCATTAG
+GGAGGGATTTGAACCCTCGACCTCGTCCTGA
+GGGAGGGATTTGAACCCTCGACCTCGTCCTG
+TCAGGCGACGGATGCCTAGATTAGCATTAGA
+TAAGAATGAAGATAATAAAATCTGATTCAGG
+GACCTCGTCCTGATTGTCCTGCATTCAGTGC
+TACTTGACCATCCGCCCTGGTGTGATCCCCT
+TCGACCTCGTCCTGATTGTCCTGCATTCAGT
+ATTAGCATTAGAGATACTTGACCATCCGCCC
+GATACTTGACCATCCGCCCTGGTGTGATCCC
+TGTCCTGCATTCAGTGCCGGTTACCAAGGAC
+GTCCTGCATTCAGTGCCGGTTACCAAGGACG
+GCGACGGATGCCTAGATTAGCATTAGAGATA
+GCCCTGGTGTGATCCCCTACGCTAACTTGGC
+TAATAAATTTCAAGAAGCCCCGGGAGGGATT
+ACGGATGCCTAGATTAGCATTAGAGATACTT
+TGATTCAGGCGACGGATGCCTAGATTAGCAT
+CCTGGTGTGATCCCCTACGCTAACTTGGCTA
+CTTTTCGGATAGGCTCTAAGAATGAAGATAA
+CCCGGGAGGGATTTGAACCCTCGACCTCGTC
+AGATAATAAAATCTGATTCAGGCGACGGATG
+CATCCGCCCTGGTGTGATCCCCTACGCTAAC
+ATTCAGGCGACGGATGCCTAGATTAGCATTA
+TCCCCTACGCTAACTTGGCTAATAAATTTCA
+GGCTCTAAGAATGAAGATAATAAAATCTGAT
+AAGAATGAAGATAATAAAATCTGATTCAGGC
+CGACCTCGTCCTGATTGTCCTGCATTCAGTG
+AAAATCTGATTCAGGCGACGGATGCCTAGAT
+CGGGAGGGATTTGAACCCTCGACCTCGTCCT
+CTCGTCCTGATTGTCCTGCATTCAGTGCCGG
+ATTTCAAGAAGCCCCGGGAGGGATTTGAACC
+ATTAGAGATACTTGACCATCCGCCCTGGTGT
+CTCTAAGAATGAAGATAATAAAATCTGATTC
+TGAACCCTCGACCTCGTCCTGATTGTCCTGC
+GATTGTCCTGCATTCAGTGCCGGTTACCAAG
+ACCTCGTCCTGATTGTCCTGCATTCAGTGCC
+AATCTGATTCAGGCGACGGATGCCTAGATTA
+CGGATAGGCTCTAAGAATGAAGATAATAAAA
+GCTTCTGGACTTTTCGGATAGGCTCTAAGAA
+AAGATAATAAAATCTGATTCAGGCGACGGAT
+TAGCATTAGAGATACTTGACCATCCGCCCTG
+GACCATCCGCCCTGGTGTGATCCCCTACGCT
+AATAAAATCTGATTCAGGCGACGGATGCCTA
+GTGCATGGATAACGTTCAGAGCTTCTGGACT
+ACTTCGCATGTGCATGGATAACGTTCAGAGC
+GCATGTGCATGGATAACGTTCAGAGCTTCTG
+GAGGGATTTGAACCCTCGACCTCGTCCTGAT
+TCCGCCCTGGTGTGATCCCCTACGCTAACTT
+TTAGAGATACTTGACCATCCGCCCTGGTGTG
+TGATTGTCCTGCATTCAGTGCCGGTTACCAA
+GATTAGCATTAGAGATACTTGACCATCCGCC
+CGTCCTGATTGTCCTGCATTCAGTGCCGGTT
+CTGATTGTCCTGCATTCAGTGCCGGTTACCA
+GCCTAGATTAGCATTAGAGATACTTGACCAT
+AACGTTCAGAGCTTCTGGACTTTTCGGATAG
+GCTCTAAGAATGAAGATAATAAAATCTGATT
+GCCCCGGGAGGGATTTGAACCCTCGACCTCG
+TGGATAACGTTCAGAGCTTCTGGACTTTTCG
+CCATCCGCCCTGGTGTGATCCCCTACGCTAA
+TAAAATCTGATTCAGGCGACGGATGCCTAGA
+CCCCTACGCTAACTTGGCTAATAAATTTCAA
+CTGCATTCAGTGCCGGTTACCAAGGACGCGC
+GAACCCTCGACCTCGTCCTGATTGTCCTGCA
+TTGAACCCTCGACCTCGTCCTGATTGTCCTG
+CTAATAAATTTCAAGAAGCCCCGGGAGGGAT
+GCATGGATAACGTTCAGAGCTTCTGGACTTT
+AGCTTCTGGACTTTTCGGATAGGCTCTAAGA
+AGATTAGCATTAGAGATACTTGACCATCCGC
+TGACCATCCGCCCTGGTGTGATCCCCTACGC
+TACACTTCGCATGTGCATGGATAACGTTCAG
+TAGAGATACTTGACCATCCGCCCTGGTGTGA
+GTGTGATCCCCTACGCTAACTTGGCTAATAA
+TGGTGTGATCCCCTACGCTAACTTGGCTAAT
+ACTTGGCTAATAAATTTCAAGAAGCCCCGGG
+TGGACTTTTCGGATAGGCTCTAAGAATGAAG
+TAGATTAGCATTAGAGATACTTGACCATCCG
+AACCCTCGACCTCGTCCTGATTGTCCTGCAT
+CCCCGGGAGGGATTTGAACCCTCGACCTCGT
+AAATTTCAAGAAGCCCCGGGAGGGATTTGAA
+TGTGATCCCCTACGCTAACTTGGCTAATAAA
+TCGCATGTGCATGGATAACGTTCAGAGCTTC
+GAGCTTCTGGACTTTTCGGATAGGCTCTAAG
+AGGGATTTGAACCCTCGACCTCGTCCTGATT
+ATGCCTAGATTAGCATTAGAGATACTTGACC
+AGAATGAAGATAATAAAATCTGATTCAGGCG
+CGTTCAGAGCTTCTGGACTTTTCGGATAGGC
+TAACGTTCAGAGCTTCTGGACTTTTCGGATA
+TGGCTAATAAATTTCAAGAAGCCCCGGGAGG
+GATAATAAAATCTGATTCAGGCGACGGATGC
+TGTGCATGGATAACGTTCAGAGCTTCTGGAC
+CAGGCGACGGATGCCTAGATTAGCATTAGAG
+TTGGCTAATAAATTTCAAGAAGCCCCGGGAG
+GGGATTTGAACCCTCGACCTCGTCCTGATTG
+CGCATGTGCATGGATAACGTTCAGAGCTTCT
+TGATCCCCTACGCTAACTTGGCTAATAAATT
+CTTCTGGACTTTTCGGATAGGCTCTAAGAAT
+TGCATGGATAACGTTCAGAGCTTCTGGACTT
+CTAAGAATGAAGATAATAAAATCTGATTCAG
+AGATACTTGACCATCCGCCCTGGTGTGATCC
+ATGGATAACGTTCAGAGCTTCTGGACTTTTC
+TCGGATAGGCTCTAAGAATGAAGATAATAAA
+CCGCCCTGGTGTGATCCCCTACGCTAACTTG
+CCTGATTGTCCTGCATTCAGTGCCGGTTACC
+ATTTGAACCCTCGACCTCGTCCTGATTGTCC
+TTGTCCTGCATTCAGTGCCGGTTACCAAGGA
+ATAAATTTCAAGAAGCCCCGGGAGGGATTTG
+AATGAAGATAATAAAATCTGATTCAGGCGAC
+TTCAGAGCTTCTGGACTTTTCGGATAGGCTC
+GGATTTGAACCCTCGACCTCGTCCTGATTGT
+CTAGATTAGCATTAGAGATACTTGACCATCC
+ATACTTGACCATCCGCCCTGGTGTGATCCCC
+GAAGCCCCGGGAGGGATTTGAACCCTCGACC
+TCAGAGCTTCTGGACTTTTCGGATAGGCTCT
+AATAAATTTCAAGAAGCCCCGGGAGGGATTT
+ATAATAAAATCTGATTCAGGCGACGGATGCC
+CCTAGATTAGCATTAGAGATACTTGACCATC
+TTCGCATGTGCATGGATAACGTTCAGAGCTT
+GGCGACGGATGCCTAGATTAGCATTAGAGAT
+CATGGATAACGTTCAGAGCTTCTGGACTTTT
+TCCTGCATTCAGTGCCGGTTACCAAGGACGC
+TTCAAGAAGCCCCGGGAGGGATTTGAACCCT

data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 ADDED

@@ -0,0 +1,220 @@
+CTCTTCTGGATTCCAATATATTCCCCAGAAA
+TATTCCCCAGAAATTCTTTATGTGGTTCAAA
+TTTATGTGGTTCAAAGAGCTCTTCTATACTG
+ATTCTTTATGTGGTTCAAAGAGCTCTTCTAT
+TTCTATACTGCTCTCTATTATCTGGGTATCA
+TGAGTTCGTTGATTGGTATAACAATCGACCT
+AAACTGGATGAACTATAGGGGATATGCCCAT
+AACTGGATGAACTATAGGGGATATGCCCATT
+TATGTGGTTCAAAGAGCTCTTCTATACTGCT
+GAACTATAGGGGATATGCCCATTACTCTTCT
+TCTATTATCTGGGTATCACCAAGCTCACTAA
+AACAAAAGAAATCTGGATAAACTGGATGAAC
+TTGAAACAAAAGAAATCTGGATAAACTGGAT
+CTATACTGCTCTCTATTATCTGGGTATCACC
+ACCTCATGGAAGCCTTAATTTTAAGGAACTT
+CTGGATAAACTGGATGAACTATAGGGGATAT
+TCTCTATTATCTGGGTATCACCAAGCTCACT
+AGCCTTAATTTTAAGGAACTTGAAACAAAAG
+CCGCAGATTCAGGAAATCCTTCTCCAGCTTT
+AATATATTCCCCAGAAATTCTTTATGTGGTT
+TCATGGAAGCCTTAATTTTAAGGAACTTGAA
+AAATCCTTCTCCAGCTTTGATGAGTTCGTTG
+CGACCTCATGGAAGCCTTAATTTTAAGGAAC
+AATTCTTTATGTGGTTCAAAGAGCTCTTCTA
+TAAGGAACTTGAAACAAAAGAAATCTGGATA
+CTTAATTTTAAGGAACTTGAAACAAAAGAAA
+AAATTCTTTATGTGGTTCAAAGAGCTCTTCT
+TCCAGCTTTGATGAGTTCGTTGATTGGTATA
+CAGGAAATCCTTCTCCAGCTTTGATGAGTTC
+GGATGAACTATAGGGGATATGCCCATTACTC
+TTTGATGAGTTCGTTGATTGGTATAACAATC
+ATAAACTGGATGAACTATAGGGGATATGCCC
+TTGATGAGTTCGTTGATTGGTATAACAATCG
+CAATCGACCTCATGGAAGCCTTAATTTTAAG
+CAGAAATTCTTTATGTGGTTCAAAGAGCTCT
+CTTTGATGAGTTCGTTGATTGGTATAACAAT
+TTCAGGAAATCCTTCTCCAGCTTTGATGAGT
+TAAACTGGATGAACTATAGGGGATATGCCCA
+ATGAGTTCGTTGATTGGTATAACAATCGACC
+CCTTAATTTTAAGGAACTTGAAACAAAAGAA
+TGATGAGTTCGTTGATTGGTATAACAATCGA
+AATCCTTCTCCAGCTTTGATGAGTTCGTTGA
+TCGTTGATTGGTATAACAATCGACCTCATGG
+TAGGGGATATGCCCATTACTCTTCTGGATTC
+AAGGAACTTGAAACAAAAGAAATCTGGATAA
+GTTCGTTGATTGGTATAACAATCGACCTCAT
+CGTTGATTGGTATAACAATCGACCTCATGGA
+GGAAGCCTTAATTTTAAGGAACTTGAAACAA
+AGGGGATATGCCCATTACTCTTCTGGATTCC
+ATACTGCTCTCTATTATCTGGGTATCACCAA
+CTGGATTCCAATATATTCCCCAGAAATTCTT
+GGGATATGCCCATTACTCTTCTGGATTCCAA
+TTGATTGGTATAACAATCGACCTCATGGAAG
+AAATCTGGATAAACTGGATGAACTATAGGGG
+TAATTTTAAGGAACTTGAAACAAAAGAAATC
+ATGAACTATAGGGGATATGCCCATTACTCTT
+TAACAATCGACCTCATGGAAGCCTTAATTTT
+TTCTCCAGCTTTGATGAGTTCGTTGATTGGT
+TCTTTATGTGGTTCAAAGAGCTCTTCTATAC
+TACTGCTCTCTATTATCTGGGTATCACCAAG
+ACAAAAGAAATCTGGATAAACTGGATGAACT
+ACTATAGGGGATATGCCCATTACTCTTCTGG
+GTTCAAAGAGCTCTTCTATACTGCTCTCTAT
+ATATGCCCATTACTCTTCTGGATTCCAATAT
+ATCTGGGTATCACCAAGCTCACTAATCTTCA
+TTCGTTGATTGGTATAACAATCGACCTCATG
+CTGGATGAACTATAGGGGATATGCCCATTAC
+CAAAAGAAATCTGGATAAACTGGATGAACTA
+TCTCCAGCTTTGATGAGTTCGTTGATTGGTA
+GAGTTCGTTGATTGGTATAACAATCGACCTC
+GATTCCAATATATTCCCCAGAAATTCTTTAT
+TACTCTTCTGGATTCCAATATATTCCCCAGA
+ATATATTCCCCAGAAATTCTTTATGTGGTTC
+ATTTTAAGGAACTTGAAACAAAAGAAATCTG
+TATAGGGGATATGCCCATTACTCTTCTGGAT
+GGATTCCAATATATTCCCCAGAAATTCTTTA
+CGCAGATTCAGGAAATCCTTCTCCAGCTTTG
+ATGTGGTTCAAAGAGCTCTTCTATACTGCTC
+AAGAAATCTGGATAAACTGGATGAACTATAG
+TTGGTATAACAATCGACCTCATGGAAGCCTT
+CAAAGAGCTCTTCTATACTGCTCTCTATTAT
+TTCAAAGAGCTCTTCTATACTGCTCTCTATT
+GAAGCCTTAATTTTAAGGAACTTGAAACAAA
+GCCTTAATTTTAAGGAACTTGAAACAAAAGA
+GCAGATTCAGGAAATCCTTCTCCAGCTTTGA
+TTAATTTTAAGGAACTTGAAACAAAAGAAAT
+GGAAATCCTTCTCCAGCTTTGATGAGTTCGT
+TGGATGAACTATAGGGGATATGCCCATTACT
+TTACTCTTCTGGATTCCAATATATTCCCCAG
+AATCGACCTCATGGAAGCCTTAATTTTAAGG
+GATATGCCCATTACTCTTCTGGATTCCAATA
+TCCAATATATTCCCCAGAAATTCTTTATGTG
+ATTATCTGGGTATCACCAAGCTCACTAATCT
+GAGCTCTTCTATACTGCTCTCTATTATCTGG
+CTATTATCTGGGTATCACCAAGCTCACTAAT
+CCCCAGAAATTCTTTATGTGGTTCAAAGAGC
+TGCCCATTACTCTTCTGGATTCCAATATATT
+TTCCAATATATTCCCCAGAAATTCTTTATGT
+AAAGAGCTCTTCTATACTGCTCTCTATTATC
+CTGCTCTCTATTATCTGGGTATCACCAAGCT
+TCTGGGTATCACCAAGCTCACTAATCTTCAT
+CTTTATGTGGTTCAAAGAGCTCTTCTATACT
+TGATTGGTATAACAATCGACCTCATGGAAGC
+TGGATTCCAATATATTCCCCAGAAATTCTTT
+GGTTCAAAGAGCTCTTCTATACTGCTCTCTA
+GGAACTTGAAACAAAAGAAATCTGGATAAAC
+GATTGGTATAACAATCGACCTCATGGAAGCC
+GCTCTTCTATACTGCTCTCTATTATCTGGGT
+ACTGCTCTCTATTATCTGGGTATCACCAAGC
+AAGCCTTAATTTTAAGGAACTTGAAACAAAA
+GCCCATTACTCTTCTGGATTCCAATATATTC
+CCTTCTCCAGCTTTGATGAGTTCGTTGATTG
+TATTATCTGGGTATCACCAAGCTCACTAATC
+CATTACTCTTCTGGATTCCAATATATTCCCC
+AAACAAAAGAAATCTGGATAAACTGGATGAA
+GAAATCTGGATAAACTGGATGAACTATAGGG
+ACTCTTCTGGATTCCAATATATTCCCCAGAA
+GAAATCCTTCTCCAGCTTTGATGAGTTCGTT
+TCTATACTGCTCTCTATTATCTGGGTATCAC
+TGTGGTTCAAAGAGCTCTTCTATACTGCTCT
+CAGCTTTGATGAGTTCGTTGATTGGTATAAC
+TCGACCTCATGGAAGCCTTAATTTTAAGGAA
+CCAATATATTCCCCAGAAATTCTTTATGTGG
+AAGAGCTCTTCTATACTGCTCTCTATTATCT
+AAAAGAAATCTGGATAAACTGGATGAACTAT
+ATAGGGGATATGCCCATTACTCTTCTGGATT
+TCTTCTGGATTCCAATATATTCCCCAGAAAT
+AAAGAAATCTGGATAAACTGGATGAACTATA
+GAACTTGAAACAAAAGAAATCTGGATAAACT
+TTCCCCAGAAATTCTTTATGTGGTTCAAAGA
+TTTTAAGGAACTTGAAACAAAAGAAATCTGG
+ATAACAATCGACCTCATGGAAGCCTTAATTT
+ACTGGATGAACTATAGGGGATATGCCCATTA
+TTATGTGGTTCAAAGAGCTCTTCTATACTGC
+ATATTCCCCAGAAATTCTTTATGTGGTTCAA
+TTATCTGGGTATCACCAAGCTCACTAATCTT
+TATGCCCATTACTCTTCTGGATTCCAATATA
+GACCTCATGGAAGCCTTAATTTTAAGGAACT
+TATAACAATCGACCTCATGGAAGCCTTAATT
+CTTGAAACAAAAGAAATCTGGATAAACTGGA
+AGCTCTTCTATACTGCTCTCTATTATCTGGG
+TATATTCCCCAGAAATTCTTTATGTGGTTCA
+GGATATGCCCATTACTCTTCTGGATTCCAAT
+CTCTTCTATACTGCTCTCTATTATCTGGGTA
+AACAATCGACCTCATGGAAGCCTTAATTTTA
+ATCCTTCTCCAGCTTTGATGAGTTCGTTGAT
+TCTGGATTCCAATATATTCCCCAGAAATTCT
+AGGAACTTGAAACAAAAGAAATCTGGATAAA
+ATCTGGATAAACTGGATGAACTATAGGGGAT
+ATTCCCCAGAAATTCTTTATGTGGTTCAAAG
+TCCTTCTCCAGCTTTGATGAGTTCGTTGATT
+CCCAGAAATTCTTTATGTGGTTCAAAGAGCT
+TGCTCTCTATTATCTGGGTATCACCAAGCTC
+GCTCTCTATTATCTGGGTATCACCAAGCTCA
+AACTTGAAACAAAAGAAATCTGGATAAACTG
+ACTTGAAACAAAAGAAATCTGGATAAACTGG
+ATTGGTATAACAATCGACCTCATGGAAGCCT
+TATCTGGGTATCACCAAGCTCACTAATCTTC
+AGCTTTGATGAGTTCGTTGATTGGTATAACA
+ACAATCGACCTCATGGAAGCCTTAATTTTAA
+CTTCTCCAGCTTTGATGAGTTCGTTGATTGG
+TTTAAGGAACTTGAAACAAAAGAAATCTGGA
+CTCTCTATTATCTGGGTATCACCAAGCTCAC
+TGAACTATAGGGGATATGCCCATTACTCTTC
+GATGAGTTCGTTGATTGGTATAACAATCGAC
+CCATTACTCTTCTGGATTCCAATATATTCCC
+TTCTGGATTCCAATATATTCCCCAGAAATTC
+TCCCCAGAAATTCTTTATGTGGTTCAAAGAG
+ATTCAGGAAATCCTTCTCCAGCTTTGATGAG
+ATGCCCATTACTCTTCTGGATTCCAATATAT
+ATTCCAATATATTCCCCAGAAATTCTTTATG
+GATTCAGGAAATCCTTCTCCAGCTTTGATGA
+AATTTTAAGGAACTTGAAACAAAAGAAATCT
+CTCCAGCTTTGATGAGTTCGTTGATTGGTAT
+ATCGACCTCATGGAAGCCTTAATTTTAAGGA
+GTTGATTGGTATAACAATCGACCTCATGGAA
+AGGAAATCCTTCTCCAGCTTTGATGAGTTCG
+GATGAACTATAGGGGATATGCCCATTACTCT
+GGGGATATGCCCATTACTCTTCTGGATTCCA
+GTGGTTCAAAGAGCTCTTCTATACTGCTCTC
+CCCATTACTCTTCTGGATTCCAATATATTCC
+CCAGAAATTCTTTATGTGGTTCAAAGAGCTC
+AGAAATCTGGATAAACTGGATGAACTATAGG
+AATCTGGATAAACTGGATGAACTATAGGGGA
+TGGTATAACAATCGACCTCATGGAAGCCTTA
+TATACTGCTCTCTATTATCTGGGTATCACCA
+CCTCATGGAAGCCTTAATTTTAAGGAACTTG
+TGGTTCAAAGAGCTCTTCTATACTGCTCTCT
+AGAAATTCTTTATGTGGTTCAAAGAGCTCTT
+CTTCTATACTGCTCTCTATTATCTGGGTATC
+TCAGGAAATCCTTCTCCAGCTTTGATGAGTT
+TCTTCTATACTGCTCTCTATTATCTGGGTAT
+TGGAAGCCTTAATTTTAAGGAACTTGAAACA
+ATGGAAGCCTTAATTTTAAGGAACTTGAAAC
+CAGATTCAGGAAATCCTTCTCCAGCTTTGAT
+TTAAGGAACTTGAAACAAAAGAAATCTGGAT
+ATTACTCTTCTGGATTCCAATATATTCCCCA
+CATGGAAGCCTTAATTTTAAGGAACTTGAAA
+GAAATTCTTTATGTGGTTCAAAGAGCTCTTC
+GATAAACTGGATGAACTATAGGGGATATGCC
+GGATAAACTGGATGAACTATAGGGGATATGC
+GTATAACAATCGACCTCATGGAAGCCTTAAT
+GAAACAAAAGAAATCTGGATAAACTGGATGA
+AACTATAGGGGATATGCCCATTACTCTTCTG
+CCAGCTTTGATGAGTTCGTTGATTGGTATAA
+CAATATATTCCCCAGAAATTCTTTATGTGGT
+TTCTTTATGTGGTTCAAAGAGCTCTTCTATA
+AGATTCAGGAAATCCTTCTCCAGCTTTGATG
+GCTTTGATGAGTTCGTTGATTGGTATAACAA
+CTATAGGGGATATGCCCATTACTCTTCTGGA
+TCAAAGAGCTCTTCTATACTGCTCTCTATTA
+AGTTCGTTGATTGGTATAACAATCGACCTCA
+GGTATAACAATCGACCTCATGGAAGCCTTAA
+CTCATGGAAGCCTTAATTTTAAGGAACTTGA
+CTTCTGGATTCCAATATATTCCCCAGAAATT
+TCTGGATAAACTGGATGAACTATAGGGGATA
+TGGATAAACTGGATGAACTATAGGGGATATG
+CTCTATTATCTGGGTATCACCAAGCTCACTA
+TGAAACAAAAGAAATCTGGATAAACTGGATG
+AGAGCTCTTCTATACTGCTCTCTATTATCTG