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 +1,225 @@
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: zlib-streams.adb,v 1.10 2004/05/31 10:53:40 vagul Exp $
10
+
11
+ with Ada.Unchecked_Deallocation;
12
+
13
+ package body ZLib.Streams is
14
+
15
+ -----------
16
+ -- Close --
17
+ -----------
18
+
19
+ procedure Close (Stream : in out Stream_Type) is
20
+ procedure Free is new Ada.Unchecked_Deallocation
21
+ (Stream_Element_Array, Buffer_Access);
22
+ begin
23
+ if Stream.Mode = Out_Stream or Stream.Mode = Duplex then
24
+ -- We should flush the data written by the writer.
25
+
26
+ Flush (Stream, Finish);
27
+
28
+ Close (Stream.Writer);
29
+ end if;
30
+
31
+ if Stream.Mode = In_Stream or Stream.Mode = Duplex then
32
+ Close (Stream.Reader);
33
+ Free (Stream.Buffer);
34
+ end if;
35
+ end Close;
36
+
37
+ ------------
38
+ -- Create --
39
+ ------------
40
+
41
+ procedure Create
42
+ (Stream : out Stream_Type;
43
+ Mode : in Stream_Mode;
44
+ Back : in Stream_Access;
45
+ Back_Compressed : in Boolean;
46
+ Level : in Compression_Level := Default_Compression;
47
+ Strategy : in Strategy_Type := Default_Strategy;
48
+ Header : in Header_Type := Default;
49
+ Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
50
+ := Default_Buffer_Size;
51
+ Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
52
+ := Default_Buffer_Size)
53
+ is
54
+
55
+ subtype Buffer_Subtype is Stream_Element_Array (1 .. Read_Buffer_Size);
56
+
57
+ procedure Init_Filter
58
+ (Filter : in out Filter_Type;
59
+ Compress : in Boolean);
60
+
61
+ -----------------
62
+ -- Init_Filter --
63
+ -----------------
64
+
65
+ procedure Init_Filter
66
+ (Filter : in out Filter_Type;
67
+ Compress : in Boolean) is
68
+ begin
69
+ if Compress then
70
+ Deflate_Init
71
+ (Filter, Level, Strategy, Header => Header);
72
+ else
73
+ Inflate_Init (Filter, Header => Header);
74
+ end if;
75
+ end Init_Filter;
76
+
77
+ begin
78
+ Stream.Back := Back;
79
+ Stream.Mode := Mode;
80
+
81
+ if Mode = Out_Stream or Mode = Duplex then
82
+ Init_Filter (Stream.Writer, Back_Compressed);
83
+ Stream.Buffer_Size := Write_Buffer_Size;
84
+ else
85
+ Stream.Buffer_Size := 0;
86
+ end if;
87
+
88
+ if Mode = In_Stream or Mode = Duplex then
89
+ Init_Filter (Stream.Reader, not Back_Compressed);
90
+
91
+ Stream.Buffer := new Buffer_Subtype;
92
+ Stream.Rest_First := Stream.Buffer'Last + 1;
93
+ Stream.Rest_Last := Stream.Buffer'Last;
94
+ end if;
95
+ end Create;
96
+
97
+ -----------
98
+ -- Flush --
99
+ -----------
100
+
101
+ procedure Flush
102
+ (Stream : in out Stream_Type;
103
+ Mode : in Flush_Mode := Sync_Flush)
104
+ is
105
+ Buffer : Stream_Element_Array (1 .. Stream.Buffer_Size);
106
+ Last : Stream_Element_Offset;
107
+ begin
108
+ loop
109
+ Flush (Stream.Writer, Buffer, Last, Mode);
110
+
111
+ Ada.Streams.Write (Stream.Back.all, Buffer (1 .. Last));
112
+
113
+ exit when Last < Buffer'Last;
114
+ end loop;
115
+ end Flush;
116
+
117
+ -------------
118
+ -- Is_Open --
119
+ -------------
120
+
121
+ function Is_Open (Stream : Stream_Type) return Boolean is
122
+ begin
123
+ return Is_Open (Stream.Reader) or else Is_Open (Stream.Writer);
124
+ end Is_Open;
125
+
126
+ ----------
127
+ -- Read --
128
+ ----------
129
+
130
+ procedure Read
131
+ (Stream : in out Stream_Type;
132
+ Item : out Stream_Element_Array;
133
+ Last : out Stream_Element_Offset)
134
+ is
135
+
136
+ procedure Read
137
+ (Item : out Stream_Element_Array;
138
+ Last : out Stream_Element_Offset);
139
+
140
+ ----------
141
+ -- Read --
142
+ ----------
143
+
144
+ procedure Read
145
+ (Item : out Stream_Element_Array;
146
+ Last : out Stream_Element_Offset) is
147
+ begin
148
+ Ada.Streams.Read (Stream.Back.all, Item, Last);
149
+ end Read;
150
+
151
+ procedure Read is new ZLib.Read
152
+ (Read => Read,
153
+ Buffer => Stream.Buffer.all,
154
+ Rest_First => Stream.Rest_First,
155
+ Rest_Last => Stream.Rest_Last);
156
+
157
+ begin
158
+ Read (Stream.Reader, Item, Last);
159
+ end Read;
160
+
161
+ -------------------
162
+ -- Read_Total_In --
163
+ -------------------
164
+
165
+ function Read_Total_In (Stream : in Stream_Type) return Count is
166
+ begin
167
+ return Total_In (Stream.Reader);
168
+ end Read_Total_In;
169
+
170
+ --------------------
171
+ -- Read_Total_Out --
172
+ --------------------
173
+
174
+ function Read_Total_Out (Stream : in Stream_Type) return Count is
175
+ begin
176
+ return Total_Out (Stream.Reader);
177
+ end Read_Total_Out;
178
+
179
+ -----------
180
+ -- Write --
181
+ -----------
182
+
183
+ procedure Write
184
+ (Stream : in out Stream_Type;
185
+ Item : in Stream_Element_Array)
186
+ is
187
+
188
+ procedure Write (Item : in Stream_Element_Array);
189
+
190
+ -----------
191
+ -- Write --
192
+ -----------
193
+
194
+ procedure Write (Item : in Stream_Element_Array) is
195
+ begin
196
+ Ada.Streams.Write (Stream.Back.all, Item);
197
+ end Write;
198
+
199
+ procedure Write is new ZLib.Write
200
+ (Write => Write,
201
+ Buffer_Size => Stream.Buffer_Size);
202
+
203
+ begin
204
+ Write (Stream.Writer, Item, No_Flush);
205
+ end Write;
206
+
207
+ --------------------
208
+ -- Write_Total_In --
209
+ --------------------
210
+
211
+ function Write_Total_In (Stream : in Stream_Type) return Count is
212
+ begin
213
+ return Total_In (Stream.Writer);
214
+ end Write_Total_In;
215
+
216
+ ---------------------
217
+ -- Write_Total_Out --
218
+ ---------------------
219
+
220
+ function Write_Total_Out (Stream : in Stream_Type) return Count is
221
+ begin
222
+ return Total_Out (Stream.Writer);
223
+ end Write_Total_Out;
224
+
225
+ end ZLib.Streams;
@@ -0,0 +1,114 @@
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: zlib-streams.ads,v 1.12 2004/05/31 10:53:40 vagul Exp $
10
+
11
+ package ZLib.Streams is
12
+
13
+ type Stream_Mode is (In_Stream, Out_Stream, Duplex);
14
+
15
+ type Stream_Access is access all Ada.Streams.Root_Stream_Type'Class;
16
+
17
+ type Stream_Type is
18
+ new Ada.Streams.Root_Stream_Type with private;
19
+
20
+ procedure Read
21
+ (Stream : in out Stream_Type;
22
+ Item : out Ada.Streams.Stream_Element_Array;
23
+ Last : out Ada.Streams.Stream_Element_Offset);
24
+
25
+ procedure Write
26
+ (Stream : in out Stream_Type;
27
+ Item : in Ada.Streams.Stream_Element_Array);
28
+
29
+ procedure Flush
30
+ (Stream : in out Stream_Type;
31
+ Mode : in Flush_Mode := Sync_Flush);
32
+ -- Flush the written data to the back stream,
33
+ -- all data placed to the compressor is flushing to the Back stream.
34
+ -- Should not be used untill necessary, becouse it is decreasing
35
+ -- compression.
36
+
37
+ function Read_Total_In (Stream : in Stream_Type) return Count;
38
+ pragma Inline (Read_Total_In);
39
+ -- Return total number of bytes read from back stream so far.
40
+
41
+ function Read_Total_Out (Stream : in Stream_Type) return Count;
42
+ pragma Inline (Read_Total_Out);
43
+ -- Return total number of bytes read so far.
44
+
45
+ function Write_Total_In (Stream : in Stream_Type) return Count;
46
+ pragma Inline (Write_Total_In);
47
+ -- Return total number of bytes written so far.
48
+
49
+ function Write_Total_Out (Stream : in Stream_Type) return Count;
50
+ pragma Inline (Write_Total_Out);
51
+ -- Return total number of bytes written to the back stream.
52
+
53
+ procedure Create
54
+ (Stream : out Stream_Type;
55
+ Mode : in Stream_Mode;
56
+ Back : in Stream_Access;
57
+ Back_Compressed : in Boolean;
58
+ Level : in Compression_Level := Default_Compression;
59
+ Strategy : in Strategy_Type := Default_Strategy;
60
+ Header : in Header_Type := Default;
61
+ Read_Buffer_Size : in Ada.Streams.Stream_Element_Offset
62
+ := Default_Buffer_Size;
63
+ Write_Buffer_Size : in Ada.Streams.Stream_Element_Offset
64
+ := Default_Buffer_Size);
65
+ -- Create the Comression/Decompression stream.
66
+ -- If mode is In_Stream then Write operation is disabled.
67
+ -- If mode is Out_Stream then Read operation is disabled.
68
+
69
+ -- If Back_Compressed is true then
70
+ -- Data written to the Stream is compressing to the Back stream
71
+ -- and data read from the Stream is decompressed data from the Back stream.
72
+
73
+ -- If Back_Compressed is false then
74
+ -- Data written to the Stream is decompressing to the Back stream
75
+ -- and data read from the Stream is compressed data from the Back stream.
76
+
77
+ -- !!! When the Need_Header is False ZLib-Ada is using undocumented
78
+ -- ZLib 1.1.4 functionality to do not create/wait for ZLib headers.
79
+
80
+ function Is_Open (Stream : Stream_Type) return Boolean;
81
+
82
+ procedure Close (Stream : in out Stream_Type);
83
+
84
+ private
85
+
86
+ use Ada.Streams;
87
+
88
+ type Buffer_Access is access all Stream_Element_Array;
89
+
90
+ type Stream_Type
91
+ is new Root_Stream_Type with
92
+ record
93
+ Mode : Stream_Mode;
94
+
95
+ Buffer : Buffer_Access;
96
+ Rest_First : Stream_Element_Offset;
97
+ Rest_Last : Stream_Element_Offset;
98
+ -- Buffer for Read operation.
99
+ -- We need to have this buffer in the record
100
+ -- becouse not all read data from back stream
101
+ -- could be processed during the read operation.
102
+
103
+ Buffer_Size : Stream_Element_Offset;
104
+ -- Buffer size for write operation.
105
+ -- We do not need to have this buffer
106
+ -- in the record becouse all data could be
107
+ -- processed in the write operation.
108
+
109
+ Back : Stream_Access;
110
+ Reader : Filter_Type;
111
+ Writer : Filter_Type;
112
+ end record;
113
+
114
+ end ZLib.Streams;
@@ -0,0 +1,141 @@
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: zlib-thin.adb,v 1.8 2003/12/14 18:27:31 vagul Exp $
10
+
11
+ package body ZLib.Thin is
12
+
13
+ ZLIB_VERSION : constant Chars_Ptr := zlibVersion;
14
+
15
+ Z_Stream_Size : constant Int := Z_Stream'Size / System.Storage_Unit;
16
+
17
+ --------------
18
+ -- Avail_In --
19
+ --------------
20
+
21
+ function Avail_In (Strm : in Z_Stream) return UInt is
22
+ begin
23
+ return Strm.Avail_In;
24
+ end Avail_In;
25
+
26
+ ---------------
27
+ -- Avail_Out --
28
+ ---------------
29
+
30
+ function Avail_Out (Strm : in Z_Stream) return UInt is
31
+ begin
32
+ return Strm.Avail_Out;
33
+ end Avail_Out;
34
+
35
+ ------------------
36
+ -- Deflate_Init --
37
+ ------------------
38
+
39
+ function Deflate_Init
40
+ (strm : Z_Streamp;
41
+ level : Int;
42
+ method : Int;
43
+ windowBits : Int;
44
+ memLevel : Int;
45
+ strategy : Int)
46
+ return Int is
47
+ begin
48
+ return deflateInit2
49
+ (strm,
50
+ level,
51
+ method,
52
+ windowBits,
53
+ memLevel,
54
+ strategy,
55
+ ZLIB_VERSION,
56
+ Z_Stream_Size);
57
+ end Deflate_Init;
58
+
59
+ ------------------
60
+ -- Inflate_Init --
61
+ ------------------
62
+
63
+ function Inflate_Init (strm : Z_Streamp; windowBits : Int) return Int is
64
+ begin
65
+ return inflateInit2 (strm, windowBits, ZLIB_VERSION, Z_Stream_Size);
66
+ end Inflate_Init;
67
+
68
+ ------------------------
69
+ -- Last_Error_Message --
70
+ ------------------------
71
+
72
+ function Last_Error_Message (Strm : in Z_Stream) return String is
73
+ use Interfaces.C.Strings;
74
+ begin
75
+ if Strm.msg = Null_Ptr then
76
+ return "";
77
+ else
78
+ return Value (Strm.msg);
79
+ end if;
80
+ end Last_Error_Message;
81
+
82
+ ------------
83
+ -- Set_In --
84
+ ------------
85
+
86
+ procedure Set_In
87
+ (Strm : in out Z_Stream;
88
+ Buffer : in Voidp;
89
+ Size : in UInt) is
90
+ begin
91
+ Strm.Next_In := Buffer;
92
+ Strm.Avail_In := Size;
93
+ end Set_In;
94
+
95
+ ------------------
96
+ -- Set_Mem_Func --
97
+ ------------------
98
+
99
+ procedure Set_Mem_Func
100
+ (Strm : in out Z_Stream;
101
+ Opaque : in Voidp;
102
+ Alloc : in alloc_func;
103
+ Free : in free_func) is
104
+ begin
105
+ Strm.opaque := Opaque;
106
+ Strm.zalloc := Alloc;
107
+ Strm.zfree := Free;
108
+ end Set_Mem_Func;
109
+
110
+ -------------
111
+ -- Set_Out --
112
+ -------------
113
+
114
+ procedure Set_Out
115
+ (Strm : in out Z_Stream;
116
+ Buffer : in Voidp;
117
+ Size : in UInt) is
118
+ begin
119
+ Strm.Next_Out := Buffer;
120
+ Strm.Avail_Out := Size;
121
+ end Set_Out;
122
+
123
+ --------------
124
+ -- Total_In --
125
+ --------------
126
+
127
+ function Total_In (Strm : in Z_Stream) return ULong is
128
+ begin
129
+ return Strm.Total_In;
130
+ end Total_In;
131
+
132
+ ---------------
133
+ -- Total_Out --
134
+ ---------------
135
+
136
+ function Total_Out (Strm : in Z_Stream) return ULong is
137
+ begin
138
+ return Strm.Total_Out;
139
+ end Total_Out;
140
+
141
+ end ZLib.Thin;