bio-velvet_underground 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (286) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +19 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +53 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/ext/bioruby.patch +60 -0
  11. data/ext/mkrf_conf.rb +50 -0
  12. data/ext/src/Makefile +125 -0
  13. data/ext/src/src/allocArray.c +305 -0
  14. data/ext/src/src/allocArray.h +86 -0
  15. data/ext/src/src/autoOpen.c +107 -0
  16. data/ext/src/src/autoOpen.h +18 -0
  17. data/ext/src/src/binarySequences.c +813 -0
  18. data/ext/src/src/binarySequences.h +125 -0
  19. data/ext/src/src/concatenatedGraph.c +233 -0
  20. data/ext/src/src/concatenatedGraph.h +30 -0
  21. data/ext/src/src/concatenatedPreGraph.c +262 -0
  22. data/ext/src/src/concatenatedPreGraph.h +29 -0
  23. data/ext/src/src/correctedGraph.c +2642 -0
  24. data/ext/src/src/correctedGraph.h +32 -0
  25. data/ext/src/src/dfib.c +509 -0
  26. data/ext/src/src/dfib.h +69 -0
  27. data/ext/src/src/dfibHeap.c +89 -0
  28. data/ext/src/src/dfibHeap.h +39 -0
  29. data/ext/src/src/dfibpriv.h +105 -0
  30. data/ext/src/src/fib.c +628 -0
  31. data/ext/src/src/fib.h +78 -0
  32. data/ext/src/src/fibHeap.c +79 -0
  33. data/ext/src/src/fibHeap.h +41 -0
  34. data/ext/src/src/fibpriv.h +110 -0
  35. data/ext/src/src/globals.h +153 -0
  36. data/ext/src/src/graph.c +3983 -0
  37. data/ext/src/src/graph.h +233 -0
  38. data/ext/src/src/graphReConstruction.c +1472 -0
  39. data/ext/src/src/graphReConstruction.h +30 -0
  40. data/ext/src/src/graphStats.c +2167 -0
  41. data/ext/src/src/graphStats.h +72 -0
  42. data/ext/src/src/kmer.c +652 -0
  43. data/ext/src/src/kmer.h +73 -0
  44. data/ext/src/src/kmerOccurenceTable.c +236 -0
  45. data/ext/src/src/kmerOccurenceTable.h +44 -0
  46. data/ext/src/src/kseq.h +223 -0
  47. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  48. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  49. data/ext/src/src/passageMarker.c +677 -0
  50. data/ext/src/src/passageMarker.h +137 -0
  51. data/ext/src/src/preGraph.c +1717 -0
  52. data/ext/src/src/preGraph.h +106 -0
  53. data/ext/src/src/preGraphConstruction.c +990 -0
  54. data/ext/src/src/preGraphConstruction.h +26 -0
  55. data/ext/src/src/readCoherentGraph.c +557 -0
  56. data/ext/src/src/readCoherentGraph.h +30 -0
  57. data/ext/src/src/readSet.c +1734 -0
  58. data/ext/src/src/readSet.h +67 -0
  59. data/ext/src/src/recycleBin.c +199 -0
  60. data/ext/src/src/recycleBin.h +58 -0
  61. data/ext/src/src/roadMap.c +342 -0
  62. data/ext/src/src/roadMap.h +65 -0
  63. data/ext/src/src/run.c +318 -0
  64. data/ext/src/src/run.h +52 -0
  65. data/ext/src/src/run2.c +712 -0
  66. data/ext/src/src/scaffold.c +1876 -0
  67. data/ext/src/src/scaffold.h +64 -0
  68. data/ext/src/src/shortReadPairs.c +1243 -0
  69. data/ext/src/src/shortReadPairs.h +32 -0
  70. data/ext/src/src/splay.c +259 -0
  71. data/ext/src/src/splay.h +43 -0
  72. data/ext/src/src/splayTable.c +1315 -0
  73. data/ext/src/src/splayTable.h +31 -0
  74. data/ext/src/src/tightString.c +362 -0
  75. data/ext/src/src/tightString.h +82 -0
  76. data/ext/src/src/utility.c +199 -0
  77. data/ext/src/src/utility.h +98 -0
  78. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  79. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  80. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  81. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  82. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  83. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  84. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  85. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  86. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  87. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  88. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  89. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  90. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  91. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  92. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  93. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  94. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  95. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  96. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  97. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  98. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  99. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  100. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  101. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  102. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  103. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  104. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  105. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  106. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  107. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  108. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  109. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  110. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  111. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  112. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  113. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  114. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  115. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  116. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  117. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  118. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  119. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  120. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  192. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  193. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  195. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  196. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  216. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  217. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  218. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  219. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  220. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  221. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  222. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  223. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  224. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  225. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  226. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  227. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  228. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
  229. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
  230. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
  231. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
  232. data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
  233. data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
  234. data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
  235. data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
  236. data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
  237. data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
  238. data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
  239. data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
  240. data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
  241. data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
  242. data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
  243. data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
  244. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
  245. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
  246. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
  247. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
  248. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
  249. data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
  250. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  251. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  252. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  253. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  254. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  255. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  256. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  257. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  258. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  259. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  260. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  261. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  262. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  263. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  264. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  265. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  266. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  267. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  268. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  269. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  270. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  271. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  272. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  273. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  274. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  275. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  276. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  277. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  278. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  279. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  280. data/lib/bio-velvet_underground.rb +12 -0
  281. data/lib/bio-velvet_underground/external/VERSION +1 -0
  282. data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
  283. data/spec/binary_sequence_store_spec.rb +27 -0
  284. data/spec/data/1/CnyUnifiedSeq +0 -0
  285. data/spec/spec_helper.rb +31 -0
  286. metadata +456 -0
@@ -0,0 +1,331 @@
1
+ * ZLIB.INC - Interface to the general purpose compression library
2
+ *
3
+ * ILE RPG400 version by Patrick Monnerat, DATASPHERE.
4
+ * Version 1.2.3
5
+ *
6
+ *
7
+ * WARNING:
8
+ * Procedures inflateInit(), inflateInit2(), deflateInit(),
9
+ * deflateInit2() and inflateBackInit() need to be called with
10
+ * two additional arguments:
11
+ * the package version string and the stream control structure.
12
+ * size. This is needed because RPG lacks some macro feature.
13
+ * Call these procedures as:
14
+ * inflateInit(...: ZLIB_VERSION: %size(z_stream))
15
+ *
16
+ /if not defined(ZLIB_H_)
17
+ /define ZLIB_H_
18
+ *
19
+ **************************************************************************
20
+ * Constants
21
+ **************************************************************************
22
+ *
23
+ * Versioning information.
24
+ *
25
+ D ZLIB_VERSION C '1.2.3'
26
+ D ZLIB_VERNUM C X'1230'
27
+ *
28
+ * Other equates.
29
+ *
30
+ D Z_NO_FLUSH C 0
31
+ D Z_SYNC_FLUSH C 2
32
+ D Z_FULL_FLUSH C 3
33
+ D Z_FINISH C 4
34
+ D Z_BLOCK C 5
35
+ *
36
+ D Z_OK C 0
37
+ D Z_STREAM_END C 1
38
+ D Z_NEED_DICT C 2
39
+ D Z_ERRNO C -1
40
+ D Z_STREAM_ERROR C -2
41
+ D Z_DATA_ERROR C -3
42
+ D Z_MEM_ERROR C -4
43
+ D Z_BUF_ERROR C -5
44
+ DZ_VERSION_ERROR C -6
45
+ *
46
+ D Z_NO_COMPRESSION...
47
+ D C 0
48
+ D Z_BEST_SPEED C 1
49
+ D Z_BEST_COMPRESSION...
50
+ D C 9
51
+ D Z_DEFAULT_COMPRESSION...
52
+ D C -1
53
+ *
54
+ D Z_FILTERED C 1
55
+ D Z_HUFFMAN_ONLY C 2
56
+ D Z_RLE C 3
57
+ D Z_DEFAULT_STRATEGY...
58
+ D C 0
59
+ *
60
+ D Z_BINARY C 0
61
+ D Z_ASCII C 1
62
+ D Z_UNKNOWN C 2
63
+ *
64
+ D Z_DEFLATED C 8
65
+ *
66
+ D Z_NULL C 0
67
+ *
68
+ **************************************************************************
69
+ * Types
70
+ **************************************************************************
71
+ *
72
+ D z_streamp S * Stream struct ptr
73
+ D gzFile S * File pointer
74
+ D z_off_t S 10i 0 Stream offsets
75
+ *
76
+ **************************************************************************
77
+ * Structures
78
+ **************************************************************************
79
+ *
80
+ * The GZIP encode/decode stream support structure.
81
+ *
82
+ D z_stream DS align based(z_streamp)
83
+ D zs_next_in * Next input byte
84
+ D zs_avail_in 10U 0 Byte cnt at next_in
85
+ D zs_total_in 10U 0 Total bytes read
86
+ D zs_next_out * Output buffer ptr
87
+ D zs_avail_out 10U 0 Room left @ next_out
88
+ D zs_total_out 10U 0 Total bytes written
89
+ D zs_msg * Last errmsg or null
90
+ D zs_state * Internal state
91
+ D zs_zalloc * procptr Int. state allocator
92
+ D zs_free * procptr Int. state dealloc.
93
+ D zs_opaque * Private alloc. data
94
+ D zs_data_type 10i 0 ASC/BIN best guess
95
+ D zs_adler 10u 0 Uncompr. adler32 val
96
+ D 10U 0 Reserved
97
+ D 10U 0 Ptr. alignment
98
+ *
99
+ **************************************************************************
100
+ * Utility function prototypes
101
+ **************************************************************************
102
+ *
103
+ D compress PR 10I 0 extproc('compress')
104
+ D dest 32767 options(*varsize) Destination buffer
105
+ D destLen 10U 0 Destination length
106
+ D source 32767 const options(*varsize) Source buffer
107
+ D sourceLen 10u 0 value Source length
108
+ *
109
+ D compress2 PR 10I 0 extproc('compress2')
110
+ D dest 32767 options(*varsize) Destination buffer
111
+ D destLen 10U 0 Destination length
112
+ D source 32767 const options(*varsize) Source buffer
113
+ D sourceLen 10U 0 value Source length
114
+ D level 10I 0 value Compression level
115
+ *
116
+ D compressBound PR 10U 0 extproc('compressBound')
117
+ D sourceLen 10U 0 value
118
+ *
119
+ D uncompress PR 10I 0 extproc('uncompress')
120
+ D dest 32767 options(*varsize) Destination buffer
121
+ D destLen 10U 0 Destination length
122
+ D source 32767 const options(*varsize) Source buffer
123
+ D sourceLen 10U 0 value Source length
124
+ *
125
+ D gzopen PR extproc('gzopen')
126
+ D like(gzFile)
127
+ D path * value options(*string) File pathname
128
+ D mode * value options(*string) Open mode
129
+ *
130
+ D gzdopen PR extproc('gzdopen')
131
+ D like(gzFile)
132
+ D fd 10i 0 value File descriptor
133
+ D mode * value options(*string) Open mode
134
+ *
135
+ D gzsetparams PR 10I 0 extproc('gzsetparams')
136
+ D file value like(gzFile) File pointer
137
+ D level 10I 0 value
138
+ D strategy 10i 0 value
139
+ *
140
+ D gzread PR 10I 0 extproc('gzread')
141
+ D file value like(gzFile) File pointer
142
+ D buf 32767 options(*varsize) Buffer
143
+ D len 10u 0 value Buffer length
144
+ *
145
+ D gzwrite PR 10I 0 extproc('gzwrite')
146
+ D file value like(gzFile) File pointer
147
+ D buf 32767 const options(*varsize) Buffer
148
+ D len 10u 0 value Buffer length
149
+ *
150
+ D gzputs PR 10I 0 extproc('gzputs')
151
+ D file value like(gzFile) File pointer
152
+ D s * value options(*string) String to output
153
+ *
154
+ D gzgets PR * extproc('gzgets')
155
+ D file value like(gzFile) File pointer
156
+ D buf 32767 options(*varsize) Read buffer
157
+ D len 10i 0 value Buffer length
158
+ *
159
+ D gzflush PR 10i 0 extproc('gzflush')
160
+ D file value like(gzFile) File pointer
161
+ D flush 10I 0 value Type of flush
162
+ *
163
+ D gzseek PR extproc('gzseek')
164
+ D like(z_off_t)
165
+ D file value like(gzFile) File pointer
166
+ D offset value like(z_off_t) Offset
167
+ D whence 10i 0 value Origin
168
+ *
169
+ D gzrewind PR 10i 0 extproc('gzrewind')
170
+ D file value like(gzFile) File pointer
171
+ *
172
+ D gztell PR extproc('gztell')
173
+ D like(z_off_t)
174
+ D file value like(gzFile) File pointer
175
+ *
176
+ D gzeof PR 10i 0 extproc('gzeof')
177
+ D file value like(gzFile) File pointer
178
+ *
179
+ D gzclose PR 10i 0 extproc('gzclose')
180
+ D file value like(gzFile) File pointer
181
+ *
182
+ D gzerror PR * extproc('gzerror') Error string
183
+ D file value like(gzFile) File pointer
184
+ D errnum 10I 0 Error code
185
+ *
186
+ D gzclearerr PR extproc('gzclearerr')
187
+ D file value like(gzFile) File pointer
188
+ *
189
+ **************************************************************************
190
+ * Basic function prototypes
191
+ **************************************************************************
192
+ *
193
+ D zlibVersion PR * extproc('zlibVersion') Version string
194
+ *
195
+ D deflateInit PR 10I 0 extproc('deflateInit_') Init. compression
196
+ D strm like(z_stream) Compression stream
197
+ D level 10I 0 value Compression level
198
+ D version * value options(*string) Version string
199
+ D stream_size 10i 0 value Stream struct. size
200
+ *
201
+ D deflate PR 10I 0 extproc('deflate') Compress data
202
+ D strm like(z_stream) Compression stream
203
+ D flush 10I 0 value Flush type required
204
+ *
205
+ D deflateEnd PR 10I 0 extproc('deflateEnd') Termin. compression
206
+ D strm like(z_stream) Compression stream
207
+ *
208
+ D inflateInit PR 10I 0 extproc('inflateInit_') Init. expansion
209
+ D strm like(z_stream) Expansion stream
210
+ D version * value options(*string) Version string
211
+ D stream_size 10i 0 value Stream struct. size
212
+ *
213
+ D inflate PR 10I 0 extproc('inflate') Expand data
214
+ D strm like(z_stream) Expansion stream
215
+ D flush 10I 0 value Flush type required
216
+ *
217
+ D inflateEnd PR 10I 0 extproc('inflateEnd') Termin. expansion
218
+ D strm like(z_stream) Expansion stream
219
+ *
220
+ **************************************************************************
221
+ * Advanced function prototypes
222
+ **************************************************************************
223
+ *
224
+ D deflateInit2 PR 10I 0 extproc('deflateInit2_') Init. compression
225
+ D strm like(z_stream) Compression stream
226
+ D level 10I 0 value Compression level
227
+ D method 10I 0 value Compression method
228
+ D windowBits 10I 0 value log2(window size)
229
+ D memLevel 10I 0 value Mem/cmpress tradeoff
230
+ D strategy 10I 0 value Compression stategy
231
+ D version * value options(*string) Version string
232
+ D stream_size 10i 0 value Stream struct. size
233
+ *
234
+ D deflateSetDictionary...
235
+ D PR 10I 0 extproc('deflateSetDictionary') Init. dictionary
236
+ D strm like(z_stream) Compression stream
237
+ D dictionary 32767 const options(*varsize) Dictionary bytes
238
+ D dictLength 10U 0 value Dictionary length
239
+ *
240
+ D deflateCopy PR 10I 0 extproc('deflateCopy') Compress strm 2 strm
241
+ D dest like(z_stream) Destination stream
242
+ D source like(z_stream) Source stream
243
+ *
244
+ D deflateReset PR 10I 0 extproc('deflateReset') End and init. stream
245
+ D strm like(z_stream) Compression stream
246
+ *
247
+ D deflateParams PR 10I 0 extproc('deflateParams') Change level & strat
248
+ D strm like(z_stream) Compression stream
249
+ D level 10I 0 value Compression level
250
+ D strategy 10I 0 value Compression stategy
251
+ *
252
+ D deflateBound PR 10U 0 extproc('deflateBound') Change level & strat
253
+ D strm like(z_stream) Compression stream
254
+ D sourcelen 10U 0 value Compression level
255
+ *
256
+ D deflatePrime PR 10I 0 extproc('deflatePrime') Change level & strat
257
+ D strm like(z_stream) Compression stream
258
+ D bits 10I 0 value Number of bits to insert
259
+ D value 10I 0 value Bits to insert
260
+ *
261
+ D inflateInit2 PR 10I 0 extproc('inflateInit2_') Init. expansion
262
+ D strm like(z_stream) Expansion stream
263
+ D windowBits 10I 0 value log2(window size)
264
+ D version * value options(*string) Version string
265
+ D stream_size 10i 0 value Stream struct. size
266
+ *
267
+ D inflateSetDictionary...
268
+ D PR 10I 0 extproc('inflateSetDictionary') Init. dictionary
269
+ D strm like(z_stream) Expansion stream
270
+ D dictionary 32767 const options(*varsize) Dictionary bytes
271
+ D dictLength 10U 0 value Dictionary length
272
+ *
273
+ D inflateSync PR 10I 0 extproc('inflateSync') Sync. expansion
274
+ D strm like(z_stream) Expansion stream
275
+ *
276
+ D inflateCopy PR 10I 0 extproc('inflateCopy')
277
+ D dest like(z_stream) Destination stream
278
+ D source like(z_stream) Source stream
279
+ *
280
+ D inflateReset PR 10I 0 extproc('inflateReset') End and init. stream
281
+ D strm like(z_stream) Expansion stream
282
+ *
283
+ D inflateBackInit...
284
+ D PR 10I 0 extproc('inflateBackInit_')
285
+ D strm like(z_stream) Expansion stream
286
+ D windowBits 10I 0 value Log2(buffer size)
287
+ D window 32767 options(*varsize) Buffer
288
+ D version * value options(*string) Version string
289
+ D stream_size 10i 0 value Stream struct. size
290
+ *
291
+ D inflateBack PR 10I 0 extproc('inflateBack')
292
+ D strm like(z_stream) Expansion stream
293
+ D in * value procptr Input function
294
+ D in_desc * value Input descriptor
295
+ D out * value procptr Output function
296
+ D out_desc * value Output descriptor
297
+ *
298
+ D inflateBackEnd PR 10I 0 extproc('inflateBackEnd')
299
+ D strm like(z_stream) Expansion stream
300
+ *
301
+ D zlibCompileFlags...
302
+ D PR 10U 0 extproc('zlibCompileFlags')
303
+ *
304
+ **************************************************************************
305
+ * Checksum function prototypes
306
+ **************************************************************************
307
+ *
308
+ D adler32 PR 10U 0 extproc('adler32') New checksum
309
+ D adler 10U 0 value Old checksum
310
+ D buf 32767 const options(*varsize) Bytes to accumulate
311
+ D len 10U 0 value Buffer length
312
+ *
313
+ D crc32 PR 10U 0 extproc('crc32') New checksum
314
+ D crc 10U 0 value Old checksum
315
+ D buf 32767 const options(*varsize) Bytes to accumulate
316
+ D len 10U 0 value Buffer length
317
+ *
318
+ **************************************************************************
319
+ * Miscellaneous function prototypes
320
+ **************************************************************************
321
+ *
322
+ D zError PR * extproc('zError') Error string
323
+ D err 10I 0 value Error code
324
+ *
325
+ D inflateSyncPoint...
326
+ D PR 10I 0 extproc('inflateSyncPoint')
327
+ D strm like(z_stream) Expansion stream
328
+ *
329
+ D get_crc_table PR * extproc('get_crc_table') Ptr to ulongs
330
+ *
331
+ /endif
@@ -0,0 +1,79 @@
1
+ /* compress.c -- compress a memory buffer
2
+ * Copyright (C) 1995-2003 Jean-loup Gailly.
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* @(#) $Id$ */
7
+
8
+ #define ZLIB_INTERNAL
9
+ #include "zlib.h"
10
+
11
+ /* ===========================================================================
12
+ Compresses the source buffer into the destination buffer. The level
13
+ parameter has the same meaning as in deflateInit. sourceLen is the byte
14
+ length of the source buffer. Upon entry, destLen is the total size of the
15
+ destination buffer, which must be at least 0.1% larger than sourceLen plus
16
+ 12 bytes. Upon exit, destLen is the actual size of the compressed buffer.
17
+
18
+ compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
19
+ memory, Z_BUF_ERROR if there was not enough room in the output buffer,
20
+ Z_STREAM_ERROR if the level parameter is invalid.
21
+ */
22
+ int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
23
+ Bytef *dest;
24
+ uLongf *destLen;
25
+ const Bytef *source;
26
+ uLong sourceLen;
27
+ int level;
28
+ {
29
+ z_stream stream;
30
+ int err;
31
+
32
+ stream.next_in = (Bytef*)source;
33
+ stream.avail_in = (uInt)sourceLen;
34
+ #ifdef MAXSEG_64K
35
+ /* Check for source > 64K on 16-bit machine: */
36
+ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
37
+ #endif
38
+ stream.next_out = dest;
39
+ stream.avail_out = (uInt)*destLen;
40
+ if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
41
+
42
+ stream.zalloc = (alloc_func)0;
43
+ stream.zfree = (free_func)0;
44
+ stream.opaque = (voidpf)0;
45
+
46
+ err = deflateInit(&stream, level);
47
+ if (err != Z_OK) return err;
48
+
49
+ err = deflate(&stream, Z_FINISH);
50
+ if (err != Z_STREAM_END) {
51
+ deflateEnd(&stream);
52
+ return err == Z_OK ? Z_BUF_ERROR : err;
53
+ }
54
+ *destLen = stream.total_out;
55
+
56
+ err = deflateEnd(&stream);
57
+ return err;
58
+ }
59
+
60
+ /* ===========================================================================
61
+ */
62
+ int ZEXPORT compress (dest, destLen, source, sourceLen)
63
+ Bytef *dest;
64
+ uLongf *destLen;
65
+ const Bytef *source;
66
+ uLong sourceLen;
67
+ {
68
+ return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION);
69
+ }
70
+
71
+ /* ===========================================================================
72
+ If the default memLevel or windowBits for deflateInit() is changed, then
73
+ this function needs to be updated.
74
+ */
75
+ uLong ZEXPORT compressBound (sourceLen)
76
+ uLong sourceLen;
77
+ {
78
+ return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) + 11;
79
+ }
@@ -0,0 +1,459 @@
1
+ #!/bin/sh
2
+ # configure script for zlib. This script is needed only if
3
+ # you wish to build a shared library and your system supports them,
4
+ # of if you need special compiler, flags or install directory.
5
+ # Otherwise, you can just use directly "make test; make install"
6
+ #
7
+ # To create a shared library, use "configure --shared"; by default a static
8
+ # library is created. If the primitive shared library support provided here
9
+ # does not work, use ftp://prep.ai.mit.edu/pub/gnu/libtool-*.tar.gz
10
+ #
11
+ # To impose specific compiler or flags or install directory, use for example:
12
+ # prefix=$HOME CC=cc CFLAGS="-O4" ./configure
13
+ # or for csh/tcsh users:
14
+ # (setenv prefix $HOME; setenv CC cc; setenv CFLAGS "-O4"; ./configure)
15
+ # LDSHARED is the command to be used to create a shared library
16
+
17
+ # Incorrect settings of CC or CFLAGS may prevent creating a shared library.
18
+ # If you have problems, try without defining CC and CFLAGS before reporting
19
+ # an error.
20
+
21
+ LIBS=libz.a
22
+ LDFLAGS="-L. ${LIBS}"
23
+ VER=`sed -n -e '/VERSION "/s/.*"\(.*\)".*/\1/p' < zlib.h`
24
+ VER2=`sed -n -e '/VERSION "/s/.*"\([0-9]*\\.[0-9]*\)\\..*/\1/p' < zlib.h`
25
+ VER1=`sed -n -e '/VERSION "/s/.*"\([0-9]*\)\\..*/\1/p' < zlib.h`
26
+ AR=${AR-"ar rc"}
27
+ RANLIB=${RANLIB-"ranlib"}
28
+ prefix=${prefix-/usr/local}
29
+ exec_prefix=${exec_prefix-'${prefix}'}
30
+ libdir=${libdir-'${exec_prefix}/lib'}
31
+ includedir=${includedir-'${prefix}/include'}
32
+ mandir=${mandir-'${prefix}/share/man'}
33
+ shared_ext='.so'
34
+ shared=0
35
+ gcc=0
36
+ old_cc="$CC"
37
+ old_cflags="$CFLAGS"
38
+
39
+ while test $# -ge 1
40
+ do
41
+ case "$1" in
42
+ -h* | --h*)
43
+ echo 'usage:'
44
+ echo ' configure [--shared] [--prefix=PREFIX] [--exec_prefix=EXPREFIX]'
45
+ echo ' [--libdir=LIBDIR] [--includedir=INCLUDEDIR]'
46
+ exit 0;;
47
+ -p*=* | --p*=*) prefix=`echo $1 | sed 's/[-a-z_]*=//'`; shift;;
48
+ -e*=* | --e*=*) exec_prefix=`echo $1 | sed 's/[-a-z_]*=//'`; shift;;
49
+ -l*=* | --libdir=*) libdir=`echo $1 | sed 's/[-a-z_]*=//'`; shift;;
50
+ -i*=* | --includedir=*) includedir=`echo $1 | sed 's/[-a-z_]*=//'`;shift;;
51
+ -p* | --p*) prefix="$2"; shift; shift;;
52
+ -e* | --e*) exec_prefix="$2"; shift; shift;;
53
+ -l* | --l*) libdir="$2"; shift; shift;;
54
+ -i* | --i*) includedir="$2"; shift; shift;;
55
+ -s* | --s*) shared=1; shift;;
56
+ *) echo "unknown option: $1"; echo "$0 --help for help"; exit 1;;
57
+ esac
58
+ done
59
+
60
+ test=ztest$$
61
+ cat > $test.c <<EOF
62
+ extern int getchar();
63
+ int hello() {return getchar();}
64
+ EOF
65
+
66
+ test -z "$CC" && echo Checking for gcc...
67
+ cc=${CC-gcc}
68
+ cflags=${CFLAGS-"-O3"}
69
+ # to force the asm version use: CFLAGS="-O3 -DASMV" ./configure
70
+ case "$cc" in
71
+ *gcc*) gcc=1;;
72
+ esac
73
+
74
+ if test "$gcc" -eq 1 && ($cc -c $cflags $test.c) 2>/dev/null; then
75
+ CC="$cc"
76
+ SFLAGS=${CFLAGS-"-fPIC -O3"}
77
+ CFLAGS="$cflags"
78
+ case `(uname -s || echo unknown) 2>/dev/null` in
79
+ Linux | linux | GNU | GNU/*) LDSHARED=${LDSHARED-"$cc -shared -Wl,-soname,libz.so.1"};;
80
+ CYGWIN* | Cygwin* | cygwin* | OS/2* )
81
+ EXE='.exe';;
82
+ QNX*) # This is for QNX6. I suppose that the QNX rule below is for QNX2,QNX4
83
+ # (alain.bonnefoy@icbt.com)
84
+ LDSHARED=${LDSHARED-"$cc -shared -Wl,-hlibz.so.1"};;
85
+ HP-UX*)
86
+ LDSHARED=${LDSHARED-"$cc -shared $SFLAGS"}
87
+ case `(uname -m || echo unknown) 2>/dev/null` in
88
+ ia64)
89
+ shared_ext='.so'
90
+ SHAREDLIB='libz.so';;
91
+ *)
92
+ shared_ext='.sl'
93
+ SHAREDLIB='libz.sl';;
94
+ esac;;
95
+ Darwin*) shared_ext='.dylib'
96
+ SHAREDLIB=libz$shared_ext
97
+ SHAREDLIBV=libz.$VER$shared_ext
98
+ SHAREDLIBM=libz.$VER1$shared_ext
99
+ LDSHARED=${LDSHARED-"$cc -dynamiclib -install_name $libdir/$SHAREDLIBM -compatibility_version $VER1 -current_version $VER"};;
100
+ *) LDSHARED=${LDSHARED-"$cc -shared"};;
101
+ esac
102
+ else
103
+ # find system name and corresponding cc options
104
+ CC=${CC-cc}
105
+ case `(uname -sr || echo unknown) 2>/dev/null` in
106
+ HP-UX*) SFLAGS=${CFLAGS-"-O +z"}
107
+ CFLAGS=${CFLAGS-"-O"}
108
+ # LDSHARED=${LDSHARED-"ld -b +vnocompatwarnings"}
109
+ LDSHARED=${LDSHARED-"ld -b"}
110
+ case `(uname -m || echo unknown) 2>/dev/null` in
111
+ ia64)
112
+ shared_ext='.so'
113
+ SHAREDLIB='libz.so';;
114
+ *)
115
+ shared_ext='.sl'
116
+ SHAREDLIB='libz.sl';;
117
+ esac;;
118
+ IRIX*) SFLAGS=${CFLAGS-"-ansi -O2 -rpath ."}
119
+ CFLAGS=${CFLAGS-"-ansi -O2"}
120
+ LDSHARED=${LDSHARED-"cc -shared"};;
121
+ OSF1\ V4*) SFLAGS=${CFLAGS-"-O -std1"}
122
+ CFLAGS=${CFLAGS-"-O -std1"}
123
+ LDSHARED=${LDSHARED-"cc -shared -Wl,-soname,libz.so -Wl,-msym -Wl,-rpath,$(libdir) -Wl,-set_version,${VER}:1.0"};;
124
+ OSF1*) SFLAGS=${CFLAGS-"-O -std1"}
125
+ CFLAGS=${CFLAGS-"-O -std1"}
126
+ LDSHARED=${LDSHARED-"cc -shared"};;
127
+ QNX*) SFLAGS=${CFLAGS-"-4 -O"}
128
+ CFLAGS=${CFLAGS-"-4 -O"}
129
+ LDSHARED=${LDSHARED-"cc"}
130
+ RANLIB=${RANLIB-"true"}
131
+ AR="cc -A";;
132
+ SCO_SV\ 3.2*) SFLAGS=${CFLAGS-"-O3 -dy -KPIC "}
133
+ CFLAGS=${CFLAGS-"-O3"}
134
+ LDSHARED=${LDSHARED-"cc -dy -KPIC -G"};;
135
+ SunOS\ 5*) SFLAGS=${CFLAGS-"-fast -xcg89 -KPIC -R."}
136
+ CFLAGS=${CFLAGS-"-fast -xcg89"}
137
+ LDSHARED=${LDSHARED-"cc -G"};;
138
+ SunOS\ 4*) SFLAGS=${CFLAGS-"-O2 -PIC"}
139
+ CFLAGS=${CFLAGS-"-O2"}
140
+ LDSHARED=${LDSHARED-"ld"};;
141
+ SunStudio\ 9*) SFLAGS=${CFLAGS-"-DUSE_MMAP -fast -xcode=pic32 -xtarget=ultra3 -xarch=v9b"}
142
+ CFLAGS=${CFLAGS-"-DUSE_MMAP -fast -xtarget=ultra3 -xarch=v9b"}
143
+ LDSHARED=${LDSHARED-"cc -xarch=v9b"};;
144
+ UNIX_System_V\ 4.2.0)
145
+ SFLAGS=${CFLAGS-"-KPIC -O"}
146
+ CFLAGS=${CFLAGS-"-O"}
147
+ LDSHARED=${LDSHARED-"cc -G"};;
148
+ UNIX_SV\ 4.2MP)
149
+ SFLAGS=${CFLAGS-"-Kconform_pic -O"}
150
+ CFLAGS=${CFLAGS-"-O"}
151
+ LDSHARED=${LDSHARED-"cc -G"};;
152
+ OpenUNIX\ 5)
153
+ SFLAGS=${CFLAGS-"-KPIC -O"}
154
+ CFLAGS=${CFLAGS-"-O"}
155
+ LDSHARED=${LDSHARED-"cc -G"};;
156
+ AIX*) # Courtesy of dbakker@arrayasolutions.com
157
+ SFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
158
+ CFLAGS=${CFLAGS-"-O -qmaxmem=8192"}
159
+ LDSHARED=${LDSHARED-"xlc -G"};;
160
+ # send working options for other systems to support@gzip.org
161
+ *) SFLAGS=${CFLAGS-"-O"}
162
+ CFLAGS=${CFLAGS-"-O"}
163
+ LDSHARED=${LDSHARED-"cc -shared"};;
164
+ esac
165
+ fi
166
+
167
+ SHAREDLIB=${SHAREDLIB-"libz$shared_ext"}
168
+ SHAREDLIBV=${SHAREDLIBV-"libz$shared_ext.$VER"}
169
+ SHAREDLIBM=${SHAREDLIBM-"libz$shared_ext.$VER1"}
170
+
171
+ if test $shared -eq 1; then
172
+ echo Checking for shared library support...
173
+ # we must test in two steps (cc then ld), required at least on SunOS 4.x
174
+ if test "`($CC -c $SFLAGS $test.c) 2>&1`" = "" &&
175
+ test "`($LDSHARED -o $test$shared_ext $test.o) 2>&1`" = ""; then
176
+ CFLAGS="$SFLAGS"
177
+ LIBS="$SHAREDLIBV"
178
+ echo Building shared library $SHAREDLIBV with $CC.
179
+ elif test -z "$old_cc" -a -z "$old_cflags"; then
180
+ echo No shared library support.
181
+ shared=0;
182
+ else
183
+ echo 'No shared library support; try without defining CC and CFLAGS'
184
+ shared=0;
185
+ fi
186
+ fi
187
+ if test $shared -eq 0; then
188
+ LDSHARED="$CC"
189
+ echo Building static library $LIBS version $VER with $CC.
190
+ else
191
+ LDFLAGS="-L. ${SHAREDLIBV}"
192
+ fi
193
+
194
+ cat > $test.c <<EOF
195
+ #include <unistd.h>
196
+ int main() { return 0; }
197
+ EOF
198
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
199
+ sed < zconf.in.h "/HAVE_UNISTD_H/s%0%1%" > zconf.h
200
+ echo "Checking for unistd.h... Yes."
201
+ else
202
+ cp -p zconf.in.h zconf.h
203
+ echo "Checking for unistd.h... No."
204
+ fi
205
+
206
+ cat > $test.c <<EOF
207
+ #include <stdio.h>
208
+ #include <stdarg.h>
209
+ #include "zconf.h"
210
+
211
+ int main()
212
+ {
213
+ #ifndef STDC
214
+ choke me
215
+ #endif
216
+
217
+ return 0;
218
+ }
219
+ EOF
220
+
221
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
222
+ echo "Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()"
223
+
224
+ cat > $test.c <<EOF
225
+ #include <stdio.h>
226
+ #include <stdarg.h>
227
+
228
+ int mytest(char *fmt, ...)
229
+ {
230
+ char buf[20];
231
+ va_list ap;
232
+
233
+ va_start(ap, fmt);
234
+ vsnprintf(buf, sizeof(buf), fmt, ap);
235
+ va_end(ap);
236
+ return 0;
237
+ }
238
+
239
+ int main()
240
+ {
241
+ return (mytest("Hello%d\n", 1));
242
+ }
243
+ EOF
244
+
245
+ if test "`($CC $CFLAGS -o $test $test.c) 2>&1`" = ""; then
246
+ echo "Checking for vsnprintf() in stdio.h... Yes."
247
+
248
+ cat >$test.c <<EOF
249
+ #include <stdio.h>
250
+ #include <stdarg.h>
251
+
252
+ int mytest(char *fmt, ...)
253
+ {
254
+ int n;
255
+ char buf[20];
256
+ va_list ap;
257
+
258
+ va_start(ap, fmt);
259
+ n = vsnprintf(buf, sizeof(buf), fmt, ap);
260
+ va_end(ap);
261
+ return n;
262
+ }
263
+
264
+ int main()
265
+ {
266
+ return (mytest("Hello%d\n", 1));
267
+ }
268
+ EOF
269
+
270
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
271
+ echo "Checking for return value of vsnprintf()... Yes."
272
+ else
273
+ CFLAGS="$CFLAGS -DHAS_vsnprintf_void"
274
+ echo "Checking for return value of vsnprintf()... No."
275
+ echo " WARNING: apparently vsnprintf() does not return a value. zlib"
276
+ echo " can build but will be open to possible string-format security"
277
+ echo " vulnerabilities."
278
+ fi
279
+ else
280
+ CFLAGS="$CFLAGS -DNO_vsnprintf"
281
+ echo "Checking for vsnprintf() in stdio.h... No."
282
+ echo " WARNING: vsnprintf() not found, falling back to vsprintf(). zlib"
283
+ echo " can build but will be open to possible buffer-overflow security"
284
+ echo " vulnerabilities."
285
+
286
+ cat >$test.c <<EOF
287
+ #include <stdio.h>
288
+ #include <stdarg.h>
289
+
290
+ int mytest(char *fmt, ...)
291
+ {
292
+ int n;
293
+ char buf[20];
294
+ va_list ap;
295
+
296
+ va_start(ap, fmt);
297
+ n = vsprintf(buf, fmt, ap);
298
+ va_end(ap);
299
+ return n;
300
+ }
301
+
302
+ int main()
303
+ {
304
+ return (mytest("Hello%d\n", 1));
305
+ }
306
+ EOF
307
+
308
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
309
+ echo "Checking for return value of vsprintf()... Yes."
310
+ else
311
+ CFLAGS="$CFLAGS -DHAS_vsprintf_void"
312
+ echo "Checking for return value of vsprintf()... No."
313
+ echo " WARNING: apparently vsprintf() does not return a value. zlib"
314
+ echo " can build but will be open to possible string-format security"
315
+ echo " vulnerabilities."
316
+ fi
317
+ fi
318
+ else
319
+ echo "Checking whether to use vs[n]printf() or s[n]printf()... using s[n]printf()"
320
+
321
+ cat >$test.c <<EOF
322
+ #include <stdio.h>
323
+
324
+ int mytest()
325
+ {
326
+ char buf[20];
327
+
328
+ snprintf(buf, sizeof(buf), "%s", "foo");
329
+ return 0;
330
+ }
331
+
332
+ int main()
333
+ {
334
+ return (mytest());
335
+ }
336
+ EOF
337
+
338
+ if test "`($CC $CFLAGS -o $test $test.c) 2>&1`" = ""; then
339
+ echo "Checking for snprintf() in stdio.h... Yes."
340
+
341
+ cat >$test.c <<EOF
342
+ #include <stdio.h>
343
+
344
+ int mytest()
345
+ {
346
+ char buf[20];
347
+
348
+ return snprintf(buf, sizeof(buf), "%s", "foo");
349
+ }
350
+
351
+ int main()
352
+ {
353
+ return (mytest());
354
+ }
355
+ EOF
356
+
357
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
358
+ echo "Checking for return value of snprintf()... Yes."
359
+ else
360
+ CFLAGS="$CFLAGS -DHAS_snprintf_void"
361
+ echo "Checking for return value of snprintf()... No."
362
+ echo " WARNING: apparently snprintf() does not return a value. zlib"
363
+ echo " can build but will be open to possible string-format security"
364
+ echo " vulnerabilities."
365
+ fi
366
+ else
367
+ CFLAGS="$CFLAGS -DNO_snprintf"
368
+ echo "Checking for snprintf() in stdio.h... No."
369
+ echo " WARNING: snprintf() not found, falling back to sprintf(). zlib"
370
+ echo " can build but will be open to possible buffer-overflow security"
371
+ echo " vulnerabilities."
372
+
373
+ cat >$test.c <<EOF
374
+ #include <stdio.h>
375
+
376
+ int mytest()
377
+ {
378
+ char buf[20];
379
+
380
+ return sprintf(buf, "%s", "foo");
381
+ }
382
+
383
+ int main()
384
+ {
385
+ return (mytest());
386
+ }
387
+ EOF
388
+
389
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
390
+ echo "Checking for return value of sprintf()... Yes."
391
+ else
392
+ CFLAGS="$CFLAGS -DHAS_sprintf_void"
393
+ echo "Checking for return value of sprintf()... No."
394
+ echo " WARNING: apparently sprintf() does not return a value. zlib"
395
+ echo " can build but will be open to possible string-format security"
396
+ echo " vulnerabilities."
397
+ fi
398
+ fi
399
+ fi
400
+
401
+ cat >$test.c <<EOF
402
+ #include <errno.h>
403
+ int main() { return 0; }
404
+ EOF
405
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
406
+ echo "Checking for errno.h... Yes."
407
+ else
408
+ echo "Checking for errno.h... No."
409
+ CFLAGS="$CFLAGS -DNO_ERRNO_H"
410
+ fi
411
+
412
+ cat > $test.c <<EOF
413
+ #include <sys/types.h>
414
+ #include <sys/mman.h>
415
+ #include <sys/stat.h>
416
+ caddr_t hello() {
417
+ return mmap((caddr_t)0, (off_t)0, PROT_READ, MAP_SHARED, 0, (off_t)0);
418
+ }
419
+ EOF
420
+ if test "`($CC -c $CFLAGS $test.c) 2>&1`" = ""; then
421
+ CFLAGS="$CFLAGS -DUSE_MMAP"
422
+ echo Checking for mmap support... Yes.
423
+ else
424
+ echo Checking for mmap support... No.
425
+ fi
426
+
427
+ CPP=${CPP-"$CC -E"}
428
+ case $CFLAGS in
429
+ *ASMV*)
430
+ if test "`nm $test.o | grep _hello`" = ""; then
431
+ CPP="$CPP -DNO_UNDERLINE"
432
+ echo Checking for underline in external names... No.
433
+ else
434
+ echo Checking for underline in external names... Yes.
435
+ fi;;
436
+ esac
437
+
438
+ rm -f $test.[co] $test $test$shared_ext
439
+
440
+ # udpate Makefile
441
+ sed < Makefile.in "
442
+ /^CC *=/s#=.*#=$CC#
443
+ /^CFLAGS *=/s#=.*#=$CFLAGS#
444
+ /^CPP *=/s#=.*#=$CPP#
445
+ /^LDSHARED *=/s#=.*#=$LDSHARED#
446
+ /^LIBS *=/s#=.*#=$LIBS#
447
+ /^SHAREDLIB *=/s#=.*#=$SHAREDLIB#
448
+ /^SHAREDLIBV *=/s#=.*#=$SHAREDLIBV#
449
+ /^SHAREDLIBM *=/s#=.*#=$SHAREDLIBM#
450
+ /^AR *=/s#=.*#=$AR#
451
+ /^RANLIB *=/s#=.*#=$RANLIB#
452
+ /^EXE *=/s#=.*#=$EXE#
453
+ /^prefix *=/s#=.*#=$prefix#
454
+ /^exec_prefix *=/s#=.*#=$exec_prefix#
455
+ /^libdir *=/s#=.*#=$libdir#
456
+ /^includedir *=/s#=.*#=$includedir#
457
+ /^mandir *=/s#=.*#=$mandir#
458
+ /^LDFLAGS *=/s#=.*#=$LDFLAGS#
459
+ " > Makefile