RubyGems - finishm - Versions diffs - 0.0.1 - Mend

finishm 0.0.1

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
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -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
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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
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data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 ADDED

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