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 +1,71 @@
1
+ All files under this contrib directory are UNSUPPORTED. There were
2
+ provided by users of zlib and were not tested by the authors of zlib.
3
+ Use at your own risk. Please contact the authors of the contributions
4
+ for help about these, not the zlib authors. Thanks.
5
+
6
+
7
+ ada/ by Dmitriy Anisimkov <anisimkov@yahoo.com>
8
+ Support for Ada
9
+ See http://zlib-ada.sourceforge.net/
10
+
11
+ asm586/
12
+ asm686/ by Brian Raiter <breadbox@muppetlabs.com>
13
+ asm code for Pentium and PPro/PII, using the AT&T (GNU as) syntax
14
+ See http://www.muppetlabs.com/~breadbox/software/assembly.html
15
+
16
+ blast/ by Mark Adler <madler@alumni.caltech.edu>
17
+ Decompressor for output of PKWare Data Compression Library (DCL)
18
+
19
+ delphi/ by Cosmin Truta <cosmint@cs.ubbcluj.ro>
20
+ Support for Delphi and C++ Builder
21
+
22
+ dotzlib/ by Henrik Ravn <henrik@ravn.com>
23
+ Support for Microsoft .Net and Visual C++ .Net
24
+
25
+ infback9/ by Mark Adler <madler@alumni.caltech.edu>
26
+ Unsupported diffs to infback to decode the deflate64 format
27
+
28
+ inflate86/ by Chris Anderson <christop@charm.net>
29
+ Tuned x86 gcc asm code to replace inflate_fast()
30
+
31
+ iostream/ by Kevin Ruland <kevin@rodin.wustl.edu>
32
+ A C++ I/O streams interface to the zlib gz* functions
33
+
34
+ iostream2/ by Tyge L�vset <Tyge.Lovset@cmr.no>
35
+ Another C++ I/O streams interface
36
+
37
+ iostream3/ by Ludwig Schwardt <schwardt@sun.ac.za>
38
+ and Kevin Ruland <kevin@rodin.wustl.edu>
39
+ Yet another C++ I/O streams interface
40
+
41
+ masm686/ by Dan Higdon <hdan@kinesoft.com>
42
+ and Chuck Walbourn <chuckw@kinesoft.com>
43
+ asm code for Pentium Pro/PII, using the MASM syntax
44
+
45
+ masmx64/ by Gilles Vollant <info@winimage.com>
46
+ x86 64-bit (AMD64 and Intel EM64t) code for x64 assembler to
47
+ replace longest_match() and inflate_fast()
48
+
49
+ masmx86/ by Gilles Vollant <info@winimage.com>
50
+ x86 asm code to replace longest_match() and inflate_fast(),
51
+ for Visual C++ and MASM
52
+
53
+ minizip/ by Gilles Vollant <info@winimage.com>
54
+ Mini zip and unzip based on zlib
55
+ See http://www.winimage.com/zLibDll/unzip.html
56
+
57
+ pascal/ by Bob Dellaca <bobdl@xtra.co.nz> et al.
58
+ Support for Pascal
59
+
60
+ puff/ by Mark Adler <madler@alumni.caltech.edu>
61
+ Small, low memory usage inflate. Also serves to provide an
62
+ unambiguous description of the deflate format.
63
+
64
+ testzlib/ by Gilles Vollant <info@winimage.com>
65
+ Example of the use of zlib
66
+
67
+ untgz/ by Pedro A. Aranda Gutierrez <paag@tid.es>
68
+ A very simple tar.gz file extractor using zlib
69
+
70
+ vstudio/ by Gilles Vollant <info@winimage.com>
71
+ Building a minizip-enhanced zlib with Microsoft Visual Studio
@@ -0,0 +1,106 @@
1
+ ----------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2004 Dmitriy Anisimkov --
5
+ -- --
6
+ -- Open source license information is in the zlib.ads file. --
7
+ ----------------------------------------------------------------
8
+ --
9
+ -- $Id: buffer_demo.adb,v 1.3 2004/09/06 06:55:35 vagul Exp $
10
+
11
+ -- This demo program provided by Dr Steve Sangwine <sjs@essex.ac.uk>
12
+ --
13
+ -- Demonstration of a problem with Zlib-Ada (already fixed) when a buffer
14
+ -- of exactly the correct size is used for decompressed data, and the last
15
+ -- few bytes passed in to Zlib are checksum bytes.
16
+
17
+ -- This program compresses a string of text, and then decompresses the
18
+ -- compressed text into a buffer of the same size as the original text.
19
+
20
+ with Ada.Streams; use Ada.Streams;
21
+ with Ada.Text_IO;
22
+
23
+ with ZLib; use ZLib;
24
+
25
+ procedure Buffer_Demo is
26
+ EOL : Character renames ASCII.LF;
27
+ Text : constant String
28
+ := "Four score and seven years ago our fathers brought forth," & EOL &
29
+ "upon this continent, a new nation, conceived in liberty," & EOL &
30
+ "and dedicated to the proposition that `all men are created equal'.";
31
+
32
+ Source : Stream_Element_Array (1 .. Text'Length);
33
+ for Source'Address use Text'Address;
34
+
35
+ begin
36
+ Ada.Text_IO.Put (Text);
37
+ Ada.Text_IO.New_Line;
38
+ Ada.Text_IO.Put_Line
39
+ ("Uncompressed size : " & Positive'Image (Text'Length) & " bytes");
40
+
41
+ declare
42
+ Compressed_Data : Stream_Element_Array (1 .. Text'Length);
43
+ L : Stream_Element_Offset;
44
+ begin
45
+ Compress : declare
46
+ Compressor : Filter_Type;
47
+ I : Stream_Element_Offset;
48
+ begin
49
+ Deflate_Init (Compressor);
50
+
51
+ -- Compress the whole of T at once.
52
+
53
+ Translate (Compressor, Source, I, Compressed_Data, L, Finish);
54
+ pragma Assert (I = Source'Last);
55
+
56
+ Close (Compressor);
57
+
58
+ Ada.Text_IO.Put_Line
59
+ ("Compressed size : "
60
+ & Stream_Element_Offset'Image (L) & " bytes");
61
+ end Compress;
62
+
63
+ -- Now we decompress the data, passing short blocks of data to Zlib
64
+ -- (because this demonstrates the problem - the last block passed will
65
+ -- contain checksum information and there will be no output, only a
66
+ -- check inside Zlib that the checksum is correct).
67
+
68
+ Decompress : declare
69
+ Decompressor : Filter_Type;
70
+
71
+ Uncompressed_Data : Stream_Element_Array (1 .. Text'Length);
72
+
73
+ Block_Size : constant := 4;
74
+ -- This makes sure that the last block contains
75
+ -- only Adler checksum data.
76
+
77
+ P : Stream_Element_Offset := Compressed_Data'First - 1;
78
+ O : Stream_Element_Offset;
79
+ begin
80
+ Inflate_Init (Decompressor);
81
+
82
+ loop
83
+ Translate
84
+ (Decompressor,
85
+ Compressed_Data
86
+ (P + 1 .. Stream_Element_Offset'Min (P + Block_Size, L)),
87
+ P,
88
+ Uncompressed_Data
89
+ (Total_Out (Decompressor) + 1 .. Uncompressed_Data'Last),
90
+ O,
91
+ No_Flush);
92
+
93
+ Ada.Text_IO.Put_Line
94
+ ("Total in : " & Count'Image (Total_In (Decompressor)) &
95
+ ", out : " & Count'Image (Total_Out (Decompressor)));
96
+
97
+ exit when P = L;
98
+ end loop;
99
+
100
+ Ada.Text_IO.New_Line;
101
+ Ada.Text_IO.Put_Line
102
+ ("Decompressed text matches original text : "
103
+ & Boolean'Image (Uncompressed_Data = Source));
104
+ end Decompress;
105
+ end;
106
+ end Buffer_Demo;
@@ -0,0 +1,156 @@
1
+ ----------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2003 Dmitriy Anisimkov --
5
+ -- --
6
+ -- Open source license information is in the zlib.ads file. --
7
+ ----------------------------------------------------------------
8
+ -- Continuous test for ZLib multithreading. If the test would fail
9
+ -- we should provide thread safe allocation routines for the Z_Stream.
10
+ --
11
+ -- $Id: mtest.adb,v 1.4 2004/07/23 07:49:54 vagul Exp $
12
+
13
+ with ZLib;
14
+ with Ada.Streams;
15
+ with Ada.Numerics.Discrete_Random;
16
+ with Ada.Text_IO;
17
+ with Ada.Exceptions;
18
+ with Ada.Task_Identification;
19
+
20
+ procedure MTest is
21
+ use Ada.Streams;
22
+ use ZLib;
23
+
24
+ Stop : Boolean := False;
25
+
26
+ pragma Atomic (Stop);
27
+
28
+ subtype Visible_Symbols is Stream_Element range 16#20# .. 16#7E#;
29
+
30
+ package Random_Elements is
31
+ new Ada.Numerics.Discrete_Random (Visible_Symbols);
32
+
33
+ task type Test_Task;
34
+
35
+ task body Test_Task is
36
+ Buffer : Stream_Element_Array (1 .. 100_000);
37
+ Gen : Random_Elements.Generator;
38
+
39
+ Buffer_First : Stream_Element_Offset;
40
+ Compare_First : Stream_Element_Offset;
41
+
42
+ Deflate : Filter_Type;
43
+ Inflate : Filter_Type;
44
+
45
+ procedure Further (Item : in Stream_Element_Array);
46
+
47
+ procedure Read_Buffer
48
+ (Item : out Ada.Streams.Stream_Element_Array;
49
+ Last : out Ada.Streams.Stream_Element_Offset);
50
+
51
+ -------------
52
+ -- Further --
53
+ -------------
54
+
55
+ procedure Further (Item : in Stream_Element_Array) is
56
+
57
+ procedure Compare (Item : in Stream_Element_Array);
58
+
59
+ -------------
60
+ -- Compare --
61
+ -------------
62
+
63
+ procedure Compare (Item : in Stream_Element_Array) is
64
+ Next_First : Stream_Element_Offset := Compare_First + Item'Length;
65
+ begin
66
+ if Buffer (Compare_First .. Next_First - 1) /= Item then
67
+ raise Program_Error;
68
+ end if;
69
+
70
+ Compare_First := Next_First;
71
+ end Compare;
72
+
73
+ procedure Compare_Write is new ZLib.Write (Write => Compare);
74
+ begin
75
+ Compare_Write (Inflate, Item, No_Flush);
76
+ end Further;
77
+
78
+ -----------------
79
+ -- Read_Buffer --
80
+ -----------------
81
+
82
+ procedure Read_Buffer
83
+ (Item : out Ada.Streams.Stream_Element_Array;
84
+ Last : out Ada.Streams.Stream_Element_Offset)
85
+ is
86
+ Buff_Diff : Stream_Element_Offset := Buffer'Last - Buffer_First;
87
+ Next_First : Stream_Element_Offset;
88
+ begin
89
+ if Item'Length <= Buff_Diff then
90
+ Last := Item'Last;
91
+
92
+ Next_First := Buffer_First + Item'Length;
93
+
94
+ Item := Buffer (Buffer_First .. Next_First - 1);
95
+
96
+ Buffer_First := Next_First;
97
+ else
98
+ Last := Item'First + Buff_Diff;
99
+ Item (Item'First .. Last) := Buffer (Buffer_First .. Buffer'Last);
100
+ Buffer_First := Buffer'Last + 1;
101
+ end if;
102
+ end Read_Buffer;
103
+
104
+ procedure Translate is new Generic_Translate
105
+ (Data_In => Read_Buffer,
106
+ Data_Out => Further);
107
+
108
+ begin
109
+ Random_Elements.Reset (Gen);
110
+
111
+ Buffer := (others => 20);
112
+
113
+ Main : loop
114
+ for J in Buffer'Range loop
115
+ Buffer (J) := Random_Elements.Random (Gen);
116
+
117
+ Deflate_Init (Deflate);
118
+ Inflate_Init (Inflate);
119
+
120
+ Buffer_First := Buffer'First;
121
+ Compare_First := Buffer'First;
122
+
123
+ Translate (Deflate);
124
+
125
+ if Compare_First /= Buffer'Last + 1 then
126
+ raise Program_Error;
127
+ end if;
128
+
129
+ Ada.Text_IO.Put_Line
130
+ (Ada.Task_Identification.Image
131
+ (Ada.Task_Identification.Current_Task)
132
+ & Stream_Element_Offset'Image (J)
133
+ & ZLib.Count'Image (Total_Out (Deflate)));
134
+
135
+ Close (Deflate);
136
+ Close (Inflate);
137
+
138
+ exit Main when Stop;
139
+ end loop;
140
+ end loop Main;
141
+ exception
142
+ when E : others =>
143
+ Ada.Text_IO.Put_Line (Ada.Exceptions.Exception_Information (E));
144
+ Stop := True;
145
+ end Test_Task;
146
+
147
+ Test : array (1 .. 4) of Test_Task;
148
+
149
+ pragma Unreferenced (Test);
150
+
151
+ Dummy : Character;
152
+
153
+ begin
154
+ Ada.Text_IO.Get_Immediate (Dummy);
155
+ Stop := True;
156
+ end MTest;
@@ -0,0 +1,156 @@
1
+ ----------------------------------------------------------------
2
+ -- ZLib for Ada thick binding. --
3
+ -- --
4
+ -- Copyright (C) 2002-2003 Dmitriy Anisimkov --
5
+ -- --
6
+ -- Open source license information is in the zlib.ads file. --
7
+ ----------------------------------------------------------------
8
+
9
+ -- $Id: read.adb,v 1.8 2004/05/31 10:53:40 vagul Exp $
10
+
11
+ -- Test/demo program for the generic read interface.
12
+
13
+ with Ada.Numerics.Discrete_Random;
14
+ with Ada.Streams;
15
+ with Ada.Text_IO;
16
+
17
+ with ZLib;
18
+
19
+ procedure Read is
20
+
21
+ use Ada.Streams;
22
+
23
+ ------------------------------------
24
+ -- Test configuration parameters --
25
+ ------------------------------------
26
+
27
+ File_Size : Stream_Element_Offset := 100_000;
28
+
29
+ Continuous : constant Boolean := False;
30
+ -- If this constant is True, the test would be repeated again and again,
31
+ -- with increment File_Size for every iteration.
32
+
33
+ Header : constant ZLib.Header_Type := ZLib.Default;
34
+ -- Do not use Header other than Default in ZLib versions 1.1.4 and older.
35
+
36
+ Init_Random : constant := 8;
37
+ -- We are using the same random sequence, in case of we catch bug,
38
+ -- so we would be able to reproduce it.
39
+
40
+ -- End --
41
+
42
+ Pack_Size : Stream_Element_Offset;
43
+ Offset : Stream_Element_Offset;
44
+
45
+ Filter : ZLib.Filter_Type;
46
+
47
+ subtype Visible_Symbols
48
+ is Stream_Element range 16#20# .. 16#7E#;
49
+
50
+ package Random_Elements is new
51
+ Ada.Numerics.Discrete_Random (Visible_Symbols);
52
+
53
+ Gen : Random_Elements.Generator;
54
+ Period : constant Stream_Element_Offset := 200;
55
+ -- Period constant variable for random generator not to be very random.
56
+ -- Bigger period, harder random.
57
+
58
+ Read_Buffer : Stream_Element_Array (1 .. 2048);
59
+ Read_First : Stream_Element_Offset;
60
+ Read_Last : Stream_Element_Offset;
61
+
62
+ procedure Reset;
63
+
64
+ procedure Read
65
+ (Item : out Stream_Element_Array;
66
+ Last : out Stream_Element_Offset);
67
+ -- this procedure is for generic instantiation of
68
+ -- ZLib.Read
69
+ -- reading data from the File_In.
70
+
71
+ procedure Read is new ZLib.Read
72
+ (Read,
73
+ Read_Buffer,
74
+ Rest_First => Read_First,
75
+ Rest_Last => Read_Last);
76
+
77
+ ----------
78
+ -- Read --
79
+ ----------
80
+
81
+ procedure Read
82
+ (Item : out Stream_Element_Array;
83
+ Last : out Stream_Element_Offset) is
84
+ begin
85
+ Last := Stream_Element_Offset'Min
86
+ (Item'Last,
87
+ Item'First + File_Size - Offset);
88
+
89
+ for J in Item'First .. Last loop
90
+ if J < Item'First + Period then
91
+ Item (J) := Random_Elements.Random (Gen);
92
+ else
93
+ Item (J) := Item (J - Period);
94
+ end if;
95
+
96
+ Offset := Offset + 1;
97
+ end loop;
98
+ end Read;
99
+
100
+ -----------
101
+ -- Reset --
102
+ -----------
103
+
104
+ procedure Reset is
105
+ begin
106
+ Random_Elements.Reset (Gen, Init_Random);
107
+ Pack_Size := 0;
108
+ Offset := 1;
109
+ Read_First := Read_Buffer'Last + 1;
110
+ Read_Last := Read_Buffer'Last;
111
+ end Reset;
112
+
113
+ begin
114
+ Ada.Text_IO.Put_Line ("ZLib " & ZLib.Version);
115
+
116
+ loop
117
+ for Level in ZLib.Compression_Level'Range loop
118
+
119
+ Ada.Text_IO.Put ("Level ="
120
+ & ZLib.Compression_Level'Image (Level));
121
+
122
+ -- Deflate using generic instantiation.
123
+
124
+ ZLib.Deflate_Init
125
+ (Filter,
126
+ Level,
127
+ Header => Header);
128
+
129
+ Reset;
130
+
131
+ Ada.Text_IO.Put
132
+ (Stream_Element_Offset'Image (File_Size) & " ->");
133
+
134
+ loop
135
+ declare
136
+ Buffer : Stream_Element_Array (1 .. 1024);
137
+ Last : Stream_Element_Offset;
138
+ begin
139
+ Read (Filter, Buffer, Last);
140
+
141
+ Pack_Size := Pack_Size + Last - Buffer'First + 1;
142
+
143
+ exit when Last < Buffer'Last;
144
+ end;
145
+ end loop;
146
+
147
+ Ada.Text_IO.Put_Line (Stream_Element_Offset'Image (Pack_Size));
148
+
149
+ ZLib.Close (Filter);
150
+ end loop;
151
+
152
+ exit when not Continuous;
153
+
154
+ File_Size := File_Size + 1;
155
+ end loop;
156
+ end Read;