finishm 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
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
  234. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
  235. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
  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
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
  262. data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
  263. data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
  264. data/ext/src/third-party/zlib-1.2.3/gzio.o +0 -0
  265. data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
  266. data/ext/src/third-party/zlib-1.2.3/infback.o +0 -0
  267. data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
  268. data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
  269. data/ext/src/third-party/zlib-1.2.3/inffast.o +0 -0
  270. data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
  271. data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
  272. data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
  273. data/ext/src/third-party/zlib-1.2.3/inflate.o +0 -0
  274. data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
  275. data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
  276. data/ext/src/third-party/zlib-1.2.3/inftrees.o +0 -0
  277. data/ext/src/third-party/zlib-1.2.3/libz.a +0 -0
  278. data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
  279. data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
  280. data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
  281. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
  282. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
  283. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
  284. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
  285. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
  286. data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
  287. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  288. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  289. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  290. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  291. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  292. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  293. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  294. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  295. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  296. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  297. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  298. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  299. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  300. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  301. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  302. data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
  303. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  304. data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
  305. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  306. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  307. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  308. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  309. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  310. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  311. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  312. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  313. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  314. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  315. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  316. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  317. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  318. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  319. data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
  320. data/lib/assembly/a_b_visualiser.rb +169 -0
  321. data/lib/assembly/acyclic_connection_finder.rb +81 -0
  322. data/lib/assembly/all_orfs.rb +615 -0
  323. data/lib/assembly/bad_format_writer.rb +46 -0
  324. data/lib/assembly/bam_probe_read_selector.rb +48 -0
  325. data/lib/assembly/bubbly_assembler.rb +842 -0
  326. data/lib/assembly/c_probe_node_finder.rb +38 -0
  327. data/lib/assembly/connection_interpreter.rb +350 -0
  328. data/lib/assembly/contig_printer.rb +400 -0
  329. data/lib/assembly/coverage_based_graph_filter.rb +68 -0
  330. data/lib/assembly/depth_first_search.rb +63 -0
  331. data/lib/assembly/dijkstra.rb +216 -0
  332. data/lib/assembly/fluffer.rb +253 -0
  333. data/lib/assembly/graph_explorer.rb +85 -0
  334. data/lib/assembly/graph_generator.rb +315 -0
  335. data/lib/assembly/height_finder.rb +355 -0
  336. data/lib/assembly/hybrid_velvet_graph.rb +70 -0
  337. data/lib/assembly/input_genome.rb +182 -0
  338. data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
  339. data/lib/assembly/node_finder.rb +171 -0
  340. data/lib/assembly/oriented_node_trail.rb +507 -0
  341. data/lib/assembly/paired_end_assembler.rb +53 -0
  342. data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
  343. data/lib/assembly/probed_graph.rb +105 -0
  344. data/lib/assembly/read_input.rb +79 -0
  345. data/lib/assembly/read_to_node.rb +37 -0
  346. data/lib/assembly/scaffold_breaker.rb +126 -0
  347. data/lib/assembly/sequence_hasher.rb +71 -0
  348. data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
  349. data/lib/assembly/single_coherent_wanderer.rb +261 -0
  350. data/lib/assembly/single_ended_assembler.rb +441 -0
  351. data/lib/assembly/velvet_c_binding.rb +54 -0
  352. data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
  353. data/lib/external/VERSION +1 -0
  354. data/lib/finishm/assemble.rb +224 -0
  355. data/lib/finishm/explore.rb +217 -0
  356. data/lib/finishm/finisher.rb +303 -0
  357. data/lib/finishm/fluff.rb +122 -0
  358. data/lib/finishm/gapfiller.rb +325 -0
  359. data/lib/finishm/orfs_finder.rb +88 -0
  360. data/lib/finishm/path_counter.rb +90 -0
  361. data/lib/finishm/primers.rb +425 -0
  362. data/lib/finishm/primers_check.rb +176 -0
  363. data/lib/finishm/roundup.rb +344 -0
  364. data/lib/finishm/sequence.rb +142 -0
  365. data/lib/finishm/visualise.rb +430 -0
  366. data/lib/finishm/wander.rb +270 -0
  367. data/lib/kmer_abundance_pattern.rb +79 -0
  368. data/lib/kmer_multi_abundance_file.rb +48 -0
  369. data/lib/oligo_designer.rb +88 -0
  370. data/lib/priner.rb +66 -0
  371. data/spec/acyclic_connection_finder_spec.rb +551 -0
  372. data/spec/all_orfs_spec.rb +443 -0
  373. data/spec/assemble_spec.rb +186 -0
  374. data/spec/bubbly_assembler_spec.rb +707 -0
  375. data/spec/c_node_finder_spec.rb +58 -0
  376. data/spec/connection_interpreter_spec.rb +284 -0
  377. data/spec/contig_printer_spec.rb +291 -0
  378. data/spec/coverage_based_graph_filter_spec.rb +102 -0
  379. data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
  380. data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
  381. data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
  382. data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
  383. data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
  384. data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
  385. data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
  386. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
  387. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
  388. data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
  389. data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
  390. data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
  391. data/spec/data/assembly_visualiser/Graph +46 -0
  392. data/spec/data/assembly_visualiser/start_kmers1 +2 -0
  393. data/spec/data/bands.csv +1 -0
  394. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
  395. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
  396. data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
  397. data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
  398. data/spec/data/c_probe_node_finder/1/Log +756 -0
  399. data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
  400. data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
  401. data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
  402. data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
  403. data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
  404. data/spec/data/contig_printer/1/contigs.fa +4 -0
  405. data/spec/data/contig_printer/1/seq.fa +2408 -0
  406. data/spec/data/contig_printer/1/seq.fa.svg +153 -0
  407. data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
  408. data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
  409. data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
  410. data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
  411. data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
  412. data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
  413. data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
  414. data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
  415. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
  416. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
  417. data/spec/data/contig_printer/1/seq.node12.fa +4 -0
  418. data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
  419. data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
  420. data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
  421. data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
  422. data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
  423. data/spec/data/explore/1/a.fa +2 -0
  424. data/spec/data/explore/1/seq1_and_a.fa +3 -0
  425. data/spec/data/explore/1/seq2.fa +2 -0
  426. data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
  427. data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
  428. data/spec/data/fluff/1/seq1.fa +2 -0
  429. data/spec/data/fluff/1/seq2.fa +2 -0
  430. data/spec/data/gapfilling/1/reads.fa +171 -0
  431. data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
  432. data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
  433. data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
  434. data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
  435. data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
  436. data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
  437. data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
  438. data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
  439. data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
  440. data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
  441. data/spec/data/gapfilling/2/reference.fa +2 -0
  442. data/spec/data/gapfilling/2/reference_part1.fa +4 -0
  443. data/spec/data/gapfilling/2/reference_part2.fa +4 -0
  444. data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
  445. data/spec/data/gapfilling/2/with_gaps.fa +4 -0
  446. data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
  447. data/spec/data/gapfilling/3/reads.fa.gz +0 -0
  448. data/spec/data/gapfilling/3/reference_part1.fa +4 -0
  449. data/spec/data/gapfilling/3/reference_part2.fa +4 -0
  450. data/spec/data/gapfilling/3/with_gaps.fa +4 -0
  451. data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
  452. data/spec/data/gapfilling/4/reads.fa.gz +0 -0
  453. data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
  454. data/spec/data/gapfilling/5/answer.fna +2 -0
  455. data/spec/data/gapfilling/5/gappy.fna +2 -0
  456. data/spec/data/gapfilling/5/reads.fa +17961 -0
  457. data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
  458. data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
  459. data/spec/data/gapfilling/6/random1.fa +28 -0
  460. data/spec/data/gapfilling/6/random2.fa +28 -0
  461. data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
  462. data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
  463. data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
  464. data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
  465. data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
  466. data/spec/data/kmers_count1.csv +2 -0
  467. data/spec/data/kmers_count2.csv +3 -0
  468. data/spec/data/out +3 -0
  469. data/spec/data/positive_latching_pair.fa +2 -0
  470. data/spec/data/primers.csv +4 -0
  471. data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
  472. data/spec/data/read_selection_by_kmer/input.fasta +6 -0
  473. data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
  474. data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
  475. data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
  476. data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
  477. data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
  478. data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
  479. data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
  480. data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
  481. data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
  482. data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
  483. data/spec/data/t/details.txt +5 -0
  484. data/spec/data/t/details.txt.srt +5 -0
  485. data/spec/data/t/location.txt +3 -0
  486. data/spec/data/t/location.txt.srt +3 -0
  487. data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
  488. data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
  489. data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
  490. data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
  491. data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
  492. data/spec/data/tweak/3_variant/answer.fa +2 -0
  493. data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
  494. data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
  495. data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
  496. data/spec/data/velvet_test_trails/Assem/Graph +17 -0
  497. data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
  498. data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
  499. data/spec/data/velvet_test_trails/Assem/Log +35 -0
  500. data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
  501. data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
  502. data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
  503. data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
  504. data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
  505. data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
  506. data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
  507. data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
  508. data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
  509. data/spec/data/velvet_test_trails/read1.fa +2 -0
  510. data/spec/data/velvet_test_trails/reads.fa +50 -0
  511. data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
  512. data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
  513. data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
  514. data/spec/data/visualise/1/LastGraph +6695 -0
  515. data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
  516. data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
  517. data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
  518. data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
  519. data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
  520. data/spec/data/wander/1/random1.fa +2 -0
  521. data/spec/data/wander/1/random1.sammy.fa +804 -0
  522. data/spec/depth_first_search_spec.rb +190 -0
  523. data/spec/dijkstra_spec.rb +143 -0
  524. data/spec/explore_spec.rb +29 -0
  525. data/spec/fluffer_spec.rb +155 -0
  526. data/spec/gapfiller_spec.rb +107 -0
  527. data/spec/graph_explorer_spec.rb +475 -0
  528. data/spec/graph_generator_spec.rb +99 -0
  529. data/spec/height_finder_spec.rb +306 -0
  530. data/spec/kmer_abundance_pattern_spec.rb +56 -0
  531. data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
  532. data/spec/kmer_profile_finder_spec.rb +38 -0
  533. data/spec/kmers_count_tabulate_spec.rb +120 -0
  534. data/spec/oriented_node_trail_spec.rb +221 -0
  535. data/spec/paired_end_neighbours_spec.rb +126 -0
  536. data/spec/paths_between_nodes_spec.rb +349 -0
  537. data/spec/priner_spec.rb +7 -0
  538. data/spec/read_input_spec.rb +23 -0
  539. data/spec/read_selection_by_kmer_spec.rb +166 -0
  540. data/spec/read_to_node_spec.rb +35 -0
  541. data/spec/roundup_spec.rb +366 -0
  542. data/spec/scaffold_breaker_spec.rb +144 -0
  543. data/spec/sequence_spec.rb +43 -0
  544. data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
  545. data/spec/single_coherent_wanderer_spec.rb +120 -0
  546. data/spec/single_ended_assembler_spec.rb +398 -0
  547. data/spec/spec_helper.rb +310 -0
  548. data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
  549. data/spec/visualise_spec.rb +105 -0
  550. data/spec/wander_spec.rb +119 -0
  551. data/spec/watch_for_changes.sh +16 -0
  552. data/validation/fasta_compare.rb +72 -0
  553. data/validation/gapfill_simulate_perfect.rb +108 -0
  554. metadata +899 -0
@@ -0,0 +1,60 @@
1
+ LIBRARY
2
+ ; zlib data compression library
3
+
4
+ EXPORTS
5
+ ; basic functions
6
+ zlibVersion
7
+ deflate
8
+ deflateEnd
9
+ inflate
10
+ inflateEnd
11
+ ; advanced functions
12
+ deflateSetDictionary
13
+ deflateCopy
14
+ deflateReset
15
+ deflateParams
16
+ deflateBound
17
+ deflatePrime
18
+ inflateSetDictionary
19
+ inflateSync
20
+ inflateCopy
21
+ inflateReset
22
+ inflateBack
23
+ inflateBackEnd
24
+ zlibCompileFlags
25
+ ; utility functions
26
+ compress
27
+ compress2
28
+ compressBound
29
+ uncompress
30
+ gzopen
31
+ gzdopen
32
+ gzsetparams
33
+ gzread
34
+ gzwrite
35
+ gzprintf
36
+ gzputs
37
+ gzgets
38
+ gzputc
39
+ gzgetc
40
+ gzungetc
41
+ gzflush
42
+ gzseek
43
+ gzrewind
44
+ gztell
45
+ gzeof
46
+ gzclose
47
+ gzerror
48
+ gzclearerr
49
+ ; checksum functions
50
+ adler32
51
+ crc32
52
+ ; various hacks, don't look :)
53
+ deflateInit_
54
+ deflateInit2_
55
+ inflateInit_
56
+ inflateInit2_
57
+ inflateBackInit_
58
+ inflateSyncPoint
59
+ get_crc_table
60
+ zError
@@ -0,0 +1,39 @@
1
+ #include <windows.h>
2
+
3
+ #ifdef GCC_WINDRES
4
+ VS_VERSION_INFO VERSIONINFO
5
+ #else
6
+ VS_VERSION_INFO VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
7
+ #endif
8
+ FILEVERSION 1,2,2,0
9
+ PRODUCTVERSION 1,2,2,0
10
+ FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
11
+ #ifdef _DEBUG
12
+ FILEFLAGS 1
13
+ #else
14
+ FILEFLAGS 0
15
+ #endif
16
+ FILEOS VOS_DOS_WINDOWS32
17
+ FILETYPE VFT_DLL
18
+ FILESUBTYPE 0 // not used
19
+ BEGIN
20
+ BLOCK "StringFileInfo"
21
+ BEGIN
22
+ BLOCK "040904E4"
23
+ //language ID = U.S. English, char set = Windows, Multilingual
24
+ BEGIN
25
+ VALUE "FileDescription", "zlib data compression library\0"
26
+ VALUE "FileVersion", "1.2.3\0"
27
+ VALUE "InternalName", "zlib1.dll\0"
28
+ VALUE "LegalCopyright", "(C) 1995-2004 Jean-loup Gailly & Mark Adler\0"
29
+ VALUE "OriginalFilename", "zlib1.dll\0"
30
+ VALUE "ProductName", "zlib\0"
31
+ VALUE "ProductVersion", "1.2.3\0"
32
+ VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
33
+ END
34
+ END
35
+ BLOCK "VarFileInfo"
36
+ BEGIN
37
+ VALUE "Translation", 0x0409, 1252
38
+ END
39
+ END
@@ -0,0 +1,332 @@
1
+ /* zconf.h -- configuration of the zlib compression library
2
+ * Copyright (C) 1995-2005 Jean-loup Gailly.
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* @(#) $Id$ */
7
+
8
+ #ifndef ZCONF_H
9
+ #define ZCONF_H
10
+
11
+ /*
12
+ * If you *really* need a unique prefix for all types and library functions,
13
+ * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
14
+ */
15
+ #ifdef Z_PREFIX
16
+ # define deflateInit_ z_deflateInit_
17
+ # define deflate z_deflate
18
+ # define deflateEnd z_deflateEnd
19
+ # define inflateInit_ z_inflateInit_
20
+ # define inflate z_inflate
21
+ # define inflateEnd z_inflateEnd
22
+ # define deflateInit2_ z_deflateInit2_
23
+ # define deflateSetDictionary z_deflateSetDictionary
24
+ # define deflateCopy z_deflateCopy
25
+ # define deflateReset z_deflateReset
26
+ # define deflateParams z_deflateParams
27
+ # define deflateBound z_deflateBound
28
+ # define deflatePrime z_deflatePrime
29
+ # define inflateInit2_ z_inflateInit2_
30
+ # define inflateSetDictionary z_inflateSetDictionary
31
+ # define inflateSync z_inflateSync
32
+ # define inflateSyncPoint z_inflateSyncPoint
33
+ # define inflateCopy z_inflateCopy
34
+ # define inflateReset z_inflateReset
35
+ # define inflateBack z_inflateBack
36
+ # define inflateBackEnd z_inflateBackEnd
37
+ # define compress z_compress
38
+ # define compress2 z_compress2
39
+ # define compressBound z_compressBound
40
+ # define uncompress z_uncompress
41
+ # define adler32 z_adler32
42
+ # define crc32 z_crc32
43
+ # define get_crc_table z_get_crc_table
44
+ # define zError z_zError
45
+
46
+ # define alloc_func z_alloc_func
47
+ # define free_func z_free_func
48
+ # define in_func z_in_func
49
+ # define out_func z_out_func
50
+ # define Byte z_Byte
51
+ # define uInt z_uInt
52
+ # define uLong z_uLong
53
+ # define Bytef z_Bytef
54
+ # define charf z_charf
55
+ # define intf z_intf
56
+ # define uIntf z_uIntf
57
+ # define uLongf z_uLongf
58
+ # define voidpf z_voidpf
59
+ # define voidp z_voidp
60
+ #endif
61
+
62
+ #if defined(__MSDOS__) && !defined(MSDOS)
63
+ # define MSDOS
64
+ #endif
65
+ #if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
66
+ # define OS2
67
+ #endif
68
+ #if defined(_WINDOWS) && !defined(WINDOWS)
69
+ # define WINDOWS
70
+ #endif
71
+ #if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
72
+ # ifndef WIN32
73
+ # define WIN32
74
+ # endif
75
+ #endif
76
+ #if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
77
+ # if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
78
+ # ifndef SYS16BIT
79
+ # define SYS16BIT
80
+ # endif
81
+ # endif
82
+ #endif
83
+
84
+ /*
85
+ * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
86
+ * than 64k bytes at a time (needed on systems with 16-bit int).
87
+ */
88
+ #ifdef SYS16BIT
89
+ # define MAXSEG_64K
90
+ #endif
91
+ #ifdef MSDOS
92
+ # define UNALIGNED_OK
93
+ #endif
94
+
95
+ #ifdef __STDC_VERSION__
96
+ # ifndef STDC
97
+ # define STDC
98
+ # endif
99
+ # if __STDC_VERSION__ >= 199901L
100
+ # ifndef STDC99
101
+ # define STDC99
102
+ # endif
103
+ # endif
104
+ #endif
105
+ #if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
106
+ # define STDC
107
+ #endif
108
+ #if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
109
+ # define STDC
110
+ #endif
111
+ #if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
112
+ # define STDC
113
+ #endif
114
+ #if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
115
+ # define STDC
116
+ #endif
117
+
118
+ #if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
119
+ # define STDC
120
+ #endif
121
+
122
+ #ifndef STDC
123
+ # ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
124
+ # define const /* note: need a more gentle solution here */
125
+ # endif
126
+ #endif
127
+
128
+ /* Some Mac compilers merge all .h files incorrectly: */
129
+ #if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
130
+ # define NO_DUMMY_DECL
131
+ #endif
132
+
133
+ /* Maximum value for memLevel in deflateInit2 */
134
+ #ifndef MAX_MEM_LEVEL
135
+ # ifdef MAXSEG_64K
136
+ # define MAX_MEM_LEVEL 8
137
+ # else
138
+ # define MAX_MEM_LEVEL 9
139
+ # endif
140
+ #endif
141
+
142
+ /* Maximum value for windowBits in deflateInit2 and inflateInit2.
143
+ * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
144
+ * created by gzip. (Files created by minigzip can still be extracted by
145
+ * gzip.)
146
+ */
147
+ #ifndef MAX_WBITS
148
+ # define MAX_WBITS 15 /* 32K LZ77 window */
149
+ #endif
150
+
151
+ /* The memory requirements for deflate are (in bytes):
152
+ (1 << (windowBits+2)) + (1 << (memLevel+9))
153
+ that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
154
+ plus a few kilobytes for small objects. For example, if you want to reduce
155
+ the default memory requirements from 256K to 128K, compile with
156
+ make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
157
+ Of course this will generally degrade compression (there's no free lunch).
158
+
159
+ The memory requirements for inflate are (in bytes) 1 << windowBits
160
+ that is, 32K for windowBits=15 (default value) plus a few kilobytes
161
+ for small objects.
162
+ */
163
+
164
+ /* Type declarations */
165
+
166
+ #ifndef OF /* function prototypes */
167
+ # ifdef STDC
168
+ # define OF(args) args
169
+ # else
170
+ # define OF(args) ()
171
+ # endif
172
+ #endif
173
+
174
+ /* The following definitions for FAR are needed only for MSDOS mixed
175
+ * model programming (small or medium model with some far allocations).
176
+ * This was tested only with MSC; for other MSDOS compilers you may have
177
+ * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
178
+ * just define FAR to be empty.
179
+ */
180
+ #ifdef SYS16BIT
181
+ # if defined(M_I86SM) || defined(M_I86MM)
182
+ /* MSC small or medium model */
183
+ # define SMALL_MEDIUM
184
+ # ifdef _MSC_VER
185
+ # define FAR _far
186
+ # else
187
+ # define FAR far
188
+ # endif
189
+ # endif
190
+ # if (defined(__SMALL__) || defined(__MEDIUM__))
191
+ /* Turbo C small or medium model */
192
+ # define SMALL_MEDIUM
193
+ # ifdef __BORLANDC__
194
+ # define FAR _far
195
+ # else
196
+ # define FAR far
197
+ # endif
198
+ # endif
199
+ #endif
200
+
201
+ #if defined(WINDOWS) || defined(WIN32)
202
+ /* If building or using zlib as a DLL, define ZLIB_DLL.
203
+ * This is not mandatory, but it offers a little performance increase.
204
+ */
205
+ # ifdef ZLIB_DLL
206
+ # if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
207
+ # ifdef ZLIB_INTERNAL
208
+ # define ZEXTERN extern __declspec(dllexport)
209
+ # else
210
+ # define ZEXTERN extern __declspec(dllimport)
211
+ # endif
212
+ # endif
213
+ # endif /* ZLIB_DLL */
214
+ /* If building or using zlib with the WINAPI/WINAPIV calling convention,
215
+ * define ZLIB_WINAPI.
216
+ * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
217
+ */
218
+ # ifdef ZLIB_WINAPI
219
+ # ifdef FAR
220
+ # undef FAR
221
+ # endif
222
+ # include <windows.h>
223
+ /* No need for _export, use ZLIB.DEF instead. */
224
+ /* For complete Windows compatibility, use WINAPI, not __stdcall. */
225
+ # define ZEXPORT WINAPI
226
+ # ifdef WIN32
227
+ # define ZEXPORTVA WINAPIV
228
+ # else
229
+ # define ZEXPORTVA FAR CDECL
230
+ # endif
231
+ # endif
232
+ #endif
233
+
234
+ #if defined (__BEOS__)
235
+ # ifdef ZLIB_DLL
236
+ # ifdef ZLIB_INTERNAL
237
+ # define ZEXPORT __declspec(dllexport)
238
+ # define ZEXPORTVA __declspec(dllexport)
239
+ # else
240
+ # define ZEXPORT __declspec(dllimport)
241
+ # define ZEXPORTVA __declspec(dllimport)
242
+ # endif
243
+ # endif
244
+ #endif
245
+
246
+ #ifndef ZEXTERN
247
+ # define ZEXTERN extern
248
+ #endif
249
+ #ifndef ZEXPORT
250
+ # define ZEXPORT
251
+ #endif
252
+ #ifndef ZEXPORTVA
253
+ # define ZEXPORTVA
254
+ #endif
255
+
256
+ #ifndef FAR
257
+ # define FAR
258
+ #endif
259
+
260
+ #if !defined(__MACTYPES__)
261
+ typedef unsigned char Byte; /* 8 bits */
262
+ #endif
263
+ typedef unsigned int uInt; /* 16 bits or more */
264
+ typedef unsigned long uLong; /* 32 bits or more */
265
+
266
+ #ifdef SMALL_MEDIUM
267
+ /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
268
+ # define Bytef Byte FAR
269
+ #else
270
+ typedef Byte FAR Bytef;
271
+ #endif
272
+ typedef char FAR charf;
273
+ typedef int FAR intf;
274
+ typedef uInt FAR uIntf;
275
+ typedef uLong FAR uLongf;
276
+
277
+ #ifdef STDC
278
+ typedef void const *voidpc;
279
+ typedef void FAR *voidpf;
280
+ typedef void *voidp;
281
+ #else
282
+ typedef Byte const *voidpc;
283
+ typedef Byte FAR *voidpf;
284
+ typedef Byte *voidp;
285
+ #endif
286
+
287
+ #if 1 /* HAVE_UNISTD_H -- this line is updated by ./configure */
288
+ # include <sys/types.h> /* for off_t */
289
+ # include <unistd.h> /* for SEEK_* and off_t */
290
+ # ifdef VMS
291
+ # include <unixio.h> /* for off_t */
292
+ # endif
293
+ # define z_off_t off_t
294
+ #endif
295
+ #ifndef SEEK_SET
296
+ # define SEEK_SET 0 /* Seek from beginning of file. */
297
+ # define SEEK_CUR 1 /* Seek from current position. */
298
+ # define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
299
+ #endif
300
+ #ifndef z_off_t
301
+ # define z_off_t long
302
+ #endif
303
+
304
+ #if defined(__OS400__)
305
+ # define NO_vsnprintf
306
+ #endif
307
+
308
+ #if defined(__MVS__)
309
+ # define NO_vsnprintf
310
+ # ifdef FAR
311
+ # undef FAR
312
+ # endif
313
+ #endif
314
+
315
+ /* MVS linker does not support external names larger than 8 bytes */
316
+ #if defined(__MVS__)
317
+ # pragma map(deflateInit_,"DEIN")
318
+ # pragma map(deflateInit2_,"DEIN2")
319
+ # pragma map(deflateEnd,"DEEND")
320
+ # pragma map(deflateBound,"DEBND")
321
+ # pragma map(inflateInit_,"ININ")
322
+ # pragma map(inflateInit2_,"ININ2")
323
+ # pragma map(inflateEnd,"INEND")
324
+ # pragma map(inflateSync,"INSY")
325
+ # pragma map(inflateSetDictionary,"INSEDI")
326
+ # pragma map(compressBound,"CMBND")
327
+ # pragma map(inflate_table,"INTABL")
328
+ # pragma map(inflate_fast,"INFA")
329
+ # pragma map(inflate_copyright,"INCOPY")
330
+ #endif
331
+
332
+ #endif /* ZCONF_H */
@@ -0,0 +1,332 @@
1
+ /* zconf.h -- configuration of the zlib compression library
2
+ * Copyright (C) 1995-2005 Jean-loup Gailly.
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* @(#) $Id$ */
7
+
8
+ #ifndef ZCONF_H
9
+ #define ZCONF_H
10
+
11
+ /*
12
+ * If you *really* need a unique prefix for all types and library functions,
13
+ * compile with -DZ_PREFIX. The "standard" zlib should be compiled without it.
14
+ */
15
+ #ifdef Z_PREFIX
16
+ # define deflateInit_ z_deflateInit_
17
+ # define deflate z_deflate
18
+ # define deflateEnd z_deflateEnd
19
+ # define inflateInit_ z_inflateInit_
20
+ # define inflate z_inflate
21
+ # define inflateEnd z_inflateEnd
22
+ # define deflateInit2_ z_deflateInit2_
23
+ # define deflateSetDictionary z_deflateSetDictionary
24
+ # define deflateCopy z_deflateCopy
25
+ # define deflateReset z_deflateReset
26
+ # define deflateParams z_deflateParams
27
+ # define deflateBound z_deflateBound
28
+ # define deflatePrime z_deflatePrime
29
+ # define inflateInit2_ z_inflateInit2_
30
+ # define inflateSetDictionary z_inflateSetDictionary
31
+ # define inflateSync z_inflateSync
32
+ # define inflateSyncPoint z_inflateSyncPoint
33
+ # define inflateCopy z_inflateCopy
34
+ # define inflateReset z_inflateReset
35
+ # define inflateBack z_inflateBack
36
+ # define inflateBackEnd z_inflateBackEnd
37
+ # define compress z_compress
38
+ # define compress2 z_compress2
39
+ # define compressBound z_compressBound
40
+ # define uncompress z_uncompress
41
+ # define adler32 z_adler32
42
+ # define crc32 z_crc32
43
+ # define get_crc_table z_get_crc_table
44
+ # define zError z_zError
45
+
46
+ # define alloc_func z_alloc_func
47
+ # define free_func z_free_func
48
+ # define in_func z_in_func
49
+ # define out_func z_out_func
50
+ # define Byte z_Byte
51
+ # define uInt z_uInt
52
+ # define uLong z_uLong
53
+ # define Bytef z_Bytef
54
+ # define charf z_charf
55
+ # define intf z_intf
56
+ # define uIntf z_uIntf
57
+ # define uLongf z_uLongf
58
+ # define voidpf z_voidpf
59
+ # define voidp z_voidp
60
+ #endif
61
+
62
+ #if defined(__MSDOS__) && !defined(MSDOS)
63
+ # define MSDOS
64
+ #endif
65
+ #if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
66
+ # define OS2
67
+ #endif
68
+ #if defined(_WINDOWS) && !defined(WINDOWS)
69
+ # define WINDOWS
70
+ #endif
71
+ #if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
72
+ # ifndef WIN32
73
+ # define WIN32
74
+ # endif
75
+ #endif
76
+ #if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
77
+ # if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
78
+ # ifndef SYS16BIT
79
+ # define SYS16BIT
80
+ # endif
81
+ # endif
82
+ #endif
83
+
84
+ /*
85
+ * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
86
+ * than 64k bytes at a time (needed on systems with 16-bit int).
87
+ */
88
+ #ifdef SYS16BIT
89
+ # define MAXSEG_64K
90
+ #endif
91
+ #ifdef MSDOS
92
+ # define UNALIGNED_OK
93
+ #endif
94
+
95
+ #ifdef __STDC_VERSION__
96
+ # ifndef STDC
97
+ # define STDC
98
+ # endif
99
+ # if __STDC_VERSION__ >= 199901L
100
+ # ifndef STDC99
101
+ # define STDC99
102
+ # endif
103
+ # endif
104
+ #endif
105
+ #if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
106
+ # define STDC
107
+ #endif
108
+ #if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
109
+ # define STDC
110
+ #endif
111
+ #if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
112
+ # define STDC
113
+ #endif
114
+ #if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
115
+ # define STDC
116
+ #endif
117
+
118
+ #if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
119
+ # define STDC
120
+ #endif
121
+
122
+ #ifndef STDC
123
+ # ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
124
+ # define const /* note: need a more gentle solution here */
125
+ # endif
126
+ #endif
127
+
128
+ /* Some Mac compilers merge all .h files incorrectly: */
129
+ #if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
130
+ # define NO_DUMMY_DECL
131
+ #endif
132
+
133
+ /* Maximum value for memLevel in deflateInit2 */
134
+ #ifndef MAX_MEM_LEVEL
135
+ # ifdef MAXSEG_64K
136
+ # define MAX_MEM_LEVEL 8
137
+ # else
138
+ # define MAX_MEM_LEVEL 9
139
+ # endif
140
+ #endif
141
+
142
+ /* Maximum value for windowBits in deflateInit2 and inflateInit2.
143
+ * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
144
+ * created by gzip. (Files created by minigzip can still be extracted by
145
+ * gzip.)
146
+ */
147
+ #ifndef MAX_WBITS
148
+ # define MAX_WBITS 15 /* 32K LZ77 window */
149
+ #endif
150
+
151
+ /* The memory requirements for deflate are (in bytes):
152
+ (1 << (windowBits+2)) + (1 << (memLevel+9))
153
+ that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
154
+ plus a few kilobytes for small objects. For example, if you want to reduce
155
+ the default memory requirements from 256K to 128K, compile with
156
+ make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
157
+ Of course this will generally degrade compression (there's no free lunch).
158
+
159
+ The memory requirements for inflate are (in bytes) 1 << windowBits
160
+ that is, 32K for windowBits=15 (default value) plus a few kilobytes
161
+ for small objects.
162
+ */
163
+
164
+ /* Type declarations */
165
+
166
+ #ifndef OF /* function prototypes */
167
+ # ifdef STDC
168
+ # define OF(args) args
169
+ # else
170
+ # define OF(args) ()
171
+ # endif
172
+ #endif
173
+
174
+ /* The following definitions for FAR are needed only for MSDOS mixed
175
+ * model programming (small or medium model with some far allocations).
176
+ * This was tested only with MSC; for other MSDOS compilers you may have
177
+ * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
178
+ * just define FAR to be empty.
179
+ */
180
+ #ifdef SYS16BIT
181
+ # if defined(M_I86SM) || defined(M_I86MM)
182
+ /* MSC small or medium model */
183
+ # define SMALL_MEDIUM
184
+ # ifdef _MSC_VER
185
+ # define FAR _far
186
+ # else
187
+ # define FAR far
188
+ # endif
189
+ # endif
190
+ # if (defined(__SMALL__) || defined(__MEDIUM__))
191
+ /* Turbo C small or medium model */
192
+ # define SMALL_MEDIUM
193
+ # ifdef __BORLANDC__
194
+ # define FAR _far
195
+ # else
196
+ # define FAR far
197
+ # endif
198
+ # endif
199
+ #endif
200
+
201
+ #if defined(WINDOWS) || defined(WIN32)
202
+ /* If building or using zlib as a DLL, define ZLIB_DLL.
203
+ * This is not mandatory, but it offers a little performance increase.
204
+ */
205
+ # ifdef ZLIB_DLL
206
+ # if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
207
+ # ifdef ZLIB_INTERNAL
208
+ # define ZEXTERN extern __declspec(dllexport)
209
+ # else
210
+ # define ZEXTERN extern __declspec(dllimport)
211
+ # endif
212
+ # endif
213
+ # endif /* ZLIB_DLL */
214
+ /* If building or using zlib with the WINAPI/WINAPIV calling convention,
215
+ * define ZLIB_WINAPI.
216
+ * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
217
+ */
218
+ # ifdef ZLIB_WINAPI
219
+ # ifdef FAR
220
+ # undef FAR
221
+ # endif
222
+ # include <windows.h>
223
+ /* No need for _export, use ZLIB.DEF instead. */
224
+ /* For complete Windows compatibility, use WINAPI, not __stdcall. */
225
+ # define ZEXPORT WINAPI
226
+ # ifdef WIN32
227
+ # define ZEXPORTVA WINAPIV
228
+ # else
229
+ # define ZEXPORTVA FAR CDECL
230
+ # endif
231
+ # endif
232
+ #endif
233
+
234
+ #if defined (__BEOS__)
235
+ # ifdef ZLIB_DLL
236
+ # ifdef ZLIB_INTERNAL
237
+ # define ZEXPORT __declspec(dllexport)
238
+ # define ZEXPORTVA __declspec(dllexport)
239
+ # else
240
+ # define ZEXPORT __declspec(dllimport)
241
+ # define ZEXPORTVA __declspec(dllimport)
242
+ # endif
243
+ # endif
244
+ #endif
245
+
246
+ #ifndef ZEXTERN
247
+ # define ZEXTERN extern
248
+ #endif
249
+ #ifndef ZEXPORT
250
+ # define ZEXPORT
251
+ #endif
252
+ #ifndef ZEXPORTVA
253
+ # define ZEXPORTVA
254
+ #endif
255
+
256
+ #ifndef FAR
257
+ # define FAR
258
+ #endif
259
+
260
+ #if !defined(__MACTYPES__)
261
+ typedef unsigned char Byte; /* 8 bits */
262
+ #endif
263
+ typedef unsigned int uInt; /* 16 bits or more */
264
+ typedef unsigned long uLong; /* 32 bits or more */
265
+
266
+ #ifdef SMALL_MEDIUM
267
+ /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
268
+ # define Bytef Byte FAR
269
+ #else
270
+ typedef Byte FAR Bytef;
271
+ #endif
272
+ typedef char FAR charf;
273
+ typedef int FAR intf;
274
+ typedef uInt FAR uIntf;
275
+ typedef uLong FAR uLongf;
276
+
277
+ #ifdef STDC
278
+ typedef void const *voidpc;
279
+ typedef void FAR *voidpf;
280
+ typedef void *voidp;
281
+ #else
282
+ typedef Byte const *voidpc;
283
+ typedef Byte FAR *voidpf;
284
+ typedef Byte *voidp;
285
+ #endif
286
+
287
+ #if 0 /* HAVE_UNISTD_H -- this line is updated by ./configure */
288
+ # include <sys/types.h> /* for off_t */
289
+ # include <unistd.h> /* for SEEK_* and off_t */
290
+ # ifdef VMS
291
+ # include <unixio.h> /* for off_t */
292
+ # endif
293
+ # define z_off_t off_t
294
+ #endif
295
+ #ifndef SEEK_SET
296
+ # define SEEK_SET 0 /* Seek from beginning of file. */
297
+ # define SEEK_CUR 1 /* Seek from current position. */
298
+ # define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
299
+ #endif
300
+ #ifndef z_off_t
301
+ # define z_off_t long
302
+ #endif
303
+
304
+ #if defined(__OS400__)
305
+ # define NO_vsnprintf
306
+ #endif
307
+
308
+ #if defined(__MVS__)
309
+ # define NO_vsnprintf
310
+ # ifdef FAR
311
+ # undef FAR
312
+ # endif
313
+ #endif
314
+
315
+ /* MVS linker does not support external names larger than 8 bytes */
316
+ #if defined(__MVS__)
317
+ # pragma map(deflateInit_,"DEIN")
318
+ # pragma map(deflateInit2_,"DEIN2")
319
+ # pragma map(deflateEnd,"DEEND")
320
+ # pragma map(deflateBound,"DEBND")
321
+ # pragma map(inflateInit_,"ININ")
322
+ # pragma map(inflateInit2_,"ININ2")
323
+ # pragma map(inflateEnd,"INEND")
324
+ # pragma map(inflateSync,"INSY")
325
+ # pragma map(inflateSetDictionary,"INSEDI")
326
+ # pragma map(compressBound,"CMBND")
327
+ # pragma map(inflate_table,"INTABL")
328
+ # pragma map(inflate_fast,"INFA")
329
+ # pragma map(inflate_copyright,"INCOPY")
330
+ #endif
331
+
332
+ #endif /* ZCONF_H */