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
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj ADDED
@@ -0,0 +1,567 @@
1
+ <?xml version="1.0" encoding="Windows-1252"?>
2
+ <VisualStudioProject
3
+ ProjectType="Visual C++"
4
+ Version="8,00"
5
+ Name="TestZlibDll"
6
+ ProjectGUID="{C52F9E7B-498A-42BE-8DB4-85A15694366A}"
7
+ Keyword="Win32Proj"
8
+ SignManifests="true"
9
+ >
10
+ <Platforms>
11
+ <Platform
12
+ Name="Win32"
13
+ />
14
+ <Platform
15
+ Name="x64"
16
+ />
17
+ <Platform
18
+ Name="Itanium"
19
+ />
20
+ </Platforms>
21
+ <ToolFiles>
22
+ </ToolFiles>
23
+ <Configurations>
24
+ <Configuration
25
+ Name="Debug|Win32"
26
+ OutputDirectory="x86\TestZlibDll$(ConfigurationName)"
27
+ IntermediateDirectory="x86\TestZlibDll$(ConfigurationName)\Tmp"
28
+ ConfigurationType="1"
29
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
30
+ CharacterSet="2"
31
+ >
32
+ <Tool
33
+ Name="VCPreBuildEventTool"
34
+ />
35
+ <Tool
36
+ Name="VCCustomBuildTool"
37
+ />
38
+ <Tool
39
+ Name="VCXMLDataGeneratorTool"
40
+ />
41
+ <Tool
42
+ Name="VCWebServiceProxyGeneratorTool"
43
+ />
44
+ <Tool
45
+ Name="VCMIDLTool"
46
+ />
47
+ <Tool
48
+ Name="VCCLCompilerTool"
49
+ Optimization="0"
50
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
51
+ PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE"
52
+ MinimalRebuild="true"
53
+ BasicRuntimeChecks="0"
54
+ RuntimeLibrary="1"
55
+ BufferSecurityCheck="false"
56
+ UsePrecompiledHeader="0"
57
+ AssemblerListingLocation="$(IntDir)\"
58
+ WarningLevel="3"
59
+ Detect64BitPortabilityProblems="true"
60
+ DebugInformationFormat="4"
61
+ />
62
+ <Tool
63
+ Name="VCManagedResourceCompilerTool"
64
+ />
65
+ <Tool
66
+ Name="VCResourceCompilerTool"
67
+ />
68
+ <Tool
69
+ Name="VCPreLinkEventTool"
70
+ />
71
+ <Tool
72
+ Name="VCLinkerTool"
73
+ AdditionalDependencies="x86\ZlibDllDebug\zlibwapi.lib"
74
+ OutputFile="$(OutDir)/testzlib.exe"
75
+ LinkIncremental="2"
76
+ GenerateManifest="false"
77
+ GenerateDebugInformation="true"
78
+ ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
79
+ SubSystem="1"
80
+ TargetMachine="1"
81
+ />
82
+ <Tool
83
+ Name="VCALinkTool"
84
+ />
85
+ <Tool
86
+ Name="VCManifestTool"
87
+ />
88
+ <Tool
89
+ Name="VCXDCMakeTool"
90
+ />
91
+ <Tool
92
+ Name="VCBscMakeTool"
93
+ />
94
+ <Tool
95
+ Name="VCFxCopTool"
96
+ />
97
+ <Tool
98
+ Name="VCAppVerifierTool"
99
+ />
100
+ <Tool
101
+ Name="VCWebDeploymentTool"
102
+ />
103
+ <Tool
104
+ Name="VCPostBuildEventTool"
105
+ />
106
+ </Configuration>
107
+ <Configuration
108
+ Name="Debug|x64"
109
+ OutputDirectory="x64\TestZlibDll$(ConfigurationName)"
110
+ IntermediateDirectory="x64\TestZlibDll$(ConfigurationName)\Tmp"
111
+ ConfigurationType="1"
112
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
113
+ CharacterSet="2"
114
+ >
115
+ <Tool
116
+ Name="VCPreBuildEventTool"
117
+ />
118
+ <Tool
119
+ Name="VCCustomBuildTool"
120
+ />
121
+ <Tool
122
+ Name="VCXMLDataGeneratorTool"
123
+ />
124
+ <Tool
125
+ Name="VCWebServiceProxyGeneratorTool"
126
+ />
127
+ <Tool
128
+ Name="VCMIDLTool"
129
+ TargetEnvironment="3"
130
+ />
131
+ <Tool
132
+ Name="VCCLCompilerTool"
133
+ Optimization="0"
134
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
135
+ PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
136
+ MinimalRebuild="true"
137
+ BasicRuntimeChecks="0"
138
+ RuntimeLibrary="3"
139
+ BufferSecurityCheck="false"
140
+ UsePrecompiledHeader="0"
141
+ AssemblerListingLocation="$(IntDir)\"
142
+ WarningLevel="3"
143
+ Detect64BitPortabilityProblems="true"
144
+ DebugInformationFormat="3"
145
+ />
146
+ <Tool
147
+ Name="VCManagedResourceCompilerTool"
148
+ />
149
+ <Tool
150
+ Name="VCResourceCompilerTool"
151
+ />
152
+ <Tool
153
+ Name="VCPreLinkEventTool"
154
+ />
155
+ <Tool
156
+ Name="VCLinkerTool"
157
+ AdditionalDependencies="x64\ZlibDllDebug\zlibwapi.lib"
158
+ OutputFile="$(OutDir)/testzlib.exe"
159
+ LinkIncremental="2"
160
+ GenerateManifest="false"
161
+ GenerateDebugInformation="true"
162
+ ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
163
+ SubSystem="1"
164
+ TargetMachine="17"
165
+ />
166
+ <Tool
167
+ Name="VCALinkTool"
168
+ />
169
+ <Tool
170
+ Name="VCManifestTool"
171
+ />
172
+ <Tool
173
+ Name="VCXDCMakeTool"
174
+ />
175
+ <Tool
176
+ Name="VCBscMakeTool"
177
+ />
178
+ <Tool
179
+ Name="VCFxCopTool"
180
+ />
181
+ <Tool
182
+ Name="VCAppVerifierTool"
183
+ />
184
+ <Tool
185
+ Name="VCWebDeploymentTool"
186
+ />
187
+ <Tool
188
+ Name="VCPostBuildEventTool"
189
+ />
190
+ </Configuration>
191
+ <Configuration
192
+ Name="Debug|Itanium"
193
+ OutputDirectory="ia64\TestZlibDll$(ConfigurationName)"
194
+ IntermediateDirectory="ia64\TestZlibDll$(ConfigurationName)\Tmp"
195
+ ConfigurationType="1"
196
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
197
+ CharacterSet="2"
198
+ >
199
+ <Tool
200
+ Name="VCPreBuildEventTool"
201
+ />
202
+ <Tool
203
+ Name="VCCustomBuildTool"
204
+ />
205
+ <Tool
206
+ Name="VCXMLDataGeneratorTool"
207
+ />
208
+ <Tool
209
+ Name="VCWebServiceProxyGeneratorTool"
210
+ />
211
+ <Tool
212
+ Name="VCMIDLTool"
213
+ TargetEnvironment="2"
214
+ />
215
+ <Tool
216
+ Name="VCCLCompilerTool"
217
+ Optimization="0"
218
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
219
+ PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;_DEBUG;_CONSOLE;WIN64"
220
+ MinimalRebuild="true"
221
+ BasicRuntimeChecks="0"
222
+ RuntimeLibrary="3"
223
+ BufferSecurityCheck="false"
224
+ UsePrecompiledHeader="0"
225
+ AssemblerListingLocation="$(IntDir)\"
226
+ WarningLevel="3"
227
+ Detect64BitPortabilityProblems="true"
228
+ DebugInformationFormat="3"
229
+ />
230
+ <Tool
231
+ Name="VCManagedResourceCompilerTool"
232
+ />
233
+ <Tool
234
+ Name="VCResourceCompilerTool"
235
+ />
236
+ <Tool
237
+ Name="VCPreLinkEventTool"
238
+ />
239
+ <Tool
240
+ Name="VCLinkerTool"
241
+ AdditionalDependencies="ia64\ZlibDllDebug\zlibwapi.lib"
242
+ OutputFile="$(OutDir)/testzlib.exe"
243
+ LinkIncremental="2"
244
+ GenerateManifest="false"
245
+ GenerateDebugInformation="true"
246
+ ProgramDatabaseFile="$(OutDir)/testzlib.pdb"
247
+ SubSystem="1"
248
+ TargetMachine="5"
249
+ />
250
+ <Tool
251
+ Name="VCALinkTool"
252
+ />
253
+ <Tool
254
+ Name="VCManifestTool"
255
+ />
256
+ <Tool
257
+ Name="VCXDCMakeTool"
258
+ />
259
+ <Tool
260
+ Name="VCBscMakeTool"
261
+ />
262
+ <Tool
263
+ Name="VCFxCopTool"
264
+ />
265
+ <Tool
266
+ Name="VCAppVerifierTool"
267
+ />
268
+ <Tool
269
+ Name="VCWebDeploymentTool"
270
+ />
271
+ <Tool
272
+ Name="VCPostBuildEventTool"
273
+ />
274
+ </Configuration>
275
+ <Configuration
276
+ Name="Release|Win32"
277
+ OutputDirectory="x86\TestZlibDll$(ConfigurationName)"
278
+ IntermediateDirectory="x86\TestZlibDll$(ConfigurationName)\Tmp"
279
+ ConfigurationType="1"
280
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
281
+ CharacterSet="2"
282
+ >
283
+ <Tool
284
+ Name="VCPreBuildEventTool"
285
+ />
286
+ <Tool
287
+ Name="VCCustomBuildTool"
288
+ />
289
+ <Tool
290
+ Name="VCXMLDataGeneratorTool"
291
+ />
292
+ <Tool
293
+ Name="VCWebServiceProxyGeneratorTool"
294
+ />
295
+ <Tool
296
+ Name="VCMIDLTool"
297
+ />
298
+ <Tool
299
+ Name="VCCLCompilerTool"
300
+ Optimization="2"
301
+ InlineFunctionExpansion="1"
302
+ OmitFramePointers="true"
303
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
304
+ PreprocessorDefinitions="WIN32;_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE"
305
+ StringPooling="true"
306
+ BasicRuntimeChecks="0"
307
+ RuntimeLibrary="0"
308
+ BufferSecurityCheck="false"
309
+ EnableFunctionLevelLinking="true"
310
+ UsePrecompiledHeader="0"
311
+ AssemblerListingLocation="$(IntDir)\"
312
+ WarningLevel="3"
313
+ Detect64BitPortabilityProblems="true"
314
+ DebugInformationFormat="3"
315
+ />
316
+ <Tool
317
+ Name="VCManagedResourceCompilerTool"
318
+ />
319
+ <Tool
320
+ Name="VCResourceCompilerTool"
321
+ />
322
+ <Tool
323
+ Name="VCPreLinkEventTool"
324
+ />
325
+ <Tool
326
+ Name="VCLinkerTool"
327
+ AdditionalDependencies="x86\ZlibDllRelease\zlibwapi.lib"
328
+ OutputFile="$(OutDir)/testzlib.exe"
329
+ LinkIncremental="1"
330
+ GenerateManifest="false"
331
+ GenerateDebugInformation="true"
332
+ SubSystem="1"
333
+ OptimizeReferences="2"
334
+ EnableCOMDATFolding="2"
335
+ OptimizeForWindows98="1"
336
+ TargetMachine="1"
337
+ />
338
+ <Tool
339
+ Name="VCALinkTool"
340
+ />
341
+ <Tool
342
+ Name="VCManifestTool"
343
+ />
344
+ <Tool
345
+ Name="VCXDCMakeTool"
346
+ />
347
+ <Tool
348
+ Name="VCBscMakeTool"
349
+ />
350
+ <Tool
351
+ Name="VCFxCopTool"
352
+ />
353
+ <Tool
354
+ Name="VCAppVerifierTool"
355
+ />
356
+ <Tool
357
+ Name="VCWebDeploymentTool"
358
+ />
359
+ <Tool
360
+ Name="VCPostBuildEventTool"
361
+ />
362
+ </Configuration>
363
+ <Configuration
364
+ Name="Release|x64"
365
+ OutputDirectory="x64\TestZlibDll$(ConfigurationName)"
366
+ IntermediateDirectory="x64\TestZlibDll$(ConfigurationName)\Tmp"
367
+ ConfigurationType="1"
368
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
369
+ CharacterSet="2"
370
+ >
371
+ <Tool
372
+ Name="VCPreBuildEventTool"
373
+ />
374
+ <Tool
375
+ Name="VCCustomBuildTool"
376
+ />
377
+ <Tool
378
+ Name="VCXMLDataGeneratorTool"
379
+ />
380
+ <Tool
381
+ Name="VCWebServiceProxyGeneratorTool"
382
+ />
383
+ <Tool
384
+ Name="VCMIDLTool"
385
+ TargetEnvironment="3"
386
+ />
387
+ <Tool
388
+ Name="VCCLCompilerTool"
389
+ Optimization="2"
390
+ InlineFunctionExpansion="1"
391
+ OmitFramePointers="true"
392
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
393
+ PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
394
+ StringPooling="true"
395
+ BasicRuntimeChecks="0"
396
+ RuntimeLibrary="2"
397
+ BufferSecurityCheck="false"
398
+ EnableFunctionLevelLinking="true"
399
+ UsePrecompiledHeader="0"
400
+ AssemblerListingLocation="$(IntDir)\"
401
+ WarningLevel="3"
402
+ Detect64BitPortabilityProblems="true"
403
+ DebugInformationFormat="3"
404
+ />
405
+ <Tool
406
+ Name="VCManagedResourceCompilerTool"
407
+ />
408
+ <Tool
409
+ Name="VCResourceCompilerTool"
410
+ />
411
+ <Tool
412
+ Name="VCPreLinkEventTool"
413
+ />
414
+ <Tool
415
+ Name="VCLinkerTool"
416
+ AdditionalDependencies="x64\ZlibDllRelease\zlibwapi.lib"
417
+ OutputFile="$(OutDir)/testzlib.exe"
418
+ LinkIncremental="1"
419
+ GenerateManifest="false"
420
+ GenerateDebugInformation="true"
421
+ SubSystem="1"
422
+ OptimizeReferences="2"
423
+ EnableCOMDATFolding="2"
424
+ OptimizeForWindows98="1"
425
+ TargetMachine="17"
426
+ />
427
+ <Tool
428
+ Name="VCALinkTool"
429
+ />
430
+ <Tool
431
+ Name="VCManifestTool"
432
+ />
433
+ <Tool
434
+ Name="VCXDCMakeTool"
435
+ />
436
+ <Tool
437
+ Name="VCBscMakeTool"
438
+ />
439
+ <Tool
440
+ Name="VCFxCopTool"
441
+ />
442
+ <Tool
443
+ Name="VCAppVerifierTool"
444
+ />
445
+ <Tool
446
+ Name="VCWebDeploymentTool"
447
+ />
448
+ <Tool
449
+ Name="VCPostBuildEventTool"
450
+ />
451
+ </Configuration>
452
+ <Configuration
453
+ Name="Release|Itanium"
454
+ OutputDirectory="ia64\TestZlibDll$(ConfigurationName)"
455
+ IntermediateDirectory="ia64\TestZlibDll$(ConfigurationName)\Tmp"
456
+ ConfigurationType="1"
457
+ InheritedPropertySheets="UpgradeFromVC70.vsprops"
458
+ CharacterSet="2"
459
+ >
460
+ <Tool
461
+ Name="VCPreBuildEventTool"
462
+ />
463
+ <Tool
464
+ Name="VCCustomBuildTool"
465
+ />
466
+ <Tool
467
+ Name="VCXMLDataGeneratorTool"
468
+ />
469
+ <Tool
470
+ Name="VCWebServiceProxyGeneratorTool"
471
+ />
472
+ <Tool
473
+ Name="VCMIDLTool"
474
+ TargetEnvironment="2"
475
+ />
476
+ <Tool
477
+ Name="VCCLCompilerTool"
478
+ Optimization="2"
479
+ InlineFunctionExpansion="1"
480
+ OmitFramePointers="true"
481
+ AdditionalIncludeDirectories="..\..\..;..\..\minizip"
482
+ PreprocessorDefinitions="_CRT_NONSTDC_NO_DEPRECATE;_CRT_SECURE_NO_DEPRECATE;ZLIB_WINAPI;NDEBUG;_CONSOLE;WIN64"
483
+ StringPooling="true"
484
+ BasicRuntimeChecks="0"
485
+ RuntimeLibrary="2"
486
+ BufferSecurityCheck="false"
487
+ EnableFunctionLevelLinking="true"
488
+ UsePrecompiledHeader="0"
489
+ AssemblerListingLocation="$(IntDir)\"
490
+ WarningLevel="3"
491
+ Detect64BitPortabilityProblems="true"
492
+ DebugInformationFormat="3"
493
+ />
494
+ <Tool
495
+ Name="VCManagedResourceCompilerTool"
496
+ />
497
+ <Tool
498
+ Name="VCResourceCompilerTool"
499
+ />
500
+ <Tool
501
+ Name="VCPreLinkEventTool"
502
+ />
503
+ <Tool
504
+ Name="VCLinkerTool"
505
+ AdditionalDependencies="ia64\ZlibDllRelease\zlibwapi.lib"
506
+ OutputFile="$(OutDir)/testzlib.exe"
507
+ LinkIncremental="1"
508
+ GenerateManifest="false"
509
+ GenerateDebugInformation="true"
510
+ SubSystem="1"
511
+ OptimizeReferences="2"
512
+ EnableCOMDATFolding="2"
513
+ OptimizeForWindows98="1"
514
+ TargetMachine="5"
515
+ />
516
+ <Tool
517
+ Name="VCALinkTool"
518
+ />
519
+ <Tool
520
+ Name="VCManifestTool"
521
+ />
522
+ <Tool
523
+ Name="VCXDCMakeTool"
524
+ />
525
+ <Tool
526
+ Name="VCBscMakeTool"
527
+ />
528
+ <Tool
529
+ Name="VCFxCopTool"
530
+ />
531
+ <Tool
532
+ Name="VCAppVerifierTool"
533
+ />
534
+ <Tool
535
+ Name="VCWebDeploymentTool"
536
+ />
537
+ <Tool
538
+ Name="VCPostBuildEventTool"
539
+ />
540
+ </Configuration>
541
+ </Configurations>
542
+ <References>
543
+ </References>
544
+ <Files>
545
+ <Filter
546
+ Name="Source Files"
547
+ Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm"
548
+ >
549
+ <File
550
+ RelativePath="..\..\testzlib\testzlib.c"
551
+ >
552
+ </File>
553
+ </Filter>
554
+ <Filter
555
+ Name="Header Files"
556
+ Filter="h;hpp;hxx;hm;inl;inc"
557
+ >
558
+ </Filter>
559
+ <Filter
560
+ Name="Resource Files"
561
+ Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
562
+ >
563
+ </Filter>
564
+ </Files>
565
+ <Globals>
566
+ </Globals>
567
+ </VisualStudioProject>