finishm 0.0.1
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
- data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
- data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
- data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
- data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
- data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
- data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- 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
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- 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
@@ -0,0 +1,500 @@
|
|
1
|
+
/* gzappend -- command to append to a gzip file
|
2
|
+
|
3
|
+
Copyright (C) 2003 Mark Adler, all rights reserved
|
4
|
+
version 1.1, 4 Nov 2003
|
5
|
+
|
6
|
+
This software is provided 'as-is', without any express or implied
|
7
|
+
warranty. In no event will the author be held liable for any damages
|
8
|
+
arising from the use of this software.
|
9
|
+
|
10
|
+
Permission is granted to anyone to use this software for any purpose,
|
11
|
+
including commercial applications, and to alter it and redistribute it
|
12
|
+
freely, subject to the following restrictions:
|
13
|
+
|
14
|
+
1. The origin of this software must not be misrepresented; you must not
|
15
|
+
claim that you wrote the original software. If you use this software
|
16
|
+
in a product, an acknowledgment in the product documentation would be
|
17
|
+
appreciated but is not required.
|
18
|
+
2. Altered source versions must be plainly marked as such, and must not be
|
19
|
+
misrepresented as being the original software.
|
20
|
+
3. This notice may not be removed or altered from any source distribution.
|
21
|
+
|
22
|
+
Mark Adler madler@alumni.caltech.edu
|
23
|
+
*/
|
24
|
+
|
25
|
+
/*
|
26
|
+
* Change history:
|
27
|
+
*
|
28
|
+
* 1.0 19 Oct 2003 - First version
|
29
|
+
* 1.1 4 Nov 2003 - Expand and clarify some comments and notes
|
30
|
+
* - Add version and copyright to help
|
31
|
+
* - Send help to stdout instead of stderr
|
32
|
+
* - Add some preemptive typecasts
|
33
|
+
* - Add L to constants in lseek() calls
|
34
|
+
* - Remove some debugging information in error messages
|
35
|
+
* - Use new data_type definition for zlib 1.2.1
|
36
|
+
* - Simplfy and unify file operations
|
37
|
+
* - Finish off gzip file in gztack()
|
38
|
+
* - Use deflatePrime() instead of adding empty blocks
|
39
|
+
* - Keep gzip file clean on appended file read errors
|
40
|
+
* - Use in-place rotate instead of auxiliary buffer
|
41
|
+
* (Why you ask? Because it was fun to write!)
|
42
|
+
*/
|
43
|
+
|
44
|
+
/*
|
45
|
+
gzappend takes a gzip file and appends to it, compressing files from the
|
46
|
+
command line or data from stdin. The gzip file is written to directly, to
|
47
|
+
avoid copying that file, in case it's large. Note that this results in the
|
48
|
+
unfriendly behavior that if gzappend fails, the gzip file is corrupted.
|
49
|
+
|
50
|
+
This program was written to illustrate the use of the new Z_BLOCK option of
|
51
|
+
zlib 1.2.x's inflate() function. This option returns from inflate() at each
|
52
|
+
block boundary to facilitate locating and modifying the last block bit at
|
53
|
+
the start of the final deflate block. Also whether using Z_BLOCK or not,
|
54
|
+
another required feature of zlib 1.2.x is that inflate() now provides the
|
55
|
+
number of unusued bits in the last input byte used. gzappend will not work
|
56
|
+
with versions of zlib earlier than 1.2.1.
|
57
|
+
|
58
|
+
gzappend first decompresses the gzip file internally, discarding all but
|
59
|
+
the last 32K of uncompressed data, and noting the location of the last block
|
60
|
+
bit and the number of unused bits in the last byte of the compressed data.
|
61
|
+
The gzip trailer containing the CRC-32 and length of the uncompressed data
|
62
|
+
is verified. This trailer will be later overwritten.
|
63
|
+
|
64
|
+
Then the last block bit is cleared by seeking back in the file and rewriting
|
65
|
+
the byte that contains it. Seeking forward, the last byte of the compressed
|
66
|
+
data is saved along with the number of unused bits to initialize deflate.
|
67
|
+
|
68
|
+
A deflate process is initialized, using the last 32K of the uncompressed
|
69
|
+
data from the gzip file to initialize the dictionary. If the total
|
70
|
+
uncompressed data was less than 32K, then all of it is used to initialize
|
71
|
+
the dictionary. The deflate output bit buffer is also initialized with the
|
72
|
+
last bits from the original deflate stream. From here on, the data to
|
73
|
+
append is simply compressed using deflate, and written to the gzip file.
|
74
|
+
When that is complete, the new CRC-32 and uncompressed length are written
|
75
|
+
as the trailer of the gzip file.
|
76
|
+
*/
|
77
|
+
|
78
|
+
#include <stdio.h>
|
79
|
+
#include <stdlib.h>
|
80
|
+
#include <string.h>
|
81
|
+
#include <fcntl.h>
|
82
|
+
#include <unistd.h>
|
83
|
+
#include "zlib.h"
|
84
|
+
|
85
|
+
#define local static
|
86
|
+
#define LGCHUNK 14
|
87
|
+
#define CHUNK (1U << LGCHUNK)
|
88
|
+
#define DSIZE 32768U
|
89
|
+
|
90
|
+
/* print an error message and terminate with extreme prejudice */
|
91
|
+
local void bye(char *msg1, char *msg2)
|
92
|
+
{
|
93
|
+
fprintf(stderr, "gzappend error: %s%s\n", msg1, msg2);
|
94
|
+
exit(1);
|
95
|
+
}
|
96
|
+
|
97
|
+
/* return the greatest common divisor of a and b using Euclid's algorithm,
|
98
|
+
modified to be fast when one argument much greater than the other, and
|
99
|
+
coded to avoid unnecessary swapping */
|
100
|
+
local unsigned gcd(unsigned a, unsigned b)
|
101
|
+
{
|
102
|
+
unsigned c;
|
103
|
+
|
104
|
+
while (a && b)
|
105
|
+
if (a > b) {
|
106
|
+
c = b;
|
107
|
+
while (a - c >= c)
|
108
|
+
c <<= 1;
|
109
|
+
a -= c;
|
110
|
+
}
|
111
|
+
else {
|
112
|
+
c = a;
|
113
|
+
while (b - c >= c)
|
114
|
+
c <<= 1;
|
115
|
+
b -= c;
|
116
|
+
}
|
117
|
+
return a + b;
|
118
|
+
}
|
119
|
+
|
120
|
+
/* rotate list[0..len-1] left by rot positions, in place */
|
121
|
+
local void rotate(unsigned char *list, unsigned len, unsigned rot)
|
122
|
+
{
|
123
|
+
unsigned char tmp;
|
124
|
+
unsigned cycles;
|
125
|
+
unsigned char *start, *last, *to, *from;
|
126
|
+
|
127
|
+
/* normalize rot and handle degenerate cases */
|
128
|
+
if (len < 2) return;
|
129
|
+
if (rot >= len) rot %= len;
|
130
|
+
if (rot == 0) return;
|
131
|
+
|
132
|
+
/* pointer to last entry in list */
|
133
|
+
last = list + (len - 1);
|
134
|
+
|
135
|
+
/* do simple left shift by one */
|
136
|
+
if (rot == 1) {
|
137
|
+
tmp = *list;
|
138
|
+
memcpy(list, list + 1, len - 1);
|
139
|
+
*last = tmp;
|
140
|
+
return;
|
141
|
+
}
|
142
|
+
|
143
|
+
/* do simple right shift by one */
|
144
|
+
if (rot == len - 1) {
|
145
|
+
tmp = *last;
|
146
|
+
memmove(list + 1, list, len - 1);
|
147
|
+
*list = tmp;
|
148
|
+
return;
|
149
|
+
}
|
150
|
+
|
151
|
+
/* otherwise do rotate as a set of cycles in place */
|
152
|
+
cycles = gcd(len, rot); /* number of cycles */
|
153
|
+
do {
|
154
|
+
start = from = list + cycles; /* start index is arbitrary */
|
155
|
+
tmp = *from; /* save entry to be overwritten */
|
156
|
+
for (;;) {
|
157
|
+
to = from; /* next step in cycle */
|
158
|
+
from += rot; /* go right rot positions */
|
159
|
+
if (from > last) from -= len; /* (pointer better not wrap) */
|
160
|
+
if (from == start) break; /* all but one shifted */
|
161
|
+
*to = *from; /* shift left */
|
162
|
+
}
|
163
|
+
*to = tmp; /* complete the circle */
|
164
|
+
} while (--cycles);
|
165
|
+
}
|
166
|
+
|
167
|
+
/* structure for gzip file read operations */
|
168
|
+
typedef struct {
|
169
|
+
int fd; /* file descriptor */
|
170
|
+
int size; /* 1 << size is bytes in buf */
|
171
|
+
unsigned left; /* bytes available at next */
|
172
|
+
unsigned char *buf; /* buffer */
|
173
|
+
unsigned char *next; /* next byte in buffer */
|
174
|
+
char *name; /* file name for error messages */
|
175
|
+
} file;
|
176
|
+
|
177
|
+
/* reload buffer */
|
178
|
+
local int readin(file *in)
|
179
|
+
{
|
180
|
+
int len;
|
181
|
+
|
182
|
+
len = read(in->fd, in->buf, 1 << in->size);
|
183
|
+
if (len == -1) bye("error reading ", in->name);
|
184
|
+
in->left = (unsigned)len;
|
185
|
+
in->next = in->buf;
|
186
|
+
return len;
|
187
|
+
}
|
188
|
+
|
189
|
+
/* read from file in, exit if end-of-file */
|
190
|
+
local int readmore(file *in)
|
191
|
+
{
|
192
|
+
if (readin(in) == 0) bye("unexpected end of ", in->name);
|
193
|
+
return 0;
|
194
|
+
}
|
195
|
+
|
196
|
+
#define read1(in) (in->left == 0 ? readmore(in) : 0, \
|
197
|
+
in->left--, *(in->next)++)
|
198
|
+
|
199
|
+
/* skip over n bytes of in */
|
200
|
+
local void skip(file *in, unsigned n)
|
201
|
+
{
|
202
|
+
unsigned bypass;
|
203
|
+
|
204
|
+
if (n > in->left) {
|
205
|
+
n -= in->left;
|
206
|
+
bypass = n & ~((1U << in->size) - 1);
|
207
|
+
if (bypass) {
|
208
|
+
if (lseek(in->fd, (off_t)bypass, SEEK_CUR) == -1)
|
209
|
+
bye("seeking ", in->name);
|
210
|
+
n -= bypass;
|
211
|
+
}
|
212
|
+
readmore(in);
|
213
|
+
if (n > in->left)
|
214
|
+
bye("unexpected end of ", in->name);
|
215
|
+
}
|
216
|
+
in->left -= n;
|
217
|
+
in->next += n;
|
218
|
+
}
|
219
|
+
|
220
|
+
/* read a four-byte unsigned integer, little-endian, from in */
|
221
|
+
unsigned long read4(file *in)
|
222
|
+
{
|
223
|
+
unsigned long val;
|
224
|
+
|
225
|
+
val = read1(in);
|
226
|
+
val += (unsigned)read1(in) << 8;
|
227
|
+
val += (unsigned long)read1(in) << 16;
|
228
|
+
val += (unsigned long)read1(in) << 24;
|
229
|
+
return val;
|
230
|
+
}
|
231
|
+
|
232
|
+
/* skip over gzip header */
|
233
|
+
local void gzheader(file *in)
|
234
|
+
{
|
235
|
+
int flags;
|
236
|
+
unsigned n;
|
237
|
+
|
238
|
+
if (read1(in) != 31 || read1(in) != 139) bye(in->name, " not a gzip file");
|
239
|
+
if (read1(in) != 8) bye("unknown compression method in", in->name);
|
240
|
+
flags = read1(in);
|
241
|
+
if (flags & 0xe0) bye("unknown header flags set in", in->name);
|
242
|
+
skip(in, 6);
|
243
|
+
if (flags & 4) {
|
244
|
+
n = read1(in);
|
245
|
+
n += (unsigned)(read1(in)) << 8;
|
246
|
+
skip(in, n);
|
247
|
+
}
|
248
|
+
if (flags & 8) while (read1(in) != 0) ;
|
249
|
+
if (flags & 16) while (read1(in) != 0) ;
|
250
|
+
if (flags & 2) skip(in, 2);
|
251
|
+
}
|
252
|
+
|
253
|
+
/* decompress gzip file "name", return strm with a deflate stream ready to
|
254
|
+
continue compression of the data in the gzip file, and return a file
|
255
|
+
descriptor pointing to where to write the compressed data -- the deflate
|
256
|
+
stream is initialized to compress using level "level" */
|
257
|
+
local int gzscan(char *name, z_stream *strm, int level)
|
258
|
+
{
|
259
|
+
int ret, lastbit, left, full;
|
260
|
+
unsigned have;
|
261
|
+
unsigned long crc, tot;
|
262
|
+
unsigned char *window;
|
263
|
+
off_t lastoff, end;
|
264
|
+
file gz;
|
265
|
+
|
266
|
+
/* open gzip file */
|
267
|
+
gz.name = name;
|
268
|
+
gz.fd = open(name, O_RDWR, 0);
|
269
|
+
if (gz.fd == -1) bye("cannot open ", name);
|
270
|
+
gz.buf = malloc(CHUNK);
|
271
|
+
if (gz.buf == NULL) bye("out of memory", "");
|
272
|
+
gz.size = LGCHUNK;
|
273
|
+
gz.left = 0;
|
274
|
+
|
275
|
+
/* skip gzip header */
|
276
|
+
gzheader(&gz);
|
277
|
+
|
278
|
+
/* prepare to decompress */
|
279
|
+
window = malloc(DSIZE);
|
280
|
+
if (window == NULL) bye("out of memory", "");
|
281
|
+
strm->zalloc = Z_NULL;
|
282
|
+
strm->zfree = Z_NULL;
|
283
|
+
strm->opaque = Z_NULL;
|
284
|
+
ret = inflateInit2(strm, -15);
|
285
|
+
if (ret != Z_OK) bye("out of memory", " or library mismatch");
|
286
|
+
|
287
|
+
/* decompress the deflate stream, saving append information */
|
288
|
+
lastbit = 0;
|
289
|
+
lastoff = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
|
290
|
+
left = 0;
|
291
|
+
strm->avail_in = gz.left;
|
292
|
+
strm->next_in = gz.next;
|
293
|
+
crc = crc32(0L, Z_NULL, 0);
|
294
|
+
have = full = 0;
|
295
|
+
do {
|
296
|
+
/* if needed, get more input */
|
297
|
+
if (strm->avail_in == 0) {
|
298
|
+
readmore(&gz);
|
299
|
+
strm->avail_in = gz.left;
|
300
|
+
strm->next_in = gz.next;
|
301
|
+
}
|
302
|
+
|
303
|
+
/* set up output to next available section of sliding window */
|
304
|
+
strm->avail_out = DSIZE - have;
|
305
|
+
strm->next_out = window + have;
|
306
|
+
|
307
|
+
/* inflate and check for errors */
|
308
|
+
ret = inflate(strm, Z_BLOCK);
|
309
|
+
if (ret == Z_STREAM_ERROR) bye("internal stream error!", "");
|
310
|
+
if (ret == Z_MEM_ERROR) bye("out of memory", "");
|
311
|
+
if (ret == Z_DATA_ERROR)
|
312
|
+
bye("invalid compressed data--format violated in", name);
|
313
|
+
|
314
|
+
/* update crc and sliding window pointer */
|
315
|
+
crc = crc32(crc, window + have, DSIZE - have - strm->avail_out);
|
316
|
+
if (strm->avail_out)
|
317
|
+
have = DSIZE - strm->avail_out;
|
318
|
+
else {
|
319
|
+
have = 0;
|
320
|
+
full = 1;
|
321
|
+
}
|
322
|
+
|
323
|
+
/* process end of block */
|
324
|
+
if (strm->data_type & 128) {
|
325
|
+
if (strm->data_type & 64)
|
326
|
+
left = strm->data_type & 0x1f;
|
327
|
+
else {
|
328
|
+
lastbit = strm->data_type & 0x1f;
|
329
|
+
lastoff = lseek(gz.fd, 0L, SEEK_CUR) - strm->avail_in;
|
330
|
+
}
|
331
|
+
}
|
332
|
+
} while (ret != Z_STREAM_END);
|
333
|
+
inflateEnd(strm);
|
334
|
+
gz.left = strm->avail_in;
|
335
|
+
gz.next = strm->next_in;
|
336
|
+
|
337
|
+
/* save the location of the end of the compressed data */
|
338
|
+
end = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
|
339
|
+
|
340
|
+
/* check gzip trailer and save total for deflate */
|
341
|
+
if (crc != read4(&gz))
|
342
|
+
bye("invalid compressed data--crc mismatch in ", name);
|
343
|
+
tot = strm->total_out;
|
344
|
+
if ((tot & 0xffffffffUL) != read4(&gz))
|
345
|
+
bye("invalid compressed data--length mismatch in", name);
|
346
|
+
|
347
|
+
/* if not at end of file, warn */
|
348
|
+
if (gz.left || readin(&gz))
|
349
|
+
fprintf(stderr,
|
350
|
+
"gzappend warning: junk at end of gzip file overwritten\n");
|
351
|
+
|
352
|
+
/* clear last block bit */
|
353
|
+
lseek(gz.fd, lastoff - (lastbit != 0), SEEK_SET);
|
354
|
+
if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
|
355
|
+
*gz.buf = (unsigned char)(*gz.buf ^ (1 << ((8 - lastbit) & 7)));
|
356
|
+
lseek(gz.fd, -1L, SEEK_CUR);
|
357
|
+
if (write(gz.fd, gz.buf, 1) != 1) bye("writing after seek to ", name);
|
358
|
+
|
359
|
+
/* if window wrapped, build dictionary from window by rotating */
|
360
|
+
if (full) {
|
361
|
+
rotate(window, DSIZE, have);
|
362
|
+
have = DSIZE;
|
363
|
+
}
|
364
|
+
|
365
|
+
/* set up deflate stream with window, crc, total_in, and leftover bits */
|
366
|
+
ret = deflateInit2(strm, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY);
|
367
|
+
if (ret != Z_OK) bye("out of memory", "");
|
368
|
+
deflateSetDictionary(strm, window, have);
|
369
|
+
strm->adler = crc;
|
370
|
+
strm->total_in = tot;
|
371
|
+
if (left) {
|
372
|
+
lseek(gz.fd, --end, SEEK_SET);
|
373
|
+
if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
|
374
|
+
deflatePrime(strm, 8 - left, *gz.buf);
|
375
|
+
}
|
376
|
+
lseek(gz.fd, end, SEEK_SET);
|
377
|
+
|
378
|
+
/* clean up and return */
|
379
|
+
free(window);
|
380
|
+
free(gz.buf);
|
381
|
+
return gz.fd;
|
382
|
+
}
|
383
|
+
|
384
|
+
/* append file "name" to gzip file gd using deflate stream strm -- if last
|
385
|
+
is true, then finish off the deflate stream at the end */
|
386
|
+
local void gztack(char *name, int gd, z_stream *strm, int last)
|
387
|
+
{
|
388
|
+
int fd, len, ret;
|
389
|
+
unsigned left;
|
390
|
+
unsigned char *in, *out;
|
391
|
+
|
392
|
+
/* open file to compress and append */
|
393
|
+
fd = 0;
|
394
|
+
if (name != NULL) {
|
395
|
+
fd = open(name, O_RDONLY, 0);
|
396
|
+
if (fd == -1)
|
397
|
+
fprintf(stderr, "gzappend warning: %s not found, skipping ...\n",
|
398
|
+
name);
|
399
|
+
}
|
400
|
+
|
401
|
+
/* allocate buffers */
|
402
|
+
in = fd == -1 ? NULL : malloc(CHUNK);
|
403
|
+
out = malloc(CHUNK);
|
404
|
+
if (out == NULL) bye("out of memory", "");
|
405
|
+
|
406
|
+
/* compress input file and append to gzip file */
|
407
|
+
do {
|
408
|
+
/* get more input */
|
409
|
+
len = fd == -1 ? 0 : read(fd, in, CHUNK);
|
410
|
+
if (len == -1) {
|
411
|
+
fprintf(stderr,
|
412
|
+
"gzappend warning: error reading %s, skipping rest ...\n",
|
413
|
+
name);
|
414
|
+
len = 0;
|
415
|
+
}
|
416
|
+
strm->avail_in = (unsigned)len;
|
417
|
+
strm->next_in = in;
|
418
|
+
if (len) strm->adler = crc32(strm->adler, in, (unsigned)len);
|
419
|
+
|
420
|
+
/* compress and write all available output */
|
421
|
+
do {
|
422
|
+
strm->avail_out = CHUNK;
|
423
|
+
strm->next_out = out;
|
424
|
+
ret = deflate(strm, last && len == 0 ? Z_FINISH : Z_NO_FLUSH);
|
425
|
+
left = CHUNK - strm->avail_out;
|
426
|
+
while (left) {
|
427
|
+
len = write(gd, out + CHUNK - strm->avail_out - left, left);
|
428
|
+
if (len == -1) bye("writing gzip file", "");
|
429
|
+
left -= (unsigned)len;
|
430
|
+
}
|
431
|
+
} while (strm->avail_out == 0 && ret != Z_STREAM_END);
|
432
|
+
} while (len != 0);
|
433
|
+
|
434
|
+
/* write trailer after last entry */
|
435
|
+
if (last) {
|
436
|
+
deflateEnd(strm);
|
437
|
+
out[0] = (unsigned char)(strm->adler);
|
438
|
+
out[1] = (unsigned char)(strm->adler >> 8);
|
439
|
+
out[2] = (unsigned char)(strm->adler >> 16);
|
440
|
+
out[3] = (unsigned char)(strm->adler >> 24);
|
441
|
+
out[4] = (unsigned char)(strm->total_in);
|
442
|
+
out[5] = (unsigned char)(strm->total_in >> 8);
|
443
|
+
out[6] = (unsigned char)(strm->total_in >> 16);
|
444
|
+
out[7] = (unsigned char)(strm->total_in >> 24);
|
445
|
+
len = 8;
|
446
|
+
do {
|
447
|
+
ret = write(gd, out + 8 - len, len);
|
448
|
+
if (ret == -1) bye("writing gzip file", "");
|
449
|
+
len -= ret;
|
450
|
+
} while (len);
|
451
|
+
close(gd);
|
452
|
+
}
|
453
|
+
|
454
|
+
/* clean up and return */
|
455
|
+
free(out);
|
456
|
+
if (in != NULL) free(in);
|
457
|
+
if (fd > 0) close(fd);
|
458
|
+
}
|
459
|
+
|
460
|
+
/* process the compression level option if present, scan the gzip file, and
|
461
|
+
append the specified files, or append the data from stdin if no other file
|
462
|
+
names are provided on the command line -- the gzip file must be writable
|
463
|
+
and seekable */
|
464
|
+
int main(int argc, char **argv)
|
465
|
+
{
|
466
|
+
int gd, level;
|
467
|
+
z_stream strm;
|
468
|
+
|
469
|
+
/* ignore command name */
|
470
|
+
argv++;
|
471
|
+
|
472
|
+
/* provide usage if no arguments */
|
473
|
+
if (*argv == NULL) {
|
474
|
+
printf("gzappend 1.1 (4 Nov 2003) Copyright (C) 2003 Mark Adler\n");
|
475
|
+
printf(
|
476
|
+
"usage: gzappend [-level] file.gz [ addthis [ andthis ... ]]\n");
|
477
|
+
return 0;
|
478
|
+
}
|
479
|
+
|
480
|
+
/* set compression level */
|
481
|
+
level = Z_DEFAULT_COMPRESSION;
|
482
|
+
if (argv[0][0] == '-') {
|
483
|
+
if (argv[0][1] < '0' || argv[0][1] > '9' || argv[0][2] != 0)
|
484
|
+
bye("invalid compression level", "");
|
485
|
+
level = argv[0][1] - '0';
|
486
|
+
if (*++argv == NULL) bye("no gzip file name after options", "");
|
487
|
+
}
|
488
|
+
|
489
|
+
/* prepare to append to gzip file */
|
490
|
+
gd = gzscan(*argv++, &strm, level);
|
491
|
+
|
492
|
+
/* append files on command line, or from stdin if none */
|
493
|
+
if (*argv == NULL)
|
494
|
+
gztack(NULL, gd, &strm, 1);
|
495
|
+
else
|
496
|
+
do {
|
497
|
+
gztack(*argv, gd, &strm, argv[1] == NULL);
|
498
|
+
} while (*++argv != NULL);
|
499
|
+
return 0;
|
500
|
+
}
|