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.
- 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
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- 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
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and Chuck Walbourn <chuckw@kinesoft.com>
|
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43
|
+
asm code for Pentium Pro/PII, using the MASM syntax
|
|
44
|
+
|
|
45
|
+
masmx64/ by Gilles Vollant <info@winimage.com>
|
|
46
|
+
x86 64-bit (AMD64 and Intel EM64t) code for x64 assembler to
|
|
47
|
+
replace longest_match() and inflate_fast()
|
|
48
|
+
|
|
49
|
+
masmx86/ by Gilles Vollant <info@winimage.com>
|
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50
|
+
x86 asm code to replace longest_match() and inflate_fast(),
|
|
51
|
+
for Visual C++ and MASM
|
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52
|
+
|
|
53
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+
minizip/ by Gilles Vollant <info@winimage.com>
|
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54
|
+
Mini zip and unzip based on zlib
|
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+
See http://www.winimage.com/zLibDll/unzip.html
|
|
56
|
+
|
|
57
|
+
pascal/ by Bob Dellaca <bobdl@xtra.co.nz> et al.
|
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58
|
+
Support for Pascal
|
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59
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+
|
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60
|
+
puff/ by Mark Adler <madler@alumni.caltech.edu>
|
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61
|
+
Small, low memory usage inflate. Also serves to provide an
|
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62
|
+
unambiguous description of the deflate format.
|
|
63
|
+
|
|
64
|
+
testzlib/ by Gilles Vollant <info@winimage.com>
|
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65
|
+
Example of the use of zlib
|
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66
|
+
|
|
67
|
+
untgz/ by Pedro A. Aranda Gutierrez <paag@tid.es>
|
|
68
|
+
A very simple tar.gz file extractor using zlib
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69
|
+
|
|
70
|
+
vstudio/ by Gilles Vollant <info@winimage.com>
|
|
71
|
+
Building a minizip-enhanced zlib with Microsoft Visual Studio
|
|
@@ -0,0 +1,106 @@
|
|
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1
|
+
----------------------------------------------------------------
|
|
2
|
+
-- ZLib for Ada thick binding. --
|
|
3
|
+
-- --
|
|
4
|
+
-- Copyright (C) 2002-2004 Dmitriy Anisimkov --
|
|
5
|
+
-- --
|
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
|
7
|
+
----------------------------------------------------------------
|
|
8
|
+
--
|
|
9
|
+
-- $Id: buffer_demo.adb,v 1.3 2004/09/06 06:55:35 vagul Exp $
|
|
10
|
+
|
|
11
|
+
-- This demo program provided by Dr Steve Sangwine <sjs@essex.ac.uk>
|
|
12
|
+
--
|
|
13
|
+
-- Demonstration of a problem with Zlib-Ada (already fixed) when a buffer
|
|
14
|
+
-- of exactly the correct size is used for decompressed data, and the last
|
|
15
|
+
-- few bytes passed in to Zlib are checksum bytes.
|
|
16
|
+
|
|
17
|
+
-- This program compresses a string of text, and then decompresses the
|
|
18
|
+
-- compressed text into a buffer of the same size as the original text.
|
|
19
|
+
|
|
20
|
+
with Ada.Streams; use Ada.Streams;
|
|
21
|
+
with Ada.Text_IO;
|
|
22
|
+
|
|
23
|
+
with ZLib; use ZLib;
|
|
24
|
+
|
|
25
|
+
procedure Buffer_Demo is
|
|
26
|
+
EOL : Character renames ASCII.LF;
|
|
27
|
+
Text : constant String
|
|
28
|
+
:= "Four score and seven years ago our fathers brought forth," & EOL &
|
|
29
|
+
"upon this continent, a new nation, conceived in liberty," & EOL &
|
|
30
|
+
"and dedicated to the proposition that `all men are created equal'.";
|
|
31
|
+
|
|
32
|
+
Source : Stream_Element_Array (1 .. Text'Length);
|
|
33
|
+
for Source'Address use Text'Address;
|
|
34
|
+
|
|
35
|
+
begin
|
|
36
|
+
Ada.Text_IO.Put (Text);
|
|
37
|
+
Ada.Text_IO.New_Line;
|
|
38
|
+
Ada.Text_IO.Put_Line
|
|
39
|
+
("Uncompressed size : " & Positive'Image (Text'Length) & " bytes");
|
|
40
|
+
|
|
41
|
+
declare
|
|
42
|
+
Compressed_Data : Stream_Element_Array (1 .. Text'Length);
|
|
43
|
+
L : Stream_Element_Offset;
|
|
44
|
+
begin
|
|
45
|
+
Compress : declare
|
|
46
|
+
Compressor : Filter_Type;
|
|
47
|
+
I : Stream_Element_Offset;
|
|
48
|
+
begin
|
|
49
|
+
Deflate_Init (Compressor);
|
|
50
|
+
|
|
51
|
+
-- Compress the whole of T at once.
|
|
52
|
+
|
|
53
|
+
Translate (Compressor, Source, I, Compressed_Data, L, Finish);
|
|
54
|
+
pragma Assert (I = Source'Last);
|
|
55
|
+
|
|
56
|
+
Close (Compressor);
|
|
57
|
+
|
|
58
|
+
Ada.Text_IO.Put_Line
|
|
59
|
+
("Compressed size : "
|
|
60
|
+
& Stream_Element_Offset'Image (L) & " bytes");
|
|
61
|
+
end Compress;
|
|
62
|
+
|
|
63
|
+
-- Now we decompress the data, passing short blocks of data to Zlib
|
|
64
|
+
-- (because this demonstrates the problem - the last block passed will
|
|
65
|
+
-- contain checksum information and there will be no output, only a
|
|
66
|
+
-- check inside Zlib that the checksum is correct).
|
|
67
|
+
|
|
68
|
+
Decompress : declare
|
|
69
|
+
Decompressor : Filter_Type;
|
|
70
|
+
|
|
71
|
+
Uncompressed_Data : Stream_Element_Array (1 .. Text'Length);
|
|
72
|
+
|
|
73
|
+
Block_Size : constant := 4;
|
|
74
|
+
-- This makes sure that the last block contains
|
|
75
|
+
-- only Adler checksum data.
|
|
76
|
+
|
|
77
|
+
P : Stream_Element_Offset := Compressed_Data'First - 1;
|
|
78
|
+
O : Stream_Element_Offset;
|
|
79
|
+
begin
|
|
80
|
+
Inflate_Init (Decompressor);
|
|
81
|
+
|
|
82
|
+
loop
|
|
83
|
+
Translate
|
|
84
|
+
(Decompressor,
|
|
85
|
+
Compressed_Data
|
|
86
|
+
(P + 1 .. Stream_Element_Offset'Min (P + Block_Size, L)),
|
|
87
|
+
P,
|
|
88
|
+
Uncompressed_Data
|
|
89
|
+
(Total_Out (Decompressor) + 1 .. Uncompressed_Data'Last),
|
|
90
|
+
O,
|
|
91
|
+
No_Flush);
|
|
92
|
+
|
|
93
|
+
Ada.Text_IO.Put_Line
|
|
94
|
+
("Total in : " & Count'Image (Total_In (Decompressor)) &
|
|
95
|
+
", out : " & Count'Image (Total_Out (Decompressor)));
|
|
96
|
+
|
|
97
|
+
exit when P = L;
|
|
98
|
+
end loop;
|
|
99
|
+
|
|
100
|
+
Ada.Text_IO.New_Line;
|
|
101
|
+
Ada.Text_IO.Put_Line
|
|
102
|
+
("Decompressed text matches original text : "
|
|
103
|
+
& Boolean'Image (Uncompressed_Data = Source));
|
|
104
|
+
end Decompress;
|
|
105
|
+
end;
|
|
106
|
+
end Buffer_Demo;
|
|
@@ -0,0 +1,156 @@
|
|
|
1
|
+
----------------------------------------------------------------
|
|
2
|
+
-- ZLib for Ada thick binding. --
|
|
3
|
+
-- --
|
|
4
|
+
-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
|
5
|
+
-- --
|
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
|
7
|
+
----------------------------------------------------------------
|
|
8
|
+
-- Continuous test for ZLib multithreading. If the test would fail
|
|
9
|
+
-- we should provide thread safe allocation routines for the Z_Stream.
|
|
10
|
+
--
|
|
11
|
+
-- $Id: mtest.adb,v 1.4 2004/07/23 07:49:54 vagul Exp $
|
|
12
|
+
|
|
13
|
+
with ZLib;
|
|
14
|
+
with Ada.Streams;
|
|
15
|
+
with Ada.Numerics.Discrete_Random;
|
|
16
|
+
with Ada.Text_IO;
|
|
17
|
+
with Ada.Exceptions;
|
|
18
|
+
with Ada.Task_Identification;
|
|
19
|
+
|
|
20
|
+
procedure MTest is
|
|
21
|
+
use Ada.Streams;
|
|
22
|
+
use ZLib;
|
|
23
|
+
|
|
24
|
+
Stop : Boolean := False;
|
|
25
|
+
|
|
26
|
+
pragma Atomic (Stop);
|
|
27
|
+
|
|
28
|
+
subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
|
|
29
|
+
|
|
30
|
+
package Random_Elements is
|
|
31
|
+
new Ada.Numerics.Discrete_Random (Visible_Symbols);
|
|
32
|
+
|
|
33
|
+
task type Test_Task;
|
|
34
|
+
|
|
35
|
+
task body Test_Task is
|
|
36
|
+
Buffer : Stream_Element_Array (1 .. 100_000);
|
|
37
|
+
Gen : Random_Elements.Generator;
|
|
38
|
+
|
|
39
|
+
Buffer_First : Stream_Element_Offset;
|
|
40
|
+
Compare_First : Stream_Element_Offset;
|
|
41
|
+
|
|
42
|
+
Deflate : Filter_Type;
|
|
43
|
+
Inflate : Filter_Type;
|
|
44
|
+
|
|
45
|
+
procedure Further (Item : in Stream_Element_Array);
|
|
46
|
+
|
|
47
|
+
procedure Read_Buffer
|
|
48
|
+
(Item : out Ada.Streams.Stream_Element_Array;
|
|
49
|
+
Last : out Ada.Streams.Stream_Element_Offset);
|
|
50
|
+
|
|
51
|
+
-------------
|
|
52
|
+
-- Further --
|
|
53
|
+
-------------
|
|
54
|
+
|
|
55
|
+
procedure Further (Item : in Stream_Element_Array) is
|
|
56
|
+
|
|
57
|
+
procedure Compare (Item : in Stream_Element_Array);
|
|
58
|
+
|
|
59
|
+
-------------
|
|
60
|
+
-- Compare --
|
|
61
|
+
-------------
|
|
62
|
+
|
|
63
|
+
procedure Compare (Item : in Stream_Element_Array) is
|
|
64
|
+
Next_First : Stream_Element_Offset := Compare_First + Item'Length;
|
|
65
|
+
begin
|
|
66
|
+
if Buffer (Compare_First .. Next_First - 1) /= Item then
|
|
67
|
+
raise Program_Error;
|
|
68
|
+
end if;
|
|
69
|
+
|
|
70
|
+
Compare_First := Next_First;
|
|
71
|
+
end Compare;
|
|
72
|
+
|
|
73
|
+
procedure Compare_Write is new ZLib.Write (Write => Compare);
|
|
74
|
+
begin
|
|
75
|
+
Compare_Write (Inflate, Item, No_Flush);
|
|
76
|
+
end Further;
|
|
77
|
+
|
|
78
|
+
-----------------
|
|
79
|
+
-- Read_Buffer --
|
|
80
|
+
-----------------
|
|
81
|
+
|
|
82
|
+
procedure Read_Buffer
|
|
83
|
+
(Item : out Ada.Streams.Stream_Element_Array;
|
|
84
|
+
Last : out Ada.Streams.Stream_Element_Offset)
|
|
85
|
+
is
|
|
86
|
+
Buff_Diff : Stream_Element_Offset := Buffer'Last - Buffer_First;
|
|
87
|
+
Next_First : Stream_Element_Offset;
|
|
88
|
+
begin
|
|
89
|
+
if Item'Length <= Buff_Diff then
|
|
90
|
+
Last := Item'Last;
|
|
91
|
+
|
|
92
|
+
Next_First := Buffer_First + Item'Length;
|
|
93
|
+
|
|
94
|
+
Item := Buffer (Buffer_First .. Next_First - 1);
|
|
95
|
+
|
|
96
|
+
Buffer_First := Next_First;
|
|
97
|
+
else
|
|
98
|
+
Last := Item'First + Buff_Diff;
|
|
99
|
+
Item (Item'First .. Last) := Buffer (Buffer_First .. Buffer'Last);
|
|
100
|
+
Buffer_First := Buffer'Last + 1;
|
|
101
|
+
end if;
|
|
102
|
+
end Read_Buffer;
|
|
103
|
+
|
|
104
|
+
procedure Translate is new Generic_Translate
|
|
105
|
+
(Data_In => Read_Buffer,
|
|
106
|
+
Data_Out => Further);
|
|
107
|
+
|
|
108
|
+
begin
|
|
109
|
+
Random_Elements.Reset (Gen);
|
|
110
|
+
|
|
111
|
+
Buffer := (others => 20);
|
|
112
|
+
|
|
113
|
+
Main : loop
|
|
114
|
+
for J in Buffer'Range loop
|
|
115
|
+
Buffer (J) := Random_Elements.Random (Gen);
|
|
116
|
+
|
|
117
|
+
Deflate_Init (Deflate);
|
|
118
|
+
Inflate_Init (Inflate);
|
|
119
|
+
|
|
120
|
+
Buffer_First := Buffer'First;
|
|
121
|
+
Compare_First := Buffer'First;
|
|
122
|
+
|
|
123
|
+
Translate (Deflate);
|
|
124
|
+
|
|
125
|
+
if Compare_First /= Buffer'Last + 1 then
|
|
126
|
+
raise Program_Error;
|
|
127
|
+
end if;
|
|
128
|
+
|
|
129
|
+
Ada.Text_IO.Put_Line
|
|
130
|
+
(Ada.Task_Identification.Image
|
|
131
|
+
(Ada.Task_Identification.Current_Task)
|
|
132
|
+
& Stream_Element_Offset'Image (J)
|
|
133
|
+
& ZLib.Count'Image (Total_Out (Deflate)));
|
|
134
|
+
|
|
135
|
+
Close (Deflate);
|
|
136
|
+
Close (Inflate);
|
|
137
|
+
|
|
138
|
+
exit Main when Stop;
|
|
139
|
+
end loop;
|
|
140
|
+
end loop Main;
|
|
141
|
+
exception
|
|
142
|
+
when E : others =>
|
|
143
|
+
Ada.Text_IO.Put_Line (Ada.Exceptions.Exception_Information (E));
|
|
144
|
+
Stop := True;
|
|
145
|
+
end Test_Task;
|
|
146
|
+
|
|
147
|
+
Test : array (1 .. 4) of Test_Task;
|
|
148
|
+
|
|
149
|
+
pragma Unreferenced (Test);
|
|
150
|
+
|
|
151
|
+
Dummy : Character;
|
|
152
|
+
|
|
153
|
+
begin
|
|
154
|
+
Ada.Text_IO.Get_Immediate (Dummy);
|
|
155
|
+
Stop := True;
|
|
156
|
+
end MTest;
|
|
@@ -0,0 +1,156 @@
|
|
|
1
|
+
----------------------------------------------------------------
|
|
2
|
+
-- ZLib for Ada thick binding. --
|
|
3
|
+
-- --
|
|
4
|
+
-- Copyright (C) 2002-2003 Dmitriy Anisimkov --
|
|
5
|
+
-- --
|
|
6
|
+
-- Open source license information is in the zlib.ads file. --
|
|
7
|
+
----------------------------------------------------------------
|
|
8
|
+
|
|
9
|
+
-- $Id: read.adb,v 1.8 2004/05/31 10:53:40 vagul Exp $
|
|
10
|
+
|
|
11
|
+
-- Test/demo program for the generic read interface.
|
|
12
|
+
|
|
13
|
+
with Ada.Numerics.Discrete_Random;
|
|
14
|
+
with Ada.Streams;
|
|
15
|
+
with Ada.Text_IO;
|
|
16
|
+
|
|
17
|
+
with ZLib;
|
|
18
|
+
|
|
19
|
+
procedure Read is
|
|
20
|
+
|
|
21
|
+
use Ada.Streams;
|
|
22
|
+
|
|
23
|
+
------------------------------------
|
|
24
|
+
-- Test configuration parameters --
|
|
25
|
+
------------------------------------
|
|
26
|
+
|
|
27
|
+
File_Size : Stream_Element_Offset := 100_000;
|
|
28
|
+
|
|
29
|
+
Continuous : constant Boolean := False;
|
|
30
|
+
-- If this constant is True, the test would be repeated again and again,
|
|
31
|
+
-- with increment File_Size for every iteration.
|
|
32
|
+
|
|
33
|
+
Header : constant ZLib.Header_Type := ZLib.Default;
|
|
34
|
+
-- Do not use Header other than Default in ZLib versions 1.1.4 and older.
|
|
35
|
+
|
|
36
|
+
Init_Random : constant := 8;
|
|
37
|
+
-- We are using the same random sequence, in case of we catch bug,
|
|
38
|
+
-- so we would be able to reproduce it.
|
|
39
|
+
|
|
40
|
+
-- End --
|
|
41
|
+
|
|
42
|
+
Pack_Size : Stream_Element_Offset;
|
|
43
|
+
Offset : Stream_Element_Offset;
|
|
44
|
+
|
|
45
|
+
Filter : ZLib.Filter_Type;
|
|
46
|
+
|
|
47
|
+
subtype Visible_Symbols
|
|
48
|
+
is Stream_Element range 16#20# .. 16#7E#;
|
|
49
|
+
|
|
50
|
+
package Random_Elements is new
|
|
51
|
+
Ada.Numerics.Discrete_Random (Visible_Symbols);
|
|
52
|
+
|
|
53
|
+
Gen : Random_Elements.Generator;
|
|
54
|
+
Period : constant Stream_Element_Offset := 200;
|
|
55
|
+
-- Period constant variable for random generator not to be very random.
|
|
56
|
+
-- Bigger period, harder random.
|
|
57
|
+
|
|
58
|
+
Read_Buffer : Stream_Element_Array (1 .. 2048);
|
|
59
|
+
Read_First : Stream_Element_Offset;
|
|
60
|
+
Read_Last : Stream_Element_Offset;
|
|
61
|
+
|
|
62
|
+
procedure Reset;
|
|
63
|
+
|
|
64
|
+
procedure Read
|
|
65
|
+
(Item : out Stream_Element_Array;
|
|
66
|
+
Last : out Stream_Element_Offset);
|
|
67
|
+
-- this procedure is for generic instantiation of
|
|
68
|
+
-- ZLib.Read
|
|
69
|
+
-- reading data from the File_In.
|
|
70
|
+
|
|
71
|
+
procedure Read is new ZLib.Read
|
|
72
|
+
(Read,
|
|
73
|
+
Read_Buffer,
|
|
74
|
+
Rest_First => Read_First,
|
|
75
|
+
Rest_Last => Read_Last);
|
|
76
|
+
|
|
77
|
+
----------
|
|
78
|
+
-- Read --
|
|
79
|
+
----------
|
|
80
|
+
|
|
81
|
+
procedure Read
|
|
82
|
+
(Item : out Stream_Element_Array;
|
|
83
|
+
Last : out Stream_Element_Offset) is
|
|
84
|
+
begin
|
|
85
|
+
Last := Stream_Element_Offset'Min
|
|
86
|
+
(Item'Last,
|
|
87
|
+
Item'First + File_Size - Offset);
|
|
88
|
+
|
|
89
|
+
for J in Item'First .. Last loop
|
|
90
|
+
if J < Item'First + Period then
|
|
91
|
+
Item (J) := Random_Elements.Random (Gen);
|
|
92
|
+
else
|
|
93
|
+
Item (J) := Item (J - Period);
|
|
94
|
+
end if;
|
|
95
|
+
|
|
96
|
+
Offset := Offset + 1;
|
|
97
|
+
end loop;
|
|
98
|
+
end Read;
|
|
99
|
+
|
|
100
|
+
-----------
|
|
101
|
+
-- Reset --
|
|
102
|
+
-----------
|
|
103
|
+
|
|
104
|
+
procedure Reset is
|
|
105
|
+
begin
|
|
106
|
+
Random_Elements.Reset (Gen, Init_Random);
|
|
107
|
+
Pack_Size := 0;
|
|
108
|
+
Offset := 1;
|
|
109
|
+
Read_First := Read_Buffer'Last + 1;
|
|
110
|
+
Read_Last := Read_Buffer'Last;
|
|
111
|
+
end Reset;
|
|
112
|
+
|
|
113
|
+
begin
|
|
114
|
+
Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
|
|
115
|
+
|
|
116
|
+
loop
|
|
117
|
+
for Level in ZLib.Compression_Level'Range loop
|
|
118
|
+
|
|
119
|
+
Ada.Text_IO.Put ("Level ="
|
|
120
|
+
& ZLib.Compression_Level'Image (Level));
|
|
121
|
+
|
|
122
|
+
-- Deflate using generic instantiation.
|
|
123
|
+
|
|
124
|
+
ZLib.Deflate_Init
|
|
125
|
+
(Filter,
|
|
126
|
+
Level,
|
|
127
|
+
Header => Header);
|
|
128
|
+
|
|
129
|
+
Reset;
|
|
130
|
+
|
|
131
|
+
Ada.Text_IO.Put
|
|
132
|
+
(Stream_Element_Offset'Image (File_Size) & " ->");
|
|
133
|
+
|
|
134
|
+
loop
|
|
135
|
+
declare
|
|
136
|
+
Buffer : Stream_Element_Array (1 .. 1024);
|
|
137
|
+
Last : Stream_Element_Offset;
|
|
138
|
+
begin
|
|
139
|
+
Read (Filter, Buffer, Last);
|
|
140
|
+
|
|
141
|
+
Pack_Size := Pack_Size + Last - Buffer'First + 1;
|
|
142
|
+
|
|
143
|
+
exit when Last < Buffer'Last;
|
|
144
|
+
end;
|
|
145
|
+
end loop;
|
|
146
|
+
|
|
147
|
+
Ada.Text_IO.Put_Line (Stream_Element_Offset'Image (Pack_Size));
|
|
148
|
+
|
|
149
|
+
ZLib.Close (Filter);
|
|
150
|
+
end loop;
|
|
151
|
+
|
|
152
|
+
exit when not Continuous;
|
|
153
|
+
|
|
154
|
+
File_Size := File_Size + 1;
|
|
155
|
+
end loop;
|
|
156
|
+
end Read;
|