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
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- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
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- 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
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- data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
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- data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
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- 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
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- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
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- data/spec/data/kmers_count1.csv +2 -0
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- 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
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- data/spec/graph_explorer_spec.rb +475 -0
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- 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
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/* puff.h
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Copyright (C) 2002, 2003 Mark Adler, all rights reserved
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version 1.7, 3 Mar 2002
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This software is provided 'as-is', without any express or implied
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warranty. In no event will the author be held liable for any damages
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arising from the use of this software.
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Permission is granted to anyone to use this software for any purpose,
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including commercial applications, and to alter it and redistribute it
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freely, subject to the following restrictions:
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claim that you wrote the original software. If you use this software
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in a product, an acknowledgment in the product documentation would be
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appreciated but is not required.
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misrepresented as being the original software.
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3. This notice may not be removed or altered from any source distribution.
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Mark Adler madler@alumni.caltech.edu
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*/
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int puff(unsigned char *dest, /* pointer to destination pointer */
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void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
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{
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R->HighPart = A.HighPart - B.HighPart;
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if (A.LowPart >= B.LowPart)
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else
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+
{
|
|
15
|
+
R->LowPart = A.LowPart - B.LowPart;
|
|
16
|
+
R->HighPart --;
|
|
17
|
+
}
|
|
18
|
+
}
|
|
19
|
+
|
|
20
|
+
#ifdef _M_X64
|
|
21
|
+
// see http://msdn2.microsoft.com/library/twchhe95(en-us,vs.80).aspx for __rdtsc
|
|
22
|
+
unsigned __int64 __rdtsc(void);
|
|
23
|
+
void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
|
|
24
|
+
{
|
|
25
|
+
// printf("rdtsc = %I64x\n",__rdtsc());
|
|
26
|
+
pbeginTime64->QuadPart=__rdtsc();
|
|
27
|
+
}
|
|
28
|
+
|
|
29
|
+
LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
|
30
|
+
{
|
|
31
|
+
LARGE_INTEGER LIres;
|
|
32
|
+
unsigned _int64 res=__rdtsc()-((unsigned _int64)(beginTime64.QuadPart));
|
|
33
|
+
LIres.QuadPart=res;
|
|
34
|
+
// printf("rdtsc = %I64x\n",__rdtsc());
|
|
35
|
+
return LIres;
|
|
36
|
+
}
|
|
37
|
+
#else
|
|
38
|
+
#ifdef _M_IX86
|
|
39
|
+
void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
|
|
40
|
+
{
|
|
41
|
+
DWORD dwEdx,dwEax;
|
|
42
|
+
_asm
|
|
43
|
+
{
|
|
44
|
+
rdtsc
|
|
45
|
+
mov dwEax,eax
|
|
46
|
+
mov dwEdx,edx
|
|
47
|
+
}
|
|
48
|
+
pbeginTime64->LowPart=dwEax;
|
|
49
|
+
pbeginTime64->HighPart=dwEdx;
|
|
50
|
+
}
|
|
51
|
+
|
|
52
|
+
void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
|
|
53
|
+
{
|
|
54
|
+
myGetRDTSC32(pbeginTime64);
|
|
55
|
+
}
|
|
56
|
+
|
|
57
|
+
LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
|
58
|
+
{
|
|
59
|
+
LARGE_INTEGER LIres,endTime64;
|
|
60
|
+
myGetRDTSC32(&endTime64);
|
|
61
|
+
|
|
62
|
+
LIres.LowPart=LIres.HighPart=0;
|
|
63
|
+
MyDoMinus64(&LIres,endTime64,beginTime64);
|
|
64
|
+
return LIres;
|
|
65
|
+
}
|
|
66
|
+
#else
|
|
67
|
+
void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
|
|
68
|
+
{
|
|
69
|
+
}
|
|
70
|
+
|
|
71
|
+
void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
|
|
72
|
+
{
|
|
73
|
+
}
|
|
74
|
+
|
|
75
|
+
LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
|
76
|
+
{
|
|
77
|
+
LARGE_INTEGER lr;
|
|
78
|
+
lr.QuadPart=0;
|
|
79
|
+
return lr;
|
|
80
|
+
}
|
|
81
|
+
#endif
|
|
82
|
+
#endif
|
|
83
|
+
|
|
84
|
+
void BeginCountPerfCounter(LARGE_INTEGER * pbeginTime64,BOOL fComputeTimeQueryPerf)
|
|
85
|
+
{
|
|
86
|
+
if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(pbeginTime64)))
|
|
87
|
+
{
|
|
88
|
+
pbeginTime64->LowPart = GetTickCount();
|
|
89
|
+
pbeginTime64->HighPart = 0;
|
|
90
|
+
}
|
|
91
|
+
}
|
|
92
|
+
|
|
93
|
+
DWORD GetMsecSincePerfCounter(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
|
|
94
|
+
{
|
|
95
|
+
LARGE_INTEGER endTime64,ticksPerSecond,ticks;
|
|
96
|
+
DWORDLONG ticksShifted,tickSecShifted;
|
|
97
|
+
DWORD dwLog=16+0;
|
|
98
|
+
DWORD dwRet;
|
|
99
|
+
if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(&endTime64)))
|
|
100
|
+
dwRet = (GetTickCount() - beginTime64.LowPart)*1;
|
|
101
|
+
else
|
|
102
|
+
{
|
|
103
|
+
MyDoMinus64(&ticks,endTime64,beginTime64);
|
|
104
|
+
QueryPerformanceFrequency(&ticksPerSecond);
|
|
105
|
+
|
|
106
|
+
|
|
107
|
+
{
|
|
108
|
+
ticksShifted = Int64ShrlMod32(*(DWORDLONG*)&ticks,dwLog);
|
|
109
|
+
tickSecShifted = Int64ShrlMod32(*(DWORDLONG*)&ticksPerSecond,dwLog);
|
|
110
|
+
|
|
111
|
+
}
|
|
112
|
+
|
|
113
|
+
dwRet = (DWORD)((((DWORD)ticksShifted)*1000)/(DWORD)(tickSecShifted));
|
|
114
|
+
dwRet *=1;
|
|
115
|
+
}
|
|
116
|
+
return dwRet;
|
|
117
|
+
}
|
|
118
|
+
|
|
119
|
+
int ReadFileMemory(const char* filename,long* plFileSize,void** pFilePtr)
|
|
120
|
+
{
|
|
121
|
+
FILE* stream;
|
|
122
|
+
void* ptr;
|
|
123
|
+
int retVal=1;
|
|
124
|
+
stream=fopen(filename, "rb");
|
|
125
|
+
if (stream==NULL)
|
|
126
|
+
return 0;
|
|
127
|
+
|
|
128
|
+
fseek(stream,0,SEEK_END);
|
|
129
|
+
|
|
130
|
+
*plFileSize=ftell(stream);
|
|
131
|
+
fseek(stream,0,SEEK_SET);
|
|
132
|
+
ptr=malloc((*plFileSize)+1);
|
|
133
|
+
if (ptr==NULL)
|
|
134
|
+
retVal=0;
|
|
135
|
+
else
|
|
136
|
+
{
|
|
137
|
+
if (fread(ptr, 1, *plFileSize,stream) != (*plFileSize))
|
|
138
|
+
retVal=0;
|
|
139
|
+
}
|
|
140
|
+
fclose(stream);
|
|
141
|
+
*pFilePtr=ptr;
|
|
142
|
+
return retVal;
|
|
143
|
+
}
|
|
144
|
+
|
|
145
|
+
int main(int argc, char *argv[])
|
|
146
|
+
{
|
|
147
|
+
int BlockSizeCompress=0x8000;
|
|
148
|
+
int BlockSizeUncompress=0x8000;
|
|
149
|
+
int cprLevel=Z_DEFAULT_COMPRESSION ;
|
|
150
|
+
long lFileSize;
|
|
151
|
+
unsigned char* FilePtr;
|
|
152
|
+
long lBufferSizeCpr;
|
|
153
|
+
long lBufferSizeUncpr;
|
|
154
|
+
long lCompressedSize=0;
|
|
155
|
+
unsigned char* CprPtr;
|
|
156
|
+
unsigned char* UncprPtr;
|
|
157
|
+
long lSizeCpr,lSizeUncpr;
|
|
158
|
+
DWORD dwGetTick,dwMsecQP;
|
|
159
|
+
LARGE_INTEGER li_qp,li_rdtsc,dwResRdtsc;
|
|
160
|
+
|
|
161
|
+
if (argc<=1)
|
|
162
|
+
{
|
|
163
|
+
printf("run TestZlib <File> [BlockSizeCompress] [BlockSizeUncompress] [compres. level]\n");
|
|
164
|
+
return 0;
|
|
165
|
+
}
|
|
166
|
+
|
|
167
|
+
if (ReadFileMemory(argv[1],&lFileSize,&FilePtr)==0)
|
|
168
|
+
{
|
|
169
|
+
printf("error reading %s\n",argv[1]);
|
|
170
|
+
return 1;
|
|
171
|
+
}
|
|
172
|
+
else printf("file %s read, %u bytes\n",argv[1],lFileSize);
|
|
173
|
+
|
|
174
|
+
if (argc>=3)
|
|
175
|
+
BlockSizeCompress=atol(argv[2]);
|
|
176
|
+
|
|
177
|
+
if (argc>=4)
|
|
178
|
+
BlockSizeUncompress=atol(argv[3]);
|
|
179
|
+
|
|
180
|
+
if (argc>=5)
|
|
181
|
+
cprLevel=(int)atol(argv[4]);
|
|
182
|
+
|
|
183
|
+
lBufferSizeCpr = lFileSize + (lFileSize/0x10) + 0x200;
|
|
184
|
+
lBufferSizeUncpr = lBufferSizeCpr;
|
|
185
|
+
|
|
186
|
+
CprPtr=(unsigned char*)malloc(lBufferSizeCpr + BlockSizeCompress);
|
|
187
|
+
|
|
188
|
+
BeginCountPerfCounter(&li_qp,TRUE);
|
|
189
|
+
dwGetTick=GetTickCount();
|
|
190
|
+
BeginCountRdtsc(&li_rdtsc);
|
|
191
|
+
{
|
|
192
|
+
z_stream zcpr;
|
|
193
|
+
int ret=Z_OK;
|
|
194
|
+
long lOrigToDo = lFileSize;
|
|
195
|
+
long lOrigDone = 0;
|
|
196
|
+
int step=0;
|
|
197
|
+
memset(&zcpr,0,sizeof(z_stream));
|
|
198
|
+
deflateInit(&zcpr,cprLevel);
|
|
199
|
+
|
|
200
|
+
zcpr.next_in = FilePtr;
|
|
201
|
+
zcpr.next_out = CprPtr;
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
do
|
|
205
|
+
{
|
|
206
|
+
long all_read_before = zcpr.total_in;
|
|
207
|
+
zcpr.avail_in = min(lOrigToDo,BlockSizeCompress);
|
|
208
|
+
zcpr.avail_out = BlockSizeCompress;
|
|
209
|
+
ret=deflate(&zcpr,(zcpr.avail_in==lOrigToDo) ? Z_FINISH : Z_SYNC_FLUSH);
|
|
210
|
+
lOrigDone += (zcpr.total_in-all_read_before);
|
|
211
|
+
lOrigToDo -= (zcpr.total_in-all_read_before);
|
|
212
|
+
step++;
|
|
213
|
+
} while (ret==Z_OK);
|
|
214
|
+
|
|
215
|
+
lSizeCpr=zcpr.total_out;
|
|
216
|
+
deflateEnd(&zcpr);
|
|
217
|
+
dwGetTick=GetTickCount()-dwGetTick;
|
|
218
|
+
dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
|
|
219
|
+
dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
|
|
220
|
+
printf("total compress size = %u, in %u step\n",lSizeCpr,step);
|
|
221
|
+
printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
|
|
222
|
+
printf("defcpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
|
|
223
|
+
printf("defcpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
|
|
224
|
+
}
|
|
225
|
+
|
|
226
|
+
CprPtr=(unsigned char*)realloc(CprPtr,lSizeCpr);
|
|
227
|
+
UncprPtr=(unsigned char*)malloc(lBufferSizeUncpr + BlockSizeUncompress);
|
|
228
|
+
|
|
229
|
+
BeginCountPerfCounter(&li_qp,TRUE);
|
|
230
|
+
dwGetTick=GetTickCount();
|
|
231
|
+
BeginCountRdtsc(&li_rdtsc);
|
|
232
|
+
{
|
|
233
|
+
z_stream zcpr;
|
|
234
|
+
int ret=Z_OK;
|
|
235
|
+
long lOrigToDo = lSizeCpr;
|
|
236
|
+
long lOrigDone = 0;
|
|
237
|
+
int step=0;
|
|
238
|
+
memset(&zcpr,0,sizeof(z_stream));
|
|
239
|
+
inflateInit(&zcpr);
|
|
240
|
+
|
|
241
|
+
zcpr.next_in = CprPtr;
|
|
242
|
+
zcpr.next_out = UncprPtr;
|
|
243
|
+
|
|
244
|
+
|
|
245
|
+
do
|
|
246
|
+
{
|
|
247
|
+
long all_read_before = zcpr.total_in;
|
|
248
|
+
zcpr.avail_in = min(lOrigToDo,BlockSizeUncompress);
|
|
249
|
+
zcpr.avail_out = BlockSizeUncompress;
|
|
250
|
+
ret=inflate(&zcpr,Z_SYNC_FLUSH);
|
|
251
|
+
lOrigDone += (zcpr.total_in-all_read_before);
|
|
252
|
+
lOrigToDo -= (zcpr.total_in-all_read_before);
|
|
253
|
+
step++;
|
|
254
|
+
} while (ret==Z_OK);
|
|
255
|
+
|
|
256
|
+
lSizeUncpr=zcpr.total_out;
|
|
257
|
+
inflateEnd(&zcpr);
|
|
258
|
+
dwGetTick=GetTickCount()-dwGetTick;
|
|
259
|
+
dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
|
|
260
|
+
dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
|
|
261
|
+
printf("total uncompress size = %u, in %u step\n",lSizeUncpr,step);
|
|
262
|
+
printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
|
|
263
|
+
printf("uncpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
|
|
264
|
+
printf("uncpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
|
|
265
|
+
}
|
|
266
|
+
|
|
267
|
+
if (lSizeUncpr==lFileSize)
|
|
268
|
+
{
|
|
269
|
+
if (memcmp(FilePtr,UncprPtr,lFileSize)==0)
|
|
270
|
+
printf("compare ok\n");
|
|
271
|
+
|
|
272
|
+
}
|
|
273
|
+
|
|
274
|
+
return 0;
|
|
275
|
+
}
|
|
@@ -0,0 +1,14 @@
|
|
|
1
|
+
CC=cc
|
|
2
|
+
CFLAGS=-g
|
|
3
|
+
|
|
4
|
+
untgz: untgz.o ../../libz.a
|
|
5
|
+
$(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
|
|
6
|
+
|
|
7
|
+
untgz.o: untgz.c ../../zlib.h
|
|
8
|
+
$(CC) $(CFLAGS) -c -I../.. untgz.c
|
|
9
|
+
|
|
10
|
+
../../libz.a:
|
|
11
|
+
cd ../..; ./configure; make
|
|
12
|
+
|
|
13
|
+
clean:
|
|
14
|
+
rm -f untgz untgz.o *~
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
CC=cl
|
|
2
|
+
CFLAGS=-MD
|
|
3
|
+
|
|
4
|
+
untgz.exe: untgz.obj ..\..\zlib.lib
|
|
5
|
+
$(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
|
|
6
|
+
|
|
7
|
+
untgz.obj: untgz.c ..\..\zlib.h
|
|
8
|
+
$(CC) $(CFLAGS) -c -I..\.. untgz.c
|
|
9
|
+
|
|
10
|
+
..\..\zlib.lib:
|
|
11
|
+
cd ..\..
|
|
12
|
+
$(MAKE) -f win32\makefile.msc
|
|
13
|
+
cd contrib\untgz
|
|
14
|
+
|
|
15
|
+
clean:
|
|
16
|
+
-del untgz.obj
|
|
17
|
+
-del untgz.exe
|
|
@@ -0,0 +1,674 @@
|
|
|
1
|
+
/*
|
|
2
|
+
* untgz.c -- Display contents and extract files from a gzip'd TAR file
|
|
3
|
+
*
|
|
4
|
+
* written by Pedro A. Aranda Gutierrez <paag@tid.es>
|
|
5
|
+
* adaptation to Unix by Jean-loup Gailly <jloup@gzip.org>
|
|
6
|
+
* various fixes by Cosmin Truta <cosmint@cs.ubbcluj.ro>
|
|
7
|
+
*/
|
|
8
|
+
|
|
9
|
+
#include <stdio.h>
|
|
10
|
+
#include <stdlib.h>
|
|
11
|
+
#include <string.h>
|
|
12
|
+
#include <time.h>
|
|
13
|
+
#include <errno.h>
|
|
14
|
+
|
|
15
|
+
#include "zlib.h"
|
|
16
|
+
|
|
17
|
+
#ifdef unix
|
|
18
|
+
# include <unistd.h>
|
|
19
|
+
#else
|
|
20
|
+
# include <direct.h>
|
|
21
|
+
# include <io.h>
|
|
22
|
+
#endif
|
|
23
|
+
|
|
24
|
+
#ifdef WIN32
|
|
25
|
+
#include <windows.h>
|
|
26
|
+
# ifndef F_OK
|
|
27
|
+
# define F_OK 0
|
|
28
|
+
# endif
|
|
29
|
+
# define mkdir(dirname,mode) _mkdir(dirname)
|
|
30
|
+
# ifdef _MSC_VER
|
|
31
|
+
# define access(path,mode) _access(path,mode)
|
|
32
|
+
# define chmod(path,mode) _chmod(path,mode)
|
|
33
|
+
# define strdup(str) _strdup(str)
|
|
34
|
+
# endif
|
|
35
|
+
#else
|
|
36
|
+
# include <utime.h>
|
|
37
|
+
#endif
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
/* values used in typeflag field */
|
|
41
|
+
|
|
42
|
+
#define REGTYPE '0' /* regular file */
|
|
43
|
+
#define AREGTYPE '\0' /* regular file */
|
|
44
|
+
#define LNKTYPE '1' /* link */
|
|
45
|
+
#define SYMTYPE '2' /* reserved */
|
|
46
|
+
#define CHRTYPE '3' /* character special */
|
|
47
|
+
#define BLKTYPE '4' /* block special */
|
|
48
|
+
#define DIRTYPE '5' /* directory */
|
|
49
|
+
#define FIFOTYPE '6' /* FIFO special */
|
|
50
|
+
#define CONTTYPE '7' /* reserved */
|
|
51
|
+
|
|
52
|
+
/* GNU tar extensions */
|
|
53
|
+
|
|
54
|
+
#define GNUTYPE_DUMPDIR 'D' /* file names from dumped directory */
|
|
55
|
+
#define GNUTYPE_LONGLINK 'K' /* long link name */
|
|
56
|
+
#define GNUTYPE_LONGNAME 'L' /* long file name */
|
|
57
|
+
#define GNUTYPE_MULTIVOL 'M' /* continuation of file from another volume */
|
|
58
|
+
#define GNUTYPE_NAMES 'N' /* file name that does not fit into main hdr */
|
|
59
|
+
#define GNUTYPE_SPARSE 'S' /* sparse file */
|
|
60
|
+
#define GNUTYPE_VOLHDR 'V' /* tape/volume header */
|
|
61
|
+
|
|
62
|
+
|
|
63
|
+
/* tar header */
|
|
64
|
+
|
|
65
|
+
#define BLOCKSIZE 512
|
|
66
|
+
#define SHORTNAMESIZE 100
|
|
67
|
+
|
|
68
|
+
struct tar_header
|
|
69
|
+
{ /* byte offset */
|
|
70
|
+
char name[100]; /* 0 */
|
|
71
|
+
char mode[8]; /* 100 */
|
|
72
|
+
char uid[8]; /* 108 */
|
|
73
|
+
char gid[8]; /* 116 */
|
|
74
|
+
char size[12]; /* 124 */
|
|
75
|
+
char mtime[12]; /* 136 */
|
|
76
|
+
char chksum[8]; /* 148 */
|
|
77
|
+
char typeflag; /* 156 */
|
|
78
|
+
char linkname[100]; /* 157 */
|
|
79
|
+
char magic[6]; /* 257 */
|
|
80
|
+
char version[2]; /* 263 */
|
|
81
|
+
char uname[32]; /* 265 */
|
|
82
|
+
char gname[32]; /* 297 */
|
|
83
|
+
char devmajor[8]; /* 329 */
|
|
84
|
+
char devminor[8]; /* 337 */
|
|
85
|
+
char prefix[155]; /* 345 */
|
|
86
|
+
/* 500 */
|
|
87
|
+
};
|
|
88
|
+
|
|
89
|
+
union tar_buffer
|
|
90
|
+
{
|
|
91
|
+
char buffer[BLOCKSIZE];
|
|
92
|
+
struct tar_header header;
|
|
93
|
+
};
|
|
94
|
+
|
|
95
|
+
struct attr_item
|
|
96
|
+
{
|
|
97
|
+
struct attr_item *next;
|
|
98
|
+
char *fname;
|
|
99
|
+
int mode;
|
|
100
|
+
time_t time;
|
|
101
|
+
};
|
|
102
|
+
|
|
103
|
+
enum { TGZ_EXTRACT, TGZ_LIST, TGZ_INVALID };
|
|
104
|
+
|
|
105
|
+
char *TGZfname OF((const char *));
|
|
106
|
+
void TGZnotfound OF((const char *));
|
|
107
|
+
|
|
108
|
+
int getoct OF((char *, int));
|
|
109
|
+
char *strtime OF((time_t *));
|
|
110
|
+
int setfiletime OF((char *, time_t));
|
|
111
|
+
void push_attr OF((struct attr_item **, char *, int, time_t));
|
|
112
|
+
void restore_attr OF((struct attr_item **));
|
|
113
|
+
|
|
114
|
+
int ExprMatch OF((char *, char *));
|
|
115
|
+
|
|
116
|
+
int makedir OF((char *));
|
|
117
|
+
int matchname OF((int, int, char **, char *));
|
|
118
|
+
|
|
119
|
+
void error OF((const char *));
|
|
120
|
+
int tar OF((gzFile, int, int, int, char **));
|
|
121
|
+
|
|
122
|
+
void help OF((int));
|
|
123
|
+
int main OF((int, char **));
|
|
124
|
+
|
|
125
|
+
char *prog;
|
|
126
|
+
|
|
127
|
+
const char *TGZsuffix[] = { "\0", ".tar", ".tar.gz", ".taz", ".tgz", NULL };
|
|
128
|
+
|
|
129
|
+
/* return the file name of the TGZ archive */
|
|
130
|
+
/* or NULL if it does not exist */
|
|
131
|
+
|
|
132
|
+
char *TGZfname (const char *arcname)
|
|
133
|
+
{
|
|
134
|
+
static char buffer[1024];
|
|
135
|
+
int origlen,i;
|
|
136
|
+
|
|
137
|
+
strcpy(buffer,arcname);
|
|
138
|
+
origlen = strlen(buffer);
|
|
139
|
+
|
|
140
|
+
for (i=0; TGZsuffix[i]; i++)
|
|
141
|
+
{
|
|
142
|
+
strcpy(buffer+origlen,TGZsuffix[i]);
|
|
143
|
+
if (access(buffer,F_OK) == 0)
|
|
144
|
+
return buffer;
|
|
145
|
+
}
|
|
146
|
+
return NULL;
|
|
147
|
+
}
|
|
148
|
+
|
|
149
|
+
|
|
150
|
+
/* error message for the filename */
|
|
151
|
+
|
|
152
|
+
void TGZnotfound (const char *arcname)
|
|
153
|
+
{
|
|
154
|
+
int i;
|
|
155
|
+
|
|
156
|
+
fprintf(stderr,"%s: Couldn't find ",prog);
|
|
157
|
+
for (i=0;TGZsuffix[i];i++)
|
|
158
|
+
fprintf(stderr,(TGZsuffix[i+1]) ? "%s%s, " : "or %s%s\n",
|
|
159
|
+
arcname,
|
|
160
|
+
TGZsuffix[i]);
|
|
161
|
+
exit(1);
|
|
162
|
+
}
|
|
163
|
+
|
|
164
|
+
|
|
165
|
+
/* convert octal digits to int */
|
|
166
|
+
/* on error return -1 */
|
|
167
|
+
|
|
168
|
+
int getoct (char *p,int width)
|
|
169
|
+
{
|
|
170
|
+
int result = 0;
|
|
171
|
+
char c;
|
|
172
|
+
|
|
173
|
+
while (width--)
|
|
174
|
+
{
|
|
175
|
+
c = *p++;
|
|
176
|
+
if (c == 0)
|
|
177
|
+
break;
|
|
178
|
+
if (c == ' ')
|
|
179
|
+
continue;
|
|
180
|
+
if (c < '0' || c > '7')
|
|
181
|
+
return -1;
|
|
182
|
+
result = result * 8 + (c - '0');
|
|
183
|
+
}
|
|
184
|
+
return result;
|
|
185
|
+
}
|
|
186
|
+
|
|
187
|
+
|
|
188
|
+
/* convert time_t to string */
|
|
189
|
+
/* use the "YYYY/MM/DD hh:mm:ss" format */
|
|
190
|
+
|
|
191
|
+
char *strtime (time_t *t)
|
|
192
|
+
{
|
|
193
|
+
struct tm *local;
|
|
194
|
+
static char result[32];
|
|
195
|
+
|
|
196
|
+
local = localtime(t);
|
|
197
|
+
sprintf(result,"%4d/%02d/%02d %02d:%02d:%02d",
|
|
198
|
+
local->tm_year+1900, local->tm_mon+1, local->tm_mday,
|
|
199
|
+
local->tm_hour, local->tm_min, local->tm_sec);
|
|
200
|
+
return result;
|
|
201
|
+
}
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
/* set file time */
|
|
205
|
+
|
|
206
|
+
int setfiletime (char *fname,time_t ftime)
|
|
207
|
+
{
|
|
208
|
+
#ifdef WIN32
|
|
209
|
+
static int isWinNT = -1;
|
|
210
|
+
SYSTEMTIME st;
|
|
211
|
+
FILETIME locft, modft;
|
|
212
|
+
struct tm *loctm;
|
|
213
|
+
HANDLE hFile;
|
|
214
|
+
int result;
|
|
215
|
+
|
|
216
|
+
loctm = localtime(&ftime);
|
|
217
|
+
if (loctm == NULL)
|
|
218
|
+
return -1;
|
|
219
|
+
|
|
220
|
+
st.wYear = (WORD)loctm->tm_year + 1900;
|
|
221
|
+
st.wMonth = (WORD)loctm->tm_mon + 1;
|
|
222
|
+
st.wDayOfWeek = (WORD)loctm->tm_wday;
|
|
223
|
+
st.wDay = (WORD)loctm->tm_mday;
|
|
224
|
+
st.wHour = (WORD)loctm->tm_hour;
|
|
225
|
+
st.wMinute = (WORD)loctm->tm_min;
|
|
226
|
+
st.wSecond = (WORD)loctm->tm_sec;
|
|
227
|
+
st.wMilliseconds = 0;
|
|
228
|
+
if (!SystemTimeToFileTime(&st, &locft) ||
|
|
229
|
+
!LocalFileTimeToFileTime(&locft, &modft))
|
|
230
|
+
return -1;
|
|
231
|
+
|
|
232
|
+
if (isWinNT < 0)
|
|
233
|
+
isWinNT = (GetVersion() < 0x80000000) ? 1 : 0;
|
|
234
|
+
hFile = CreateFile(fname, GENERIC_WRITE, 0, NULL, OPEN_EXISTING,
|
|
235
|
+
(isWinNT ? FILE_FLAG_BACKUP_SEMANTICS : 0),
|
|
236
|
+
NULL);
|
|
237
|
+
if (hFile == INVALID_HANDLE_VALUE)
|
|
238
|
+
return -1;
|
|
239
|
+
result = SetFileTime(hFile, NULL, NULL, &modft) ? 0 : -1;
|
|
240
|
+
CloseHandle(hFile);
|
|
241
|
+
return result;
|
|
242
|
+
#else
|
|
243
|
+
struct utimbuf settime;
|
|
244
|
+
|
|
245
|
+
settime.actime = settime.modtime = ftime;
|
|
246
|
+
return utime(fname,&settime);
|
|
247
|
+
#endif
|
|
248
|
+
}
|
|
249
|
+
|
|
250
|
+
|
|
251
|
+
/* push file attributes */
|
|
252
|
+
|
|
253
|
+
void push_attr(struct attr_item **list,char *fname,int mode,time_t time)
|
|
254
|
+
{
|
|
255
|
+
struct attr_item *item;
|
|
256
|
+
|
|
257
|
+
item = (struct attr_item *)malloc(sizeof(struct attr_item));
|
|
258
|
+
if (item == NULL)
|
|
259
|
+
error("Out of memory");
|
|
260
|
+
item->fname = strdup(fname);
|
|
261
|
+
item->mode = mode;
|
|
262
|
+
item->time = time;
|
|
263
|
+
item->next = *list;
|
|
264
|
+
*list = item;
|
|
265
|
+
}
|
|
266
|
+
|
|
267
|
+
|
|
268
|
+
/* restore file attributes */
|
|
269
|
+
|
|
270
|
+
void restore_attr(struct attr_item **list)
|
|
271
|
+
{
|
|
272
|
+
struct attr_item *item, *prev;
|
|
273
|
+
|
|
274
|
+
for (item = *list; item != NULL; )
|
|
275
|
+
{
|
|
276
|
+
setfiletime(item->fname,item->time);
|
|
277
|
+
chmod(item->fname,item->mode);
|
|
278
|
+
prev = item;
|
|
279
|
+
item = item->next;
|
|
280
|
+
free(prev);
|
|
281
|
+
}
|
|
282
|
+
*list = NULL;
|
|
283
|
+
}
|
|
284
|
+
|
|
285
|
+
|
|
286
|
+
/* match regular expression */
|
|
287
|
+
|
|
288
|
+
#define ISSPECIAL(c) (((c) == '*') || ((c) == '/'))
|
|
289
|
+
|
|
290
|
+
int ExprMatch (char *string,char *expr)
|
|
291
|
+
{
|
|
292
|
+
while (1)
|
|
293
|
+
{
|
|
294
|
+
if (ISSPECIAL(*expr))
|
|
295
|
+
{
|
|
296
|
+
if (*expr == '/')
|
|
297
|
+
{
|
|
298
|
+
if (*string != '\\' && *string != '/')
|
|
299
|
+
return 0;
|
|
300
|
+
string ++; expr++;
|
|
301
|
+
}
|
|
302
|
+
else if (*expr == '*')
|
|
303
|
+
{
|
|
304
|
+
if (*expr ++ == 0)
|
|
305
|
+
return 1;
|
|
306
|
+
while (*++string != *expr)
|
|
307
|
+
if (*string == 0)
|
|
308
|
+
return 0;
|
|
309
|
+
}
|
|
310
|
+
}
|
|
311
|
+
else
|
|
312
|
+
{
|
|
313
|
+
if (*string != *expr)
|
|
314
|
+
return 0;
|
|
315
|
+
if (*expr++ == 0)
|
|
316
|
+
return 1;
|
|
317
|
+
string++;
|
|
318
|
+
}
|
|
319
|
+
}
|
|
320
|
+
}
|
|
321
|
+
|
|
322
|
+
|
|
323
|
+
/* recursive mkdir */
|
|
324
|
+
/* abort on ENOENT; ignore other errors like "directory already exists" */
|
|
325
|
+
/* return 1 if OK */
|
|
326
|
+
/* 0 on error */
|
|
327
|
+
|
|
328
|
+
int makedir (char *newdir)
|
|
329
|
+
{
|
|
330
|
+
char *buffer = strdup(newdir);
|
|
331
|
+
char *p;
|
|
332
|
+
int len = strlen(buffer);
|
|
333
|
+
|
|
334
|
+
if (len <= 0) {
|
|
335
|
+
free(buffer);
|
|
336
|
+
return 0;
|
|
337
|
+
}
|
|
338
|
+
if (buffer[len-1] == '/') {
|
|
339
|
+
buffer[len-1] = '\0';
|
|
340
|
+
}
|
|
341
|
+
if (mkdir(buffer, 0755) == 0)
|
|
342
|
+
{
|
|
343
|
+
free(buffer);
|
|
344
|
+
return 1;
|
|
345
|
+
}
|
|
346
|
+
|
|
347
|
+
p = buffer+1;
|
|
348
|
+
while (1)
|
|
349
|
+
{
|
|
350
|
+
char hold;
|
|
351
|
+
|
|
352
|
+
while(*p && *p != '\\' && *p != '/')
|
|
353
|
+
p++;
|
|
354
|
+
hold = *p;
|
|
355
|
+
*p = 0;
|
|
356
|
+
if ((mkdir(buffer, 0755) == -1) && (errno == ENOENT))
|
|
357
|
+
{
|
|
358
|
+
fprintf(stderr,"%s: Couldn't create directory %s\n",prog,buffer);
|
|
359
|
+
free(buffer);
|
|
360
|
+
return 0;
|
|
361
|
+
}
|
|
362
|
+
if (hold == 0)
|
|
363
|
+
break;
|
|
364
|
+
*p++ = hold;
|
|
365
|
+
}
|
|
366
|
+
free(buffer);
|
|
367
|
+
return 1;
|
|
368
|
+
}
|
|
369
|
+
|
|
370
|
+
|
|
371
|
+
int matchname (int arg,int argc,char **argv,char *fname)
|
|
372
|
+
{
|
|
373
|
+
if (arg == argc) /* no arguments given (untgz tgzarchive) */
|
|
374
|
+
return 1;
|
|
375
|
+
|
|
376
|
+
while (arg < argc)
|
|
377
|
+
if (ExprMatch(fname,argv[arg++]))
|
|
378
|
+
return 1;
|
|
379
|
+
|
|
380
|
+
return 0; /* ignore this for the moment being */
|
|
381
|
+
}
|
|
382
|
+
|
|
383
|
+
|
|
384
|
+
/* tar file list or extract */
|
|
385
|
+
|
|
386
|
+
int tar (gzFile in,int action,int arg,int argc,char **argv)
|
|
387
|
+
{
|
|
388
|
+
union tar_buffer buffer;
|
|
389
|
+
int len;
|
|
390
|
+
int err;
|
|
391
|
+
int getheader = 1;
|
|
392
|
+
int remaining = 0;
|
|
393
|
+
FILE *outfile = NULL;
|
|
394
|
+
char fname[BLOCKSIZE];
|
|
395
|
+
int tarmode;
|
|
396
|
+
time_t tartime;
|
|
397
|
+
struct attr_item *attributes = NULL;
|
|
398
|
+
|
|
399
|
+
if (action == TGZ_LIST)
|
|
400
|
+
printf(" date time size file\n"
|
|
401
|
+
" ---------- -------- --------- -------------------------------------\n");
|
|
402
|
+
while (1)
|
|
403
|
+
{
|
|
404
|
+
len = gzread(in, &buffer, BLOCKSIZE);
|
|
405
|
+
if (len < 0)
|
|
406
|
+
error(gzerror(in, &err));
|
|
407
|
+
/*
|
|
408
|
+
* Always expect complete blocks to process
|
|
409
|
+
* the tar information.
|
|
410
|
+
*/
|
|
411
|
+
if (len != BLOCKSIZE)
|
|
412
|
+
{
|
|
413
|
+
action = TGZ_INVALID; /* force error exit */
|
|
414
|
+
remaining = 0; /* force I/O cleanup */
|
|
415
|
+
}
|
|
416
|
+
|
|
417
|
+
/*
|
|
418
|
+
* If we have to get a tar header
|
|
419
|
+
*/
|
|
420
|
+
if (getheader >= 1)
|
|
421
|
+
{
|
|
422
|
+
/*
|
|
423
|
+
* if we met the end of the tar
|
|
424
|
+
* or the end-of-tar block,
|
|
425
|
+
* we are done
|
|
426
|
+
*/
|
|
427
|
+
if (len == 0 || buffer.header.name[0] == 0)
|
|
428
|
+
break;
|
|
429
|
+
|
|
430
|
+
tarmode = getoct(buffer.header.mode,8);
|
|
431
|
+
tartime = (time_t)getoct(buffer.header.mtime,12);
|
|
432
|
+
if (tarmode == -1 || tartime == (time_t)-1)
|
|
433
|
+
{
|
|
434
|
+
buffer.header.name[0] = 0;
|
|
435
|
+
action = TGZ_INVALID;
|
|
436
|
+
}
|
|
437
|
+
|
|
438
|
+
if (getheader == 1)
|
|
439
|
+
{
|
|
440
|
+
strncpy(fname,buffer.header.name,SHORTNAMESIZE);
|
|
441
|
+
if (fname[SHORTNAMESIZE-1] != 0)
|
|
442
|
+
fname[SHORTNAMESIZE] = 0;
|
|
443
|
+
}
|
|
444
|
+
else
|
|
445
|
+
{
|
|
446
|
+
/*
|
|
447
|
+
* The file name is longer than SHORTNAMESIZE
|
|
448
|
+
*/
|
|
449
|
+
if (strncmp(fname,buffer.header.name,SHORTNAMESIZE-1) != 0)
|
|
450
|
+
error("bad long name");
|
|
451
|
+
getheader = 1;
|
|
452
|
+
}
|
|
453
|
+
|
|
454
|
+
/*
|
|
455
|
+
* Act according to the type flag
|
|
456
|
+
*/
|
|
457
|
+
switch (buffer.header.typeflag)
|
|
458
|
+
{
|
|
459
|
+
case DIRTYPE:
|
|
460
|
+
if (action == TGZ_LIST)
|
|
461
|
+
printf(" %s <dir> %s\n",strtime(&tartime),fname);
|
|
462
|
+
if (action == TGZ_EXTRACT)
|
|
463
|
+
{
|
|
464
|
+
makedir(fname);
|
|
465
|
+
push_attr(&attributes,fname,tarmode,tartime);
|
|
466
|
+
}
|
|
467
|
+
break;
|
|
468
|
+
case REGTYPE:
|
|
469
|
+
case AREGTYPE:
|
|
470
|
+
remaining = getoct(buffer.header.size,12);
|
|
471
|
+
if (remaining == -1)
|
|
472
|
+
{
|
|
473
|
+
action = TGZ_INVALID;
|
|
474
|
+
break;
|
|
475
|
+
}
|
|
476
|
+
if (action == TGZ_LIST)
|
|
477
|
+
printf(" %s %9d %s\n",strtime(&tartime),remaining,fname);
|
|
478
|
+
else if (action == TGZ_EXTRACT)
|
|
479
|
+
{
|
|
480
|
+
if (matchname(arg,argc,argv,fname))
|
|
481
|
+
{
|
|
482
|
+
outfile = fopen(fname,"wb");
|
|
483
|
+
if (outfile == NULL) {
|
|
484
|
+
/* try creating directory */
|
|
485
|
+
char *p = strrchr(fname, '/');
|
|
486
|
+
if (p != NULL) {
|
|
487
|
+
*p = '\0';
|
|
488
|
+
makedir(fname);
|
|
489
|
+
*p = '/';
|
|
490
|
+
outfile = fopen(fname,"wb");
|
|
491
|
+
}
|
|
492
|
+
}
|
|
493
|
+
if (outfile != NULL)
|
|
494
|
+
printf("Extracting %s\n",fname);
|
|
495
|
+
else
|
|
496
|
+
fprintf(stderr, "%s: Couldn't create %s",prog,fname);
|
|
497
|
+
}
|
|
498
|
+
else
|
|
499
|
+
outfile = NULL;
|
|
500
|
+
}
|
|
501
|
+
getheader = 0;
|
|
502
|
+
break;
|
|
503
|
+
case GNUTYPE_LONGLINK:
|
|
504
|
+
case GNUTYPE_LONGNAME:
|
|
505
|
+
remaining = getoct(buffer.header.size,12);
|
|
506
|
+
if (remaining < 0 || remaining >= BLOCKSIZE)
|
|
507
|
+
{
|
|
508
|
+
action = TGZ_INVALID;
|
|
509
|
+
break;
|
|
510
|
+
}
|
|
511
|
+
len = gzread(in, fname, BLOCKSIZE);
|
|
512
|
+
if (len < 0)
|
|
513
|
+
error(gzerror(in, &err));
|
|
514
|
+
if (fname[BLOCKSIZE-1] != 0 || (int)strlen(fname) > remaining)
|
|
515
|
+
{
|
|
516
|
+
action = TGZ_INVALID;
|
|
517
|
+
break;
|
|
518
|
+
}
|
|
519
|
+
getheader = 2;
|
|
520
|
+
break;
|
|
521
|
+
default:
|
|
522
|
+
if (action == TGZ_LIST)
|
|
523
|
+
printf(" %s <---> %s\n",strtime(&tartime),fname);
|
|
524
|
+
break;
|
|
525
|
+
}
|
|
526
|
+
}
|
|
527
|
+
else
|
|
528
|
+
{
|
|
529
|
+
unsigned int bytes = (remaining > BLOCKSIZE) ? BLOCKSIZE : remaining;
|
|
530
|
+
|
|
531
|
+
if (outfile != NULL)
|
|
532
|
+
{
|
|
533
|
+
if (fwrite(&buffer,sizeof(char),bytes,outfile) != bytes)
|
|
534
|
+
{
|
|
535
|
+
fprintf(stderr,
|
|
536
|
+
"%s: Error writing %s -- skipping\n",prog,fname);
|
|
537
|
+
fclose(outfile);
|
|
538
|
+
outfile = NULL;
|
|
539
|
+
remove(fname);
|
|
540
|
+
}
|
|
541
|
+
}
|
|
542
|
+
remaining -= bytes;
|
|
543
|
+
}
|
|
544
|
+
|
|
545
|
+
if (remaining == 0)
|
|
546
|
+
{
|
|
547
|
+
getheader = 1;
|
|
548
|
+
if (outfile != NULL)
|
|
549
|
+
{
|
|
550
|
+
fclose(outfile);
|
|
551
|
+
outfile = NULL;
|
|
552
|
+
if (action != TGZ_INVALID)
|
|
553
|
+
push_attr(&attributes,fname,tarmode,tartime);
|
|
554
|
+
}
|
|
555
|
+
}
|
|
556
|
+
|
|
557
|
+
/*
|
|
558
|
+
* Abandon if errors are found
|
|
559
|
+
*/
|
|
560
|
+
if (action == TGZ_INVALID)
|
|
561
|
+
{
|
|
562
|
+
error("broken archive");
|
|
563
|
+
break;
|
|
564
|
+
}
|
|
565
|
+
}
|
|
566
|
+
|
|
567
|
+
/*
|
|
568
|
+
* Restore file modes and time stamps
|
|
569
|
+
*/
|
|
570
|
+
restore_attr(&attributes);
|
|
571
|
+
|
|
572
|
+
if (gzclose(in) != Z_OK)
|
|
573
|
+
error("failed gzclose");
|
|
574
|
+
|
|
575
|
+
return 0;
|
|
576
|
+
}
|
|
577
|
+
|
|
578
|
+
|
|
579
|
+
/* ============================================================ */
|
|
580
|
+
|
|
581
|
+
void help(int exitval)
|
|
582
|
+
{
|
|
583
|
+
printf("untgz version 0.2.1\n"
|
|
584
|
+
" using zlib version %s\n\n",
|
|
585
|
+
zlibVersion());
|
|
586
|
+
printf("Usage: untgz file.tgz extract all files\n"
|
|
587
|
+
" untgz file.tgz fname ... extract selected files\n"
|
|
588
|
+
" untgz -l file.tgz list archive contents\n"
|
|
589
|
+
" untgz -h display this help\n");
|
|
590
|
+
exit(exitval);
|
|
591
|
+
}
|
|
592
|
+
|
|
593
|
+
void error(const char *msg)
|
|
594
|
+
{
|
|
595
|
+
fprintf(stderr, "%s: %s\n", prog, msg);
|
|
596
|
+
exit(1);
|
|
597
|
+
}
|
|
598
|
+
|
|
599
|
+
|
|
600
|
+
/* ============================================================ */
|
|
601
|
+
|
|
602
|
+
#if defined(WIN32) && defined(__GNUC__)
|
|
603
|
+
int _CRT_glob = 0; /* disable argument globbing in MinGW */
|
|
604
|
+
#endif
|
|
605
|
+
|
|
606
|
+
int main(int argc,char **argv)
|
|
607
|
+
{
|
|
608
|
+
int action = TGZ_EXTRACT;
|
|
609
|
+
int arg = 1;
|
|
610
|
+
char *TGZfile;
|
|
611
|
+
gzFile *f;
|
|
612
|
+
|
|
613
|
+
prog = strrchr(argv[0],'\\');
|
|
614
|
+
if (prog == NULL)
|
|
615
|
+
{
|
|
616
|
+
prog = strrchr(argv[0],'/');
|
|
617
|
+
if (prog == NULL)
|
|
618
|
+
{
|
|
619
|
+
prog = strrchr(argv[0],':');
|
|
620
|
+
if (prog == NULL)
|
|
621
|
+
prog = argv[0];
|
|
622
|
+
else
|
|
623
|
+
prog++;
|
|
624
|
+
}
|
|
625
|
+
else
|
|
626
|
+
prog++;
|
|
627
|
+
}
|
|
628
|
+
else
|
|
629
|
+
prog++;
|
|
630
|
+
|
|
631
|
+
if (argc == 1)
|
|
632
|
+
help(0);
|
|
633
|
+
|
|
634
|
+
if (strcmp(argv[arg],"-l") == 0)
|
|
635
|
+
{
|
|
636
|
+
action = TGZ_LIST;
|
|
637
|
+
if (argc == ++arg)
|
|
638
|
+
help(0);
|
|
639
|
+
}
|
|
640
|
+
else if (strcmp(argv[arg],"-h") == 0)
|
|
641
|
+
{
|
|
642
|
+
help(0);
|
|
643
|
+
}
|
|
644
|
+
|
|
645
|
+
if ((TGZfile = TGZfname(argv[arg])) == NULL)
|
|
646
|
+
TGZnotfound(argv[arg]);
|
|
647
|
+
|
|
648
|
+
++arg;
|
|
649
|
+
if ((action == TGZ_LIST) && (arg != argc))
|
|
650
|
+
help(1);
|
|
651
|
+
|
|
652
|
+
/*
|
|
653
|
+
* Process the TGZ file
|
|
654
|
+
*/
|
|
655
|
+
switch(action)
|
|
656
|
+
{
|
|
657
|
+
case TGZ_LIST:
|
|
658
|
+
case TGZ_EXTRACT:
|
|
659
|
+
f = gzopen(TGZfile,"rb");
|
|
660
|
+
if (f == NULL)
|
|
661
|
+
{
|
|
662
|
+
fprintf(stderr,"%s: Couldn't gzopen %s\n",prog,TGZfile);
|
|
663
|
+
return 1;
|
|
664
|
+
}
|
|
665
|
+
exit(tar(f, action, arg, argc, argv));
|
|
666
|
+
break;
|
|
667
|
+
|
|
668
|
+
default:
|
|
669
|
+
error("Unknown option");
|
|
670
|
+
exit(1);
|
|
671
|
+
}
|
|
672
|
+
|
|
673
|
+
return 0;
|
|
674
|
+
}
|