finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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@@ -0,0 +1,66 @@
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+ # Amiga powerUP (TM) Makefile
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+ # makefile for libpng and SAS C V6.58/7.00 PPC compiler
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+ # Copyright (C) 1998 by Andreas R. Kleinert
4
+
5
+ LIBNAME = libzip.a
6
+
7
+ CC = scppc
8
+ CFLAGS = NOSTKCHK NOSINT OPTIMIZE OPTGO OPTPEEP OPTINLOCAL OPTINL \
9
+ OPTLOOP OPTRDEP=8 OPTDEP=8 OPTCOMP=8 NOVER
10
+ AR = ppc-amigaos-ar cr
11
+ RANLIB = ppc-amigaos-ranlib
12
+ LD = ppc-amigaos-ld -r
13
+ LDFLAGS = -o
14
+ LDLIBS = LIB:scppc.a LIB:end.o
15
+ RM = delete quiet
16
+
17
+ OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
18
+ zutil.o inflate.o infback.o inftrees.o inffast.o
19
+
20
+ TEST_OBJS = example.o minigzip.o
21
+
22
+ all: example minigzip
23
+
24
+ check: test
25
+ test: all
26
+ example
27
+ echo hello world | minigzip | minigzip -d
28
+
29
+ $(LIBNAME): $(OBJS)
30
+ $(AR) $@ $(OBJS)
31
+ -$(RANLIB) $@
32
+
33
+ example: example.o $(LIBNAME)
34
+ $(LD) $(LDFLAGS) $@ LIB:c_ppc.o $@.o $(LIBNAME) $(LDLIBS)
35
+
36
+ minigzip: minigzip.o $(LIBNAME)
37
+ $(LD) $(LDFLAGS) $@ LIB:c_ppc.o $@.o $(LIBNAME) $(LDLIBS)
38
+
39
+ mostlyclean: clean
40
+ clean:
41
+ $(RM) *.o example minigzip $(LIBNAME) foo.gz
42
+
43
+ zip:
44
+ zip -ul9 zlib README ChangeLog Makefile Make????.??? Makefile.?? \
45
+ 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
+
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.