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
  192. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  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
  195. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  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
  216. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  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
  225. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  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
  229. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  230. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  231. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  232. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  233. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
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  236. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  237. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  238. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  239. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  240. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  241. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  242. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  243. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  244. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  246. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  247. data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  249. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  250. data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
  252. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  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
  259. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
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@@ -0,0 +1,461 @@
1
+ $! make libz under VMS written by
2
+ $! Martin P.J. Zinser
3
+ $! <zinser@zinser.no-ip.info or zinser@sysdev.deutsche-boerse.com>
4
+ $!
5
+ $ on error then goto err_exit
6
+ $!
7
+ $!
8
+ $! Just some general constants...
9
+ $!
10
+ $ true = 1
11
+ $ false = 0
12
+ $ tmpnam = "temp_" + f$getjpi("","pid")
13
+ $ SAY = "WRITE SYS$OUTPUT"
14
+ $!
15
+ $! Setup variables holding "config" information
16
+ $!
17
+ $ Make = ""
18
+ $ name = "Zlib"
19
+ $ version = "?.?.?"
20
+ $ v_string = "ZLIB_VERSION"
21
+ $ v_file = "zlib.h"
22
+ $ ccopt = ""
23
+ $ lopts = ""
24
+ $ linkonly = false
25
+ $ optfile = name + ".opt"
26
+ $ its_decc = false
27
+ $ its_vaxc = false
28
+ $ its_gnuc = false
29
+ $ axp = f$getsyi("HW_MODEL").ge.1024
30
+ $ s_case = false
31
+ $! Check for MMK/MMS
32
+ $!
33
+ $ If F$Search ("Sys$System:MMS.EXE") .nes. "" Then Make = "MMS"
34
+ $ If F$Type (MMK) .eqs. "STRING" Then Make = "MMK"
35
+ $!
36
+ $!
37
+ $ gosub find_version
38
+ $!
39
+ $ gosub check_opts
40
+ $!
41
+ $! Look for the compiler used
42
+ $!
43
+ $ gosub check_compiler
44
+ $ if its_decc
45
+ $ then
46
+ $ ccopt = "/prefix=all" + ccopt
47
+ $ if f$trnlnm("SYS") .eqs. ""
48
+ $ then
49
+ $ if axp
50
+ $ then
51
+ $ define sys sys$library:
52
+ $ else
53
+ $ ccopt = "/decc" + ccopt
54
+ $ define sys decc$library_include:
55
+ $ endif
56
+ $ endif
57
+ $ endif
58
+ $ if its_vaxc .or. its_gnuc
59
+ $ then
60
+ $ if f$trnlnm("SYS").eqs."" then define sys sys$library:
61
+ $ endif
62
+ $!
63
+ $! Build the thing plain or with mms
64
+ $!
65
+ $ write sys$output "Compiling Zlib sources ..."
66
+ $ if make.eqs.""
67
+ $ then
68
+ $ dele example.obj;*,minigzip.obj;*
69
+ $ CALL MAKE adler32.OBJ "CC ''CCOPT' adler32" -
70
+ adler32.c zlib.h zconf.h
71
+ $ CALL MAKE compress.OBJ "CC ''CCOPT' compress" -
72
+ compress.c zlib.h zconf.h
73
+ $ CALL MAKE crc32.OBJ "CC ''CCOPT' crc32" -
74
+ crc32.c zlib.h zconf.h
75
+ $ CALL MAKE deflate.OBJ "CC ''CCOPT' deflate" -
76
+ deflate.c deflate.h zutil.h zlib.h zconf.h
77
+ $ CALL MAKE gzio.OBJ "CC ''CCOPT' gzio" -
78
+ gzio.c zutil.h zlib.h zconf.h
79
+ $ CALL MAKE infback.OBJ "CC ''CCOPT' infback" -
80
+ infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
81
+ $ CALL MAKE inffast.OBJ "CC ''CCOPT' inffast" -
82
+ inffast.c zutil.h zlib.h zconf.h inffast.h
83
+ $ CALL MAKE inflate.OBJ "CC ''CCOPT' inflate" -
84
+ inflate.c zutil.h zlib.h zconf.h infblock.h
85
+ $ CALL MAKE inftrees.OBJ "CC ''CCOPT' inftrees" -
86
+ inftrees.c zutil.h zlib.h zconf.h inftrees.h
87
+ $ CALL MAKE trees.OBJ "CC ''CCOPT' trees" -
88
+ trees.c deflate.h zutil.h zlib.h zconf.h
89
+ $ CALL MAKE uncompr.OBJ "CC ''CCOPT' uncompr" -
90
+ uncompr.c zlib.h zconf.h
91
+ $ CALL MAKE zutil.OBJ "CC ''CCOPT' zutil" -
92
+ zutil.c zutil.h zlib.h zconf.h
93
+ $ write sys$output "Building Zlib ..."
94
+ $ CALL MAKE libz.OLB "lib/crea libz.olb *.obj" *.OBJ
95
+ $ write sys$output "Building example..."
96
+ $ CALL MAKE example.OBJ "CC ''CCOPT' example" -
97
+ example.c zlib.h zconf.h
98
+ $ call make example.exe "LINK example,libz.olb/lib" example.obj libz.olb
99
+ $ if f$search("x11vms:xvmsutils.olb") .nes. ""
100
+ $ then
101
+ $ write sys$output "Building minigzip..."
102
+ $ CALL MAKE minigzip.OBJ "CC ''CCOPT' minigzip" -
103
+ minigzip.c zlib.h zconf.h
104
+ $ call make minigzip.exe -
105
+ "LINK minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib" -
106
+ minigzip.obj libz.olb
107
+ $ endif
108
+ $ else
109
+ $ gosub crea_mms
110
+ $ SAY "Make ''name' ''version' with ''Make' "
111
+ $ 'make'
112
+ $ endif
113
+ $!
114
+ $! Alpha gets a shareable image
115
+ $!
116
+ $ If axp
117
+ $ Then
118
+ $ gosub crea_olist
119
+ $ write sys$output "Creating libzshr.exe"
120
+ $ call anal_obj_axp modules.opt _link.opt
121
+ $ if s_case
122
+ $ then
123
+ $ open/append optf modules.opt
124
+ $ write optf "case_sensitive=YES"
125
+ $ close optf
126
+ $ endif
127
+ $ LINK_'lopts'/SHARE=libzshr.exe modules.opt/opt,_link.opt/opt
128
+ $ endif
129
+ $ write sys$output "Zlib build completed"
130
+ $ exit
131
+ $CC_ERR:
132
+ $ write sys$output "C compiler required to build ''name'"
133
+ $ goto err_exit
134
+ $ERR_EXIT:
135
+ $ set message/facil/ident/sever/text
136
+ $ write sys$output "Exiting..."
137
+ $ exit 2
138
+ $!
139
+ $!
140
+ $MAKE: SUBROUTINE !SUBROUTINE TO CHECK DEPENDENCIES
141
+ $ V = 'F$Verify(0)
142
+ $! P1 = What we are trying to make
143
+ $! P2 = Command to make it
144
+ $! P3 - P8 What it depends on
145
+ $
146
+ $ If F$Search(P1) .Eqs. "" Then Goto Makeit
147
+ $ Time = F$CvTime(F$File(P1,"RDT"))
148
+ $arg=3
149
+ $Loop:
150
+ $ Argument = P'arg
151
+ $ If Argument .Eqs. "" Then Goto Exit
152
+ $ El=0
153
+ $Loop2:
154
+ $ File = F$Element(El," ",Argument)
155
+ $ If File .Eqs. " " Then Goto Endl
156
+ $ AFile = ""
157
+ $Loop3:
158
+ $ OFile = AFile
159
+ $ AFile = F$Search(File)
160
+ $ If AFile .Eqs. "" .Or. AFile .Eqs. OFile Then Goto NextEl
161
+ $ If F$CvTime(F$File(AFile,"RDT")) .Ges. Time Then Goto Makeit
162
+ $ Goto Loop3
163
+ $NextEL:
164
+ $ El = El + 1
165
+ $ Goto Loop2
166
+ $EndL:
167
+ $ arg=arg+1
168
+ $ If arg .Le. 8 Then Goto Loop
169
+ $ Goto Exit
170
+ $
171
+ $Makeit:
172
+ $ VV=F$VERIFY(0)
173
+ $ write sys$output P2
174
+ $ 'P2
175
+ $ VV='F$Verify(VV)
176
+ $Exit:
177
+ $ If V Then Set Verify
178
+ $ENDSUBROUTINE
179
+ $!------------------------------------------------------------------------------
180
+ $!
181
+ $! Check command line options and set symbols accordingly
182
+ $!
183
+ $ CHECK_OPTS:
184
+ $ i = 1
185
+ $ OPT_LOOP:
186
+ $ if i .lt. 9
187
+ $ then
188
+ $ cparm = f$edit(p'i',"upcase")
189
+ $ if cparm .eqs. "DEBUG"
190
+ $ then
191
+ $ ccopt = ccopt + "/noopt/deb"
192
+ $ lopts = lopts + "/deb"
193
+ $ endif
194
+ $ if f$locate("CCOPT=",cparm) .lt. f$length(cparm)
195
+ $ then
196
+ $ start = f$locate("=",cparm) + 1
197
+ $ len = f$length(cparm) - start
198
+ $ ccopt = ccopt + f$extract(start,len,cparm)
199
+ $ if f$locate("AS_IS",f$edit(ccopt,"UPCASE")) .lt. f$length(ccopt) -
200
+ then s_case = true
201
+ $ endif
202
+ $ if cparm .eqs. "LINK" then linkonly = true
203
+ $ if f$locate("LOPTS=",cparm) .lt. f$length(cparm)
204
+ $ then
205
+ $ start = f$locate("=",cparm) + 1
206
+ $ len = f$length(cparm) - start
207
+ $ lopts = lopts + f$extract(start,len,cparm)
208
+ $ endif
209
+ $ if f$locate("CC=",cparm) .lt. f$length(cparm)
210
+ $ then
211
+ $ start = f$locate("=",cparm) + 1
212
+ $ len = f$length(cparm) - start
213
+ $ cc_com = f$extract(start,len,cparm)
214
+ if (cc_com .nes. "DECC") .and. -
215
+ (cc_com .nes. "VAXC") .and. -
216
+ (cc_com .nes. "GNUC")
217
+ $ then
218
+ $ write sys$output "Unsupported compiler choice ''cc_com' ignored"
219
+ $ write sys$output "Use DECC, VAXC, or GNUC instead"
220
+ $ else
221
+ $ if cc_com .eqs. "DECC" then its_decc = true
222
+ $ if cc_com .eqs. "VAXC" then its_vaxc = true
223
+ $ if cc_com .eqs. "GNUC" then its_gnuc = true
224
+ $ endif
225
+ $ endif
226
+ $ if f$locate("MAKE=",cparm) .lt. f$length(cparm)
227
+ $ then
228
+ $ start = f$locate("=",cparm) + 1
229
+ $ len = f$length(cparm) - start
230
+ $ mmks = f$extract(start,len,cparm)
231
+ $ if (mmks .eqs. "MMK") .or. (mmks .eqs. "MMS")
232
+ $ then
233
+ $ make = mmks
234
+ $ else
235
+ $ write sys$output "Unsupported make choice ''mmks' ignored"
236
+ $ write sys$output "Use MMK or MMS instead"
237
+ $ endif
238
+ $ endif
239
+ $ i = i + 1
240
+ $ goto opt_loop
241
+ $ endif
242
+ $ return
243
+ $!------------------------------------------------------------------------------
244
+ $!
245
+ $! Look for the compiler used
246
+ $!
247
+ $CHECK_COMPILER:
248
+ $ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
249
+ $ then
250
+ $ its_decc = (f$search("SYS$SYSTEM:DECC$COMPILER.EXE") .nes. "")
251
+ $ its_vaxc = .not. its_decc .and. (F$Search("SYS$System:VAXC.Exe") .nes. "")
252
+ $ its_gnuc = .not. (its_decc .or. its_vaxc) .and. (f$trnlnm("gnu_cc") .nes. "")
253
+ $ endif
254
+ $!
255
+ $! Exit if no compiler available
256
+ $!
257
+ $ if (.not. (its_decc .or. its_vaxc .or. its_gnuc))
258
+ $ then goto CC_ERR
259
+ $ else
260
+ $ if its_decc then write sys$output "CC compiler check ... Compaq C"
261
+ $ if its_vaxc then write sys$output "CC compiler check ... VAX C"
262
+ $ if its_gnuc then write sys$output "CC compiler check ... GNU C"
263
+ $ endif
264
+ $ return
265
+ $!------------------------------------------------------------------------------
266
+ $!
267
+ $! If MMS/MMK are available dump out the descrip.mms if required
268
+ $!
269
+ $CREA_MMS:
270
+ $ write sys$output "Creating descrip.mms..."
271
+ $ create descrip.mms
272
+ $ open/append out descrip.mms
273
+ $ copy sys$input: out
274
+ $ deck
275
+ # descrip.mms: MMS description file for building zlib on VMS
276
+ # written by Martin P.J. Zinser
277
+ # <zinser@zinser.no-ip.info or zinser@sysdev.deutsche-boerse.com>
278
+
279
+ OBJS = adler32.obj, compress.obj, crc32.obj, gzio.obj, uncompr.obj, infback.obj\
280
+ deflate.obj, trees.obj, zutil.obj, inflate.obj, \
281
+ inftrees.obj, inffast.obj
282
+
283
+ $ eod
284
+ $ write out "CFLAGS=", ccopt
285
+ $ write out "LOPTS=", lopts
286
+ $ copy sys$input: out
287
+ $ deck
288
+
289
+ all : example.exe minigzip.exe libz.olb
290
+ @ write sys$output " Example applications available"
291
+
292
+ libz.olb : libz.olb($(OBJS))
293
+ @ write sys$output " libz available"
294
+
295
+ example.exe : example.obj libz.olb
296
+ link $(LOPTS) example,libz.olb/lib
297
+
298
+ minigzip.exe : minigzip.obj libz.olb
299
+ link $(LOPTS) minigzip,libz.olb/lib,x11vms:xvmsutils.olb/lib
300
+
301
+ clean :
302
+ delete *.obj;*,libz.olb;*,*.opt;*,*.exe;*
303
+
304
+
305
+ # Other dependencies.
306
+ adler32.obj : adler32.c zutil.h zlib.h zconf.h
307
+ compress.obj : compress.c zlib.h zconf.h
308
+ crc32.obj : crc32.c zutil.h zlib.h zconf.h
309
+ deflate.obj : deflate.c deflate.h zutil.h zlib.h zconf.h
310
+ example.obj : example.c zlib.h zconf.h
311
+ gzio.obj : gzio.c zutil.h zlib.h zconf.h
312
+ inffast.obj : inffast.c zutil.h zlib.h zconf.h inftrees.h inffast.h
313
+ inflate.obj : inflate.c zutil.h zlib.h zconf.h
314
+ inftrees.obj : inftrees.c zutil.h zlib.h zconf.h inftrees.h
315
+ minigzip.obj : minigzip.c zlib.h zconf.h
316
+ trees.obj : trees.c deflate.h zutil.h zlib.h zconf.h
317
+ uncompr.obj : uncompr.c zlib.h zconf.h
318
+ zutil.obj : zutil.c zutil.h zlib.h zconf.h
319
+ infback.obj : infback.c zutil.h inftrees.h inflate.h inffast.h inffixed.h
320
+ $ eod
321
+ $ close out
322
+ $ return
323
+ $!------------------------------------------------------------------------------
324
+ $!
325
+ $! Read list of core library sources from makefile.in and create options
326
+ $! needed to build shareable image
327
+ $!
328
+ $CREA_OLIST:
329
+ $ open/read min makefile.in
330
+ $ open/write mod modules.opt
331
+ $ src_check = "OBJS ="
332
+ $MRLOOP:
333
+ $ read/end=mrdone min rec
334
+ $ if (f$extract(0,6,rec) .nes. src_check) then goto mrloop
335
+ $ rec = rec - src_check
336
+ $ gosub extra_filnam
337
+ $ if (f$element(1,"\",rec) .eqs. "\") then goto mrdone
338
+ $MRSLOOP:
339
+ $ read/end=mrdone min rec
340
+ $ gosub extra_filnam
341
+ $ if (f$element(1,"\",rec) .nes. "\") then goto mrsloop
342
+ $MRDONE:
343
+ $ close min
344
+ $ close mod
345
+ $ return
346
+ $!------------------------------------------------------------------------------
347
+ $!
348
+ $! Take record extracted in crea_olist and split it into single filenames
349
+ $!
350
+ $EXTRA_FILNAM:
351
+ $ myrec = f$edit(rec - "\", "trim,compress")
352
+ $ i = 0
353
+ $FELOOP:
354
+ $ srcfil = f$element(i," ", myrec)
355
+ $ if (srcfil .nes. " ")
356
+ $ then
357
+ $ write mod f$parse(srcfil,,,"NAME"), ".obj"
358
+ $ i = i + 1
359
+ $ goto feloop
360
+ $ endif
361
+ $ return
362
+ $!------------------------------------------------------------------------------
363
+ $!
364
+ $! Find current Zlib version number
365
+ $!
366
+ $FIND_VERSION:
367
+ $ open/read h_in 'v_file'
368
+ $hloop:
369
+ $ read/end=hdone h_in rec
370
+ $ rec = f$edit(rec,"TRIM")
371
+ $ if (f$extract(0,1,rec) .nes. "#") then goto hloop
372
+ $ rec = f$edit(rec - "#", "TRIM")
373
+ $ if f$element(0," ",rec) .nes. "define" then goto hloop
374
+ $ if f$element(1," ",rec) .eqs. v_string
375
+ $ then
376
+ $ version = 'f$element(2," ",rec)'
377
+ $ goto hdone
378
+ $ endif
379
+ $ goto hloop
380
+ $hdone:
381
+ $ close h_in
382
+ $ return
383
+ $!------------------------------------------------------------------------------
384
+ $!
385
+ $! Analyze Object files for OpenVMS AXP to extract Procedure and Data
386
+ $! information to build a symbol vector for a shareable image
387
+ $! All the "brains" of this logic was suggested by Hartmut Becker
388
+ $! (Hartmut.Becker@compaq.com). All the bugs were introduced by me
389
+ $! (zinser@decus.de), so if you do have problem reports please do not
390
+ $! bother Hartmut/HP, but get in touch with me
391
+ $!
392
+ $ ANAL_OBJ_AXP: Subroutine
393
+ $ V = 'F$Verify(0)
394
+ $ SAY := "WRITE_ SYS$OUTPUT"
395
+ $
396
+ $ IF F$SEARCH("''P1'") .EQS. ""
397
+ $ THEN
398
+ $ SAY "ANAL_OBJ_AXP-E-NOSUCHFILE: Error, inputfile ''p1' not available"
399
+ $ goto exit_aa
400
+ $ ENDIF
401
+ $ IF "''P2'" .EQS. ""
402
+ $ THEN
403
+ $ SAY "ANAL_OBJ_AXP: Error, no output file provided"
404
+ $ goto exit_aa
405
+ $ ENDIF
406
+ $
407
+ $ open/read in 'p1
408
+ $ create a.tmp
409
+ $ open/append atmp a.tmp
410
+ $ loop:
411
+ $ read/end=end_loop in line
412
+ $ f= f$search(line)
413
+ $ if f .eqs. ""
414
+ $ then
415
+ $ write sys$output "ANAL_OBJ_AXP-w-nosuchfile, ''line'"
416
+ $ goto loop
417
+ $ endif
418
+ $ define/user sys$output nl:
419
+ $ define/user sys$error nl:
420
+ $ anal/obj/gsd 'f /out=x.tmp
421
+ $ open/read xtmp x.tmp
422
+ $ XLOOP:
423
+ $ read/end=end_xloop xtmp xline
424
+ $ xline = f$edit(xline,"compress")
425
+ $ write atmp xline
426
+ $ goto xloop
427
+ $ END_XLOOP:
428
+ $ close xtmp
429
+ $ goto loop
430
+ $ end_loop:
431
+ $ close in
432
+ $ close atmp
433
+ $ if f$search("a.tmp") .eqs. "" -
434
+ then $ exit
435
+ $ ! all global definitions
436
+ $ search a.tmp "symbol:","EGSY$V_DEF 1","EGSY$V_NORM 1"/out=b.tmp
437
+ $ ! all procedures
438
+ $ search b.tmp "EGSY$V_NORM 1"/wind=(0,1) /out=c.tmp
439
+ $ search c.tmp "symbol:"/out=d.tmp
440
+ $ define/user sys$output nl:
441
+ $ edito/edt/command=sys$input d.tmp
442
+ sub/symbol: "/symbol_vector=(/whole
443
+ sub/"/=PROCEDURE)/whole
444
+ exit
445
+ $ ! all data
446
+ $ search b.tmp "EGSY$V_DEF 1"/wind=(0,1) /out=e.tmp
447
+ $ search e.tmp "symbol:"/out=f.tmp
448
+ $ define/user sys$output nl:
449
+ $ edito/edt/command=sys$input f.tmp
450
+ sub/symbol: "/symbol_vector=(/whole
451
+ sub/"/=DATA)/whole
452
+ exit
453
+ $ sort/nodupl d.tmp,f.tmp 'p2'
454
+ $ delete a.tmp;*,b.tmp;*,c.tmp;*,d.tmp;*,e.tmp;*,f.tmp;*
455
+ $ if f$search("x.tmp") .nes. "" -
456
+ then $ delete x.tmp;*
457
+ $!
458
+ $ EXIT_AA:
459
+ $ if V then set verify
460
+ $ endsubroutine
461
+ $!------------------------------------------------------------------------------