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/lib/assembly/a_b_visualiser.rb +169 -0
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- 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
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- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
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- data/lib/assembly/single_ended_assembler.rb +441 -0
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- data/lib/external/VERSION +1 -0
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- 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
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- data/lib/finishm/roundup.rb +344 -0
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- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
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- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -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/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/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
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- 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
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- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
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descrip.mms *.[ch]
|
|
46
|
+
|
|
47
|
+
tgz:
|
|
48
|
+
cd ..; tar cfz zlib/zlib.tgz zlib/README zlib/ChangeLog zlib/Makefile \
|
|
49
|
+
zlib/Make????.??? zlib/Makefile.?? zlib/descrip.mms zlib/*.[ch]
|
|
50
|
+
|
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51
|
+
# DO NOT DELETE THIS LINE -- make depend depends on it.
|
|
52
|
+
|
|
53
|
+
adler32.o: zlib.h zconf.h
|
|
54
|
+
compress.o: zlib.h zconf.h
|
|
55
|
+
crc32.o: crc32.h zlib.h zconf.h
|
|
56
|
+
deflate.o: deflate.h zutil.h zlib.h zconf.h
|
|
57
|
+
example.o: zlib.h zconf.h
|
|
58
|
+
gzio.o: zutil.h zlib.h zconf.h
|
|
59
|
+
inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
60
|
+
inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
61
|
+
infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
62
|
+
inftrees.o: zutil.h zlib.h zconf.h inftrees.h
|
|
63
|
+
minigzip.o: zlib.h zconf.h
|
|
64
|
+
trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
|
|
65
|
+
uncompr.o: zlib.h zconf.h
|
|
66
|
+
zutil.o: zutil.h zlib.h zconf.h
|
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
# SMakefile for zlib
|
|
2
|
+
# Modified from the standard UNIX Makefile Copyright Jean-loup Gailly
|
|
3
|
+
# Osma Ahvenlampi <Osma.Ahvenlampi@hut.fi>
|
|
4
|
+
# Amiga, SAS/C 6.56 & Smake
|
|
5
|
+
|
|
6
|
+
CC=sc
|
|
7
|
+
CFLAGS=OPT
|
|
8
|
+
#CFLAGS=OPT CPU=68030
|
|
9
|
+
#CFLAGS=DEBUG=LINE
|
|
10
|
+
LDFLAGS=LIB z.lib
|
|
11
|
+
|
|
12
|
+
SCOPTIONS=OPTSCHED OPTINLINE OPTALIAS OPTTIME OPTINLOCAL STRMERGE \
|
|
13
|
+
NOICONS PARMS=BOTH NOSTACKCHECK UTILLIB NOVERSION ERRORREXX \
|
|
14
|
+
DEF=POSTINC
|
|
15
|
+
|
|
16
|
+
OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
|
|
17
|
+
zutil.o inflate.o infback.o inftrees.o inffast.o
|
|
18
|
+
|
|
19
|
+
TEST_OBJS = example.o minigzip.o
|
|
20
|
+
|
|
21
|
+
all: SCOPTIONS example minigzip
|
|
22
|
+
|
|
23
|
+
check: test
|
|
24
|
+
test: all
|
|
25
|
+
example
|
|
26
|
+
echo hello world | minigzip | minigzip -d
|
|
27
|
+
|
|
28
|
+
install: z.lib
|
|
29
|
+
copy clone zlib.h zconf.h INCLUDE:
|
|
30
|
+
copy clone z.lib LIB:
|
|
31
|
+
|
|
32
|
+
z.lib: $(OBJS)
|
|
33
|
+
oml z.lib r $(OBJS)
|
|
34
|
+
|
|
35
|
+
example: example.o z.lib
|
|
36
|
+
$(CC) $(CFLAGS) LINK TO $@ example.o $(LDFLAGS)
|
|
37
|
+
|
|
38
|
+
minigzip: minigzip.o z.lib
|
|
39
|
+
$(CC) $(CFLAGS) LINK TO $@ minigzip.o $(LDFLAGS)
|
|
40
|
+
|
|
41
|
+
mostlyclean: clean
|
|
42
|
+
clean:
|
|
43
|
+
-delete force quiet example minigzip *.o z.lib foo.gz *.lnk SCOPTIONS
|
|
44
|
+
|
|
45
|
+
SCOPTIONS: Makefile.sas
|
|
46
|
+
copy to $@ <from <
|
|
47
|
+
$(SCOPTIONS)
|
|
48
|
+
<
|
|
49
|
+
|
|
50
|
+
# DO NOT DELETE THIS LINE -- make depend depends on it.
|
|
51
|
+
|
|
52
|
+
adler32.o: zlib.h zconf.h
|
|
53
|
+
compress.o: zlib.h zconf.h
|
|
54
|
+
crc32.o: crc32.h zlib.h zconf.h
|
|
55
|
+
deflate.o: deflate.h zutil.h zlib.h zconf.h
|
|
56
|
+
example.o: zlib.h zconf.h
|
|
57
|
+
gzio.o: zutil.h zlib.h zconf.h
|
|
58
|
+
inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
59
|
+
inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
60
|
+
infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
|
|
61
|
+
inftrees.o: zutil.h zlib.h zconf.h inftrees.h
|
|
62
|
+
minigzip.o: zlib.h zconf.h
|
|
63
|
+
trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
|
|
64
|
+
uncompr.o: zlib.h zconf.h
|
|
65
|
+
zutil.o: zutil.h zlib.h zconf.h
|
|
@@ -0,0 +1,132 @@
|
|
|
1
|
+
STRPGMEXP PGMLVL(*CURRENT) SIGNATURE('ZLIB')
|
|
2
|
+
|
|
3
|
+
/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
|
|
4
|
+
/* Version 1.1.3 entry points. */
|
|
5
|
+
/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
|
|
6
|
+
|
|
7
|
+
/********************************************************************/
|
|
8
|
+
/* *MODULE ADLER32 ZLIB 01/02/01 00:15:09 */
|
|
9
|
+
/********************************************************************/
|
|
10
|
+
|
|
11
|
+
EXPORT SYMBOL("adler32")
|
|
12
|
+
|
|
13
|
+
/********************************************************************/
|
|
14
|
+
/* *MODULE COMPRESS ZLIB 01/02/01 00:15:09 */
|
|
15
|
+
/********************************************************************/
|
|
16
|
+
|
|
17
|
+
EXPORT SYMBOL("compress")
|
|
18
|
+
EXPORT SYMBOL("compress2")
|
|
19
|
+
|
|
20
|
+
/********************************************************************/
|
|
21
|
+
/* *MODULE CRC32 ZLIB 01/02/01 00:15:09 */
|
|
22
|
+
/********************************************************************/
|
|
23
|
+
|
|
24
|
+
EXPORT SYMBOL("crc32")
|
|
25
|
+
EXPORT SYMBOL("get_crc_table")
|
|
26
|
+
|
|
27
|
+
/********************************************************************/
|
|
28
|
+
/* *MODULE DEFLATE ZLIB 01/02/01 00:15:09 */
|
|
29
|
+
/********************************************************************/
|
|
30
|
+
|
|
31
|
+
EXPORT SYMBOL("deflate")
|
|
32
|
+
EXPORT SYMBOL("deflateEnd")
|
|
33
|
+
EXPORT SYMBOL("deflateSetDictionary")
|
|
34
|
+
EXPORT SYMBOL("deflateCopy")
|
|
35
|
+
EXPORT SYMBOL("deflateReset")
|
|
36
|
+
EXPORT SYMBOL("deflateParams")
|
|
37
|
+
EXPORT SYMBOL("deflatePrime")
|
|
38
|
+
EXPORT SYMBOL("deflateInit_")
|
|
39
|
+
EXPORT SYMBOL("deflateInit2_")
|
|
40
|
+
|
|
41
|
+
/********************************************************************/
|
|
42
|
+
/* *MODULE GZIO ZLIB 01/02/01 00:15:09 */
|
|
43
|
+
/********************************************************************/
|
|
44
|
+
|
|
45
|
+
EXPORT SYMBOL("gzopen")
|
|
46
|
+
EXPORT SYMBOL("gzdopen")
|
|
47
|
+
EXPORT SYMBOL("gzsetparams")
|
|
48
|
+
EXPORT SYMBOL("gzread")
|
|
49
|
+
EXPORT SYMBOL("gzwrite")
|
|
50
|
+
EXPORT SYMBOL("gzprintf")
|
|
51
|
+
EXPORT SYMBOL("gzputs")
|
|
52
|
+
EXPORT SYMBOL("gzgets")
|
|
53
|
+
EXPORT SYMBOL("gzputc")
|
|
54
|
+
EXPORT SYMBOL("gzgetc")
|
|
55
|
+
EXPORT SYMBOL("gzflush")
|
|
56
|
+
EXPORT SYMBOL("gzseek")
|
|
57
|
+
EXPORT SYMBOL("gzrewind")
|
|
58
|
+
EXPORT SYMBOL("gztell")
|
|
59
|
+
EXPORT SYMBOL("gzeof")
|
|
60
|
+
EXPORT SYMBOL("gzclose")
|
|
61
|
+
EXPORT SYMBOL("gzerror")
|
|
62
|
+
|
|
63
|
+
/********************************************************************/
|
|
64
|
+
/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
|
|
65
|
+
/********************************************************************/
|
|
66
|
+
|
|
67
|
+
EXPORT SYMBOL("inflate")
|
|
68
|
+
EXPORT SYMBOL("inflateEnd")
|
|
69
|
+
EXPORT SYMBOL("inflateSetDictionary")
|
|
70
|
+
EXPORT SYMBOL("inflateSync")
|
|
71
|
+
EXPORT SYMBOL("inflateReset")
|
|
72
|
+
EXPORT SYMBOL("inflateInit_")
|
|
73
|
+
EXPORT SYMBOL("inflateInit2_")
|
|
74
|
+
EXPORT SYMBOL("inflateSyncPoint")
|
|
75
|
+
|
|
76
|
+
/********************************************************************/
|
|
77
|
+
/* *MODULE UNCOMPR ZLIB 01/02/01 00:15:09 */
|
|
78
|
+
/********************************************************************/
|
|
79
|
+
|
|
80
|
+
EXPORT SYMBOL("uncompress")
|
|
81
|
+
|
|
82
|
+
/********************************************************************/
|
|
83
|
+
/* *MODULE ZUTIL ZLIB 01/02/01 00:15:09 */
|
|
84
|
+
/********************************************************************/
|
|
85
|
+
|
|
86
|
+
EXPORT SYMBOL("zlibVersion")
|
|
87
|
+
EXPORT SYMBOL("zError")
|
|
88
|
+
|
|
89
|
+
/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
|
|
90
|
+
/* Version 1.2.1 additional entry points. */
|
|
91
|
+
/*@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@*/
|
|
92
|
+
|
|
93
|
+
/********************************************************************/
|
|
94
|
+
/* *MODULE COMPRESS ZLIB 01/02/01 00:15:09 */
|
|
95
|
+
/********************************************************************/
|
|
96
|
+
|
|
97
|
+
EXPORT SYMBOL("compressBound")
|
|
98
|
+
|
|
99
|
+
/********************************************************************/
|
|
100
|
+
/* *MODULE DEFLATE ZLIB 01/02/01 00:15:09 */
|
|
101
|
+
/********************************************************************/
|
|
102
|
+
|
|
103
|
+
EXPORT SYMBOL("deflateBound")
|
|
104
|
+
|
|
105
|
+
/********************************************************************/
|
|
106
|
+
/* *MODULE GZIO ZLIB 01/02/01 00:15:09 */
|
|
107
|
+
/********************************************************************/
|
|
108
|
+
|
|
109
|
+
EXPORT SYMBOL("gzungetc")
|
|
110
|
+
EXPORT SYMBOL("gzclearerr")
|
|
111
|
+
|
|
112
|
+
/********************************************************************/
|
|
113
|
+
/* *MODULE INFBACK ZLIB 01/02/01 00:15:09 */
|
|
114
|
+
/********************************************************************/
|
|
115
|
+
|
|
116
|
+
EXPORT SYMBOL("inflateBack")
|
|
117
|
+
EXPORT SYMBOL("inflateBackEnd")
|
|
118
|
+
EXPORT SYMBOL("inflateBackInit_")
|
|
119
|
+
|
|
120
|
+
/********************************************************************/
|
|
121
|
+
/* *MODULE INFLATE ZLIB 01/02/01 00:15:09 */
|
|
122
|
+
/********************************************************************/
|
|
123
|
+
|
|
124
|
+
EXPORT SYMBOL("inflateCopy")
|
|
125
|
+
|
|
126
|
+
/********************************************************************/
|
|
127
|
+
/* *MODULE ZUTIL ZLIB 01/02/01 00:15:09 */
|
|
128
|
+
/********************************************************************/
|
|
129
|
+
|
|
130
|
+
EXPORT SYMBOL("zlibCompileFlags")
|
|
131
|
+
|
|
132
|
+
ENDPGMEXP
|
|
@@ -0,0 +1,123 @@
|
|
|
1
|
+
/******************************************************************************/
|
|
2
|
+
/* */
|
|
3
|
+
/* ZLIB */
|
|
4
|
+
/* */
|
|
5
|
+
/* Compile sources into modules and link them into a service program. */
|
|
6
|
+
/* */
|
|
7
|
+
/******************************************************************************/
|
|
8
|
+
|
|
9
|
+
PGM
|
|
10
|
+
|
|
11
|
+
/* Configuration adjustable parameters. */
|
|
12
|
+
|
|
13
|
+
DCL VAR(&SRCLIB) TYPE(*CHAR) LEN(10) +
|
|
14
|
+
VALUE('ZLIB') /* Source library. */
|
|
15
|
+
DCL VAR(&SRCFILE) TYPE(*CHAR) LEN(10) +
|
|
16
|
+
VALUE('SOURCES') /* Source member file. */
|
|
17
|
+
DCL VAR(&CTLFILE) TYPE(*CHAR) LEN(10) +
|
|
18
|
+
VALUE('TOOLS') /* Control member file. */
|
|
19
|
+
|
|
20
|
+
DCL VAR(&MODLIB) TYPE(*CHAR) LEN(10) +
|
|
21
|
+
VALUE('ZLIB') /* Module library. */
|
|
22
|
+
|
|
23
|
+
DCL VAR(&SRVLIB) TYPE(*CHAR) LEN(10) +
|
|
24
|
+
VALUE('LGPL') /* Service program library. */
|
|
25
|
+
|
|
26
|
+
DCL VAR(&CFLAGS) TYPE(*CHAR) +
|
|
27
|
+
VALUE('OPTIMIZE(40)') /* Compile options. */
|
|
28
|
+
|
|
29
|
+
|
|
30
|
+
/* Working storage. */
|
|
31
|
+
|
|
32
|
+
DCL VAR(&CMDLEN) TYPE(*DEC) LEN(15 5) VALUE(300) /* Command length. */
|
|
33
|
+
DCL VAR(&CMD) TYPE(*CHAR) LEN(512)
|
|
34
|
+
|
|
35
|
+
|
|
36
|
+
/* Compile sources into modules. */
|
|
37
|
+
|
|
38
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
39
|
+
'/ADLER32) SRCFILE(' *TCAT +
|
|
40
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
41
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
42
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
43
|
+
|
|
44
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
45
|
+
'/COMPRESS) SRCFILE(' *TCAT +
|
|
46
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
47
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
48
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
49
|
+
|
|
50
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
51
|
+
'/CRC32) SRCFILE(' *TCAT +
|
|
52
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
53
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
54
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
55
|
+
|
|
56
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
57
|
+
'/DEFLATE) SRCFILE(' *TCAT +
|
|
58
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
59
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
60
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
61
|
+
|
|
62
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
63
|
+
'/GZIO) SRCFILE(' *TCAT +
|
|
64
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
65
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
66
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
67
|
+
|
|
68
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
69
|
+
'/INFBACK) SRCFILE(' *TCAT +
|
|
70
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
71
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
72
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
73
|
+
|
|
74
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
75
|
+
'/INFFAST) SRCFILE(' *TCAT +
|
|
76
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
77
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
78
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
79
|
+
|
|
80
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
81
|
+
'/INFLATE) SRCFILE(' *TCAT +
|
|
82
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
83
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
84
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
85
|
+
|
|
86
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
87
|
+
'/INFTREES) SRCFILE(' *TCAT +
|
|
88
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
89
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
90
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
91
|
+
|
|
92
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
93
|
+
'/TREES) SRCFILE(' *TCAT +
|
|
94
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
95
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
96
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
97
|
+
|
|
98
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
99
|
+
'/UNCOMPR) SRCFILE(' *TCAT +
|
|
100
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
101
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
102
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
103
|
+
|
|
104
|
+
CHGVAR VAR(&CMD) VALUE('CRTCMOD MODULE(' *TCAT &MODLIB *TCAT +
|
|
105
|
+
'/ZUTIL) SRCFILE(' *TCAT +
|
|
106
|
+
&SRCLIB *TCAT '/' *TCAT &SRCFILE *TCAT +
|
|
107
|
+
') SYSIFCOPT(*IFSIO)' *BCAT &CFLAGS)
|
|
108
|
+
CALL PGM(QCMDEXC) PARM(&CMD &CMDLEN)
|
|
109
|
+
|
|
110
|
+
|
|
111
|
+
/* Link modules into a service program. */
|
|
112
|
+
|
|
113
|
+
CRTSRVPGM SRVPGM(&SRVLIB/ZLIB) +
|
|
114
|
+
MODULE(&MODLIB/ADLER32 &MODLIB/COMPRESS +
|
|
115
|
+
&MODLIB/CRC32 &MODLIB/DEFLATE +
|
|
116
|
+
&MODLIB/GZIO &MODLIB/INFBACK +
|
|
117
|
+
&MODLIB/INFFAST &MODLIB/INFLATE +
|
|
118
|
+
&MODLIB/INFTREES &MODLIB/TREES +
|
|
119
|
+
&MODLIB/UNCOMPR &MODLIB/ZUTIL) +
|
|
120
|
+
SRCFILE(&SRCLIB/&CTLFILE) SRCMBR(BNDSRC) +
|
|
121
|
+
TEXT('ZLIB 1.2.3') TGTRLS(V4R4M0)
|
|
122
|
+
|
|
123
|
+
ENDPGM
|
|
@@ -0,0 +1,111 @@
|
|
|
1
|
+
ZLIB version 1.2.3 for AS400 installation instructions
|
|
2
|
+
|
|
3
|
+
I) From an AS400 *SAVF file:
|
|
4
|
+
|
|
5
|
+
1) Unpacking archive to an AS400 save file
|
|
6
|
+
|
|
7
|
+
On the AS400:
|
|
8
|
+
|
|
9
|
+
_ Create the ZLIB AS400 library:
|
|
10
|
+
|
|
11
|
+
CRTLIB LIB(ZLIB) TYPE(PROD) TEXT('ZLIB compression API library')
|
|
12
|
+
|
|
13
|
+
_ Create a work save file, for example:
|
|
14
|
+
|
|
15
|
+
CRTSAVF FILE(ZLIB/ZLIBSAVF)
|
|
16
|
+
|
|
17
|
+
On a PC connected to the target AS400:
|
|
18
|
+
|
|
19
|
+
_ Unpack the save file image to a PC file "ZLIBSAVF"
|
|
20
|
+
_ Upload this file into the save file on the AS400, for example
|
|
21
|
+
using ftp in BINARY mode.
|
|
22
|
+
|
|
23
|
+
|
|
24
|
+
2) Populating the ZLIB AS400 source library
|
|
25
|
+
|
|
26
|
+
On the AS400:
|
|
27
|
+
|
|
28
|
+
_ Extract the saved objects into the ZLIB AS400 library using:
|
|
29
|
+
|
|
30
|
+
RSTOBJ OBJ(*ALL) SAVLIB(ZLIB) DEV(*SAVF) SAVF(ZLIB/ZLIBSAVF) RSTLIB(ZLIB)
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
3) Customize installation:
|
|
34
|
+
|
|
35
|
+
_ Edit CL member ZLIB/TOOLS(COMPILE) and change parameters if needed,
|
|
36
|
+
according to the comments.
|
|
37
|
+
|
|
38
|
+
_ Compile this member with:
|
|
39
|
+
|
|
40
|
+
CRTCLPGM PGM(ZLIB/COMPILE) SRCFILE(ZLIB/TOOLS) SRCMBR(COMPILE)
|
|
41
|
+
|
|
42
|
+
|
|
43
|
+
4) Compile and generate the service program:
|
|
44
|
+
|
|
45
|
+
_ This can now be done by executing:
|
|
46
|
+
|
|
47
|
+
CALL PGM(ZLIB/COMPILE)
|
|
48
|
+
|
|
49
|
+
|
|
50
|
+
|
|
51
|
+
II) From the original source distribution:
|
|
52
|
+
|
|
53
|
+
1) On the AS400, create the source library:
|
|
54
|
+
|
|
55
|
+
CRTLIB LIB(ZLIB) TYPE(PROD) TEXT('ZLIB compression API library')
|
|
56
|
+
|
|
57
|
+
2) Create the source files:
|
|
58
|
+
|
|
59
|
+
CRTSRCPF FILE(ZLIB/SOURCES) RCDLEN(112) TEXT('ZLIB library modules')
|
|
60
|
+
CRTSRCPF FILE(ZLIB/H) RCDLEN(112) TEXT('ZLIB library includes')
|
|
61
|
+
CRTSRCPF FILE(ZLIB/TOOLS) RCDLEN(112) TEXT('ZLIB library control utilities')
|
|
62
|
+
|
|
63
|
+
3) From the machine hosting the distribution files, upload them (with
|
|
64
|
+
FTP in text mode, for example) according to the following table:
|
|
65
|
+
|
|
66
|
+
Original AS400 AS400 AS400 AS400
|
|
67
|
+
file file member type description
|
|
68
|
+
SOURCES Original ZLIB C subprogram sources
|
|
69
|
+
adler32.c ADLER32 C ZLIB - Compute the Adler-32 checksum of a dta strm
|
|
70
|
+
compress.c COMPRESS C ZLIB - Compress a memory buffer
|
|
71
|
+
crc32.c CRC32 C ZLIB - Compute the CRC-32 of a data stream
|
|
72
|
+
deflate.c DEFLATE C ZLIB - Compress data using the deflation algorithm
|
|
73
|
+
gzio.c GZIO C ZLIB - IO on .gz files
|
|
74
|
+
infback.c INFBACK C ZLIB - Inflate using a callback interface
|
|
75
|
+
inffast.c INFFAST C ZLIB - Fast proc. literals & length/distance pairs
|
|
76
|
+
inflate.c INFLATE C ZLIB - Interface to inflate modules
|
|
77
|
+
inftrees.c INFTREES C ZLIB - Generate Huffman trees for efficient decode
|
|
78
|
+
trees.c TREES C ZLIB - Output deflated data using Huffman coding
|
|
79
|
+
uncompr.c UNCOMPR C ZLIB - Decompress a memory buffer
|
|
80
|
+
zutil.c ZUTIL C ZLIB - Target dependent utility functions
|
|
81
|
+
H Original ZLIB C and ILE/RPG include files
|
|
82
|
+
crc32.h CRC32 C ZLIB - CRC32 tables
|
|
83
|
+
deflate.h DEFLATE C ZLIB - Internal compression state
|
|
84
|
+
inffast.h INFFAST C ZLIB - Header to use inffast.c
|
|
85
|
+
inffixed.h INFFIXED C ZLIB - Table for decoding fixed codes
|
|
86
|
+
inflate.h INFLATE C ZLIB - Internal inflate state definitions
|
|
87
|
+
inftrees.h INFTREES C ZLIB - Header to use inftrees.c
|
|
88
|
+
trees.h TREES C ZLIB - Created automatically with -DGEN_TREES_H
|
|
89
|
+
zconf.h ZCONF C ZLIB - Compression library configuration
|
|
90
|
+
zlib.h ZLIB C ZLIB - Compression library C user interface
|
|
91
|
+
as400/zlib.inc ZLIB.INC RPGLE ZLIB - Compression library ILE RPG user interface
|
|
92
|
+
zutil.h ZUTIL C ZLIB - Internal interface and configuration
|
|
93
|
+
TOOLS Building source software & AS/400 README
|
|
94
|
+
as400/bndsrc BNDSRC Entry point exportation list
|
|
95
|
+
as400/compile.clp COMPILE CLP Compile sources & generate service program
|
|
96
|
+
as400/readme.txt README TXT Installation instructions
|
|
97
|
+
|
|
98
|
+
4) Continue as in I)3).
|
|
99
|
+
|
|
100
|
+
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
Notes: For AS400 ILE RPG programmers, a /copy member defining the ZLIB
|
|
104
|
+
API prototypes for ILE RPG can be found in ZLIB/H(ZLIB.INC).
|
|
105
|
+
Please read comments in this member for more information.
|
|
106
|
+
|
|
107
|
+
Remember that most foreign textual data are ASCII coded: this
|
|
108
|
+
implementation does not handle conversion from/to ASCII, so
|
|
109
|
+
text data code conversions must be done explicitely.
|
|
110
|
+
|
|
111
|
+
Always open zipped files in binary mode.
|