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 +1,76 @@
1
+
2
+ This directory contains a Pascal (Delphi, Kylix) interface to the
3
+ zlib data compression library.
4
+
5
+
6
+ Directory listing
7
+ =================
8
+
9
+ zlibd32.mak makefile for Borland C++
10
+ example.pas usage example of zlib
11
+ zlibpas.pas the Pascal interface to zlib
12
+ readme.txt this file
13
+
14
+
15
+ Compatibility notes
16
+ ===================
17
+
18
+ - Although the name "zlib" would have been more normal for the
19
+ zlibpas unit, this name is already taken by Borland's ZLib unit.
20
+ This is somehow unfortunate, because that unit is not a genuine
21
+ interface to the full-fledged zlib functionality, but a suite of
22
+ class wrappers around zlib streams. Other essential features,
23
+ such as checksums, are missing.
24
+ It would have been more appropriate for that unit to have a name
25
+ like "ZStreams", or something similar.
26
+
27
+ - The C and zlib-supplied types int, uInt, long, uLong, etc. are
28
+ translated directly into Pascal types of similar sizes (Integer,
29
+ LongInt, etc.), to avoid namespace pollution. In particular,
30
+ there is no conversion of unsigned int into a Pascal unsigned
31
+ integer. The Word type is non-portable and has the same size
32
+ (16 bits) both in a 16-bit and in a 32-bit environment, unlike
33
+ Integer. Even if there is a 32-bit Cardinal type, there is no
34
+ real need for unsigned int in zlib under a 32-bit environment.
35
+
36
+ - Except for the callbacks, the zlib function interfaces are
37
+ assuming the calling convention normally used in Pascal
38
+ (__pascal for DOS and Windows16, __fastcall for Windows32).
39
+ Since the cdecl keyword is used, the old Turbo Pascal does
40
+ not work with this interface.
41
+
42
+ - The gz* function interfaces are not translated, to avoid
43
+ interfacing problems with the C runtime library. Besides,
44
+ gzprintf(gzFile file, const char *format, ...)
45
+ cannot be translated into Pascal.
46
+
47
+
48
+ Legal issues
49
+ ============
50
+
51
+ The zlibpas interface is:
52
+ Copyright (C) 1995-2003 Jean-loup Gailly and Mark Adler.
53
+ Copyright (C) 1998 by Bob Dellaca.
54
+ Copyright (C) 2003 by Cosmin Truta.
55
+
56
+ The example program is:
57
+ Copyright (C) 1995-2003 by Jean-loup Gailly.
58
+ Copyright (C) 1998,1999,2000 by Jacques Nomssi Nzali.
59
+ Copyright (C) 2003 by Cosmin Truta.
60
+
61
+ This software is provided 'as-is', without any express or implied
62
+ warranty. In no event will the author be held liable for any damages
63
+ arising from the use of this software.
64
+
65
+ Permission is granted to anyone to use this software for any purpose,
66
+ including commercial applications, and to alter it and redistribute it
67
+ freely, subject to the following restrictions:
68
+
69
+ 1. The origin of this software must not be misrepresented; you must not
70
+ claim that you wrote the original software. If you use this software
71
+ in a product, an acknowledgment in the product documentation would be
72
+ appreciated but is not required.
73
+ 2. Altered source versions must be plainly marked as such, and must not be
74
+ misrepresented as being the original software.
75
+ 3. This notice may not be removed or altered from any source distribution.
76
+
@@ -0,0 +1,93 @@
1
+ # Makefile for zlib
2
+ # For use with Delphi and C++ Builder under Win32
3
+ # Updated for zlib 1.2.x by Cosmin Truta
4
+
5
+ # ------------ Borland C++ ------------
6
+
7
+ # This project uses the Delphi (fastcall/register) calling convention:
8
+ LOC = -DZEXPORT=__fastcall -DZEXPORTVA=__cdecl
9
+
10
+ CC = bcc32
11
+ LD = bcc32
12
+ AR = tlib
13
+ # do not use "-pr" in CFLAGS
14
+ CFLAGS = -a -d -k- -O2 $(LOC)
15
+ LDFLAGS =
16
+
17
+
18
+ # variables
19
+ ZLIB_LIB = zlib.lib
20
+
21
+ OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
22
+ OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
23
+ OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
24
+ OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
25
+
26
+
27
+ # targets
28
+ all: $(ZLIB_LIB) example.exe minigzip.exe
29
+
30
+ .c.obj:
31
+ $(CC) -c $(CFLAGS) $*.c
32
+
33
+ adler32.obj: adler32.c zlib.h zconf.h
34
+
35
+ compress.obj: compress.c zlib.h zconf.h
36
+
37
+ crc32.obj: crc32.c zlib.h zconf.h crc32.h
38
+
39
+ deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
40
+
41
+ gzio.obj: gzio.c zutil.h zlib.h zconf.h
42
+
43
+ infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
44
+ inffast.h inffixed.h
45
+
46
+ inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
47
+ inffast.h
48
+
49
+ inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
50
+ inffast.h inffixed.h
51
+
52
+ inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
53
+
54
+ trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
55
+
56
+ uncompr.obj: uncompr.c zlib.h zconf.h
57
+
58
+ zutil.obj: zutil.c zutil.h zlib.h zconf.h
59
+
60
+ example.obj: example.c zlib.h zconf.h
61
+
62
+ minigzip.obj: minigzip.c zlib.h zconf.h
63
+
64
+
65
+ # For the sake of the old Borland make,
66
+ # the command line is cut to fit in the MS-DOS 128 byte limit:
67
+ $(ZLIB_LIB): $(OBJ1) $(OBJ2)
68
+ -del $(ZLIB_LIB)
69
+ $(AR) $(ZLIB_LIB) $(OBJP1)
70
+ $(AR) $(ZLIB_LIB) $(OBJP2)
71
+
72
+
73
+ # testing
74
+ test: example.exe minigzip.exe
75
+ example
76
+ echo hello world | minigzip | minigzip -d
77
+
78
+ example.exe: example.obj $(ZLIB_LIB)
79
+ $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
80
+
81
+ minigzip.exe: minigzip.obj $(ZLIB_LIB)
82
+ $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
83
+
84
+
85
+ # cleanup
86
+ clean:
87
+ -del *.obj
88
+ -del *.exe
89
+ -del *.lib
90
+ -del *.tds
91
+ -del zlib.bak
92
+ -del foo.gz
93
+
@@ -0,0 +1,236 @@
1
+ (* zlibpas -- Pascal interface to the zlib data compression library
2
+ *
3
+ * Copyright (C) 2003 Cosmin Truta.
4
+ * Derived from original sources by Bob Dellaca.
5
+ * For conditions of distribution and use, see copyright notice in readme.txt
6
+ *)
7
+
8
+ unit zlibpas;
9
+
10
+ interface
11
+
12
+ const
13
+ ZLIB_VERSION = '1.2.3';
14
+
15
+ type
16
+ alloc_func = function(opaque: Pointer; items, size: Integer): Pointer;
17
+ cdecl;
18
+ free_func = procedure(opaque, address: Pointer);
19
+ cdecl;
20
+
21
+ in_func = function(opaque: Pointer; var buf: PByte): Integer;
22
+ cdecl;
23
+ out_func = function(opaque: Pointer; buf: PByte; size: Integer): Integer;
24
+ cdecl;
25
+
26
+ z_streamp = ^z_stream;
27
+ z_stream = packed record
28
+ next_in: PChar; (* next input byte *)
29
+ avail_in: Integer; (* number of bytes available at next_in *)
30
+ total_in: LongInt; (* total nb of input bytes read so far *)
31
+
32
+ next_out: PChar; (* next output byte should be put there *)
33
+ avail_out: Integer; (* remaining free space at next_out *)
34
+ total_out: LongInt; (* total nb of bytes output so far *)
35
+
36
+ msg: PChar; (* last error message, NULL if no error *)
37
+ state: Pointer; (* not visible by applications *)
38
+
39
+ zalloc: alloc_func; (* used to allocate the internal state *)
40
+ zfree: free_func; (* used to free the internal state *)
41
+ opaque: Pointer; (* private data object passed to zalloc and zfree *)
42
+
43
+ data_type: Integer; (* best guess about the data type: ascii or binary *)
44
+ adler: LongInt; (* adler32 value of the uncompressed data *)
45
+ reserved: LongInt; (* reserved for future use *)
46
+ end;
47
+
48
+ (* constants *)
49
+ const
50
+ Z_NO_FLUSH = 0;
51
+ Z_PARTIAL_FLUSH = 1;
52
+ Z_SYNC_FLUSH = 2;
53
+ Z_FULL_FLUSH = 3;
54
+ Z_FINISH = 4;
55
+
56
+ Z_OK = 0;
57
+ Z_STREAM_END = 1;
58
+ Z_NEED_DICT = 2;
59
+ Z_ERRNO = -1;
60
+ Z_STREAM_ERROR = -2;
61
+ Z_DATA_ERROR = -3;
62
+ Z_MEM_ERROR = -4;
63
+ Z_BUF_ERROR = -5;
64
+ Z_VERSION_ERROR = -6;
65
+
66
+ Z_NO_COMPRESSION = 0;
67
+ Z_BEST_SPEED = 1;
68
+ Z_BEST_COMPRESSION = 9;
69
+ Z_DEFAULT_COMPRESSION = -1;
70
+
71
+ Z_FILTERED = 1;
72
+ Z_HUFFMAN_ONLY = 2;
73
+ Z_RLE = 3;
74
+ Z_DEFAULT_STRATEGY = 0;
75
+
76
+ Z_BINARY = 0;
77
+ Z_ASCII = 1;
78
+ Z_UNKNOWN = 2;
79
+
80
+ Z_DEFLATED = 8;
81
+
82
+ (* basic functions *)
83
+ function zlibVersion: PChar;
84
+ function deflateInit(var strm: z_stream; level: Integer): Integer;
85
+ function deflate(var strm: z_stream; flush: Integer): Integer;
86
+ function deflateEnd(var strm: z_stream): Integer;
87
+ function inflateInit(var strm: z_stream): Integer;
88
+ function inflate(var strm: z_stream; flush: Integer): Integer;
89
+ function inflateEnd(var strm: z_stream): Integer;
90
+
91
+ (* advanced functions *)
92
+ function deflateInit2(var strm: z_stream; level, method, windowBits,
93
+ memLevel, strategy: Integer): Integer;
94
+ function deflateSetDictionary(var strm: z_stream; const dictionary: PChar;
95
+ dictLength: Integer): Integer;
96
+ function deflateCopy(var dest, source: z_stream): Integer;
97
+ function deflateReset(var strm: z_stream): Integer;
98
+ function deflateParams(var strm: z_stream; level, strategy: Integer): Integer;
99
+ function deflateBound(var strm: z_stream; sourceLen: LongInt): LongInt;
100
+ function deflatePrime(var strm: z_stream; bits, value: Integer): Integer;
101
+ function inflateInit2(var strm: z_stream; windowBits: Integer): Integer;
102
+ function inflateSetDictionary(var strm: z_stream; const dictionary: PChar;
103
+ dictLength: Integer): Integer;
104
+ function inflateSync(var strm: z_stream): Integer;
105
+ function inflateCopy(var dest, source: z_stream): Integer;
106
+ function inflateReset(var strm: z_stream): Integer;
107
+ function inflateBackInit(var strm: z_stream;
108
+ windowBits: Integer; window: PChar): Integer;
109
+ function inflateBack(var strm: z_stream; in_fn: in_func; in_desc: Pointer;
110
+ out_fn: out_func; out_desc: Pointer): Integer;
111
+ function inflateBackEnd(var strm: z_stream): Integer;
112
+ function zlibCompileFlags: LongInt;
113
+
114
+ (* utility functions *)
115
+ function compress(dest: PChar; var destLen: LongInt;
116
+ const source: PChar; sourceLen: LongInt): Integer;
117
+ function compress2(dest: PChar; var destLen: LongInt;
118
+ const source: PChar; sourceLen: LongInt;
119
+ level: Integer): Integer;
120
+ function compressBound(sourceLen: LongInt): LongInt;
121
+ function uncompress(dest: PChar; var destLen: LongInt;
122
+ const source: PChar; sourceLen: LongInt): Integer;
123
+
124
+ (* checksum functions *)
125
+ function adler32(adler: LongInt; const buf: PChar; len: Integer): LongInt;
126
+ function crc32(crc: LongInt; const buf: PChar; len: Integer): LongInt;
127
+
128
+ (* various hacks, don't look :) *)
129
+ function deflateInit_(var strm: z_stream; level: Integer;
130
+ const version: PChar; stream_size: Integer): Integer;
131
+ function inflateInit_(var strm: z_stream; const version: PChar;
132
+ stream_size: Integer): Integer;
133
+ function deflateInit2_(var strm: z_stream;
134
+ level, method, windowBits, memLevel, strategy: Integer;
135
+ const version: PChar; stream_size: Integer): Integer;
136
+ function inflateInit2_(var strm: z_stream; windowBits: Integer;
137
+ const version: PChar; stream_size: Integer): Integer;
138
+ function inflateBackInit_(var strm: z_stream;
139
+ windowBits: Integer; window: PChar;
140
+ const version: PChar; stream_size: Integer): Integer;
141
+
142
+
143
+ implementation
144
+
145
+ {$L adler32.obj}
146
+ {$L compress.obj}
147
+ {$L crc32.obj}
148
+ {$L deflate.obj}
149
+ {$L infback.obj}
150
+ {$L inffast.obj}
151
+ {$L inflate.obj}
152
+ {$L inftrees.obj}
153
+ {$L trees.obj}
154
+ {$L uncompr.obj}
155
+ {$L zutil.obj}
156
+
157
+ function adler32; external;
158
+ function compress; external;
159
+ function compress2; external;
160
+ function compressBound; external;
161
+ function crc32; external;
162
+ function deflate; external;
163
+ function deflateBound; external;
164
+ function deflateCopy; external;
165
+ function deflateEnd; external;
166
+ function deflateInit_; external;
167
+ function deflateInit2_; external;
168
+ function deflateParams; external;
169
+ function deflatePrime; external;
170
+ function deflateReset; external;
171
+ function deflateSetDictionary; external;
172
+ function inflate; external;
173
+ function inflateBack; external;
174
+ function inflateBackEnd; external;
175
+ function inflateBackInit_; external;
176
+ function inflateCopy; external;
177
+ function inflateEnd; external;
178
+ function inflateInit_; external;
179
+ function inflateInit2_; external;
180
+ function inflateReset; external;
181
+ function inflateSetDictionary; external;
182
+ function inflateSync; external;
183
+ function uncompress; external;
184
+ function zlibCompileFlags; external;
185
+ function zlibVersion; external;
186
+
187
+ function deflateInit(var strm: z_stream; level: Integer): Integer;
188
+ begin
189
+ Result := deflateInit_(strm, level, ZLIB_VERSION, sizeof(z_stream));
190
+ end;
191
+
192
+ function deflateInit2(var strm: z_stream; level, method, windowBits, memLevel,
193
+ strategy: Integer): Integer;
194
+ begin
195
+ Result := deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
196
+ ZLIB_VERSION, sizeof(z_stream));
197
+ end;
198
+
199
+ function inflateInit(var strm: z_stream): Integer;
200
+ begin
201
+ Result := inflateInit_(strm, ZLIB_VERSION, sizeof(z_stream));
202
+ end;
203
+
204
+ function inflateInit2(var strm: z_stream; windowBits: Integer): Integer;
205
+ begin
206
+ Result := inflateInit2_(strm, windowBits, ZLIB_VERSION, sizeof(z_stream));
207
+ end;
208
+
209
+ function inflateBackInit(var strm: z_stream;
210
+ windowBits: Integer; window: PChar): Integer;
211
+ begin
212
+ Result := inflateBackInit_(strm, windowBits, window,
213
+ ZLIB_VERSION, sizeof(z_stream));
214
+ end;
215
+
216
+ function _malloc(Size: Integer): Pointer; cdecl;
217
+ begin
218
+ GetMem(Result, Size);
219
+ end;
220
+
221
+ procedure _free(Block: Pointer); cdecl;
222
+ begin
223
+ FreeMem(Block);
224
+ end;
225
+
226
+ procedure _memset(P: Pointer; B: Byte; count: Integer); cdecl;
227
+ begin
228
+ FillChar(P^, count, B);
229
+ end;
230
+
231
+ procedure _memcpy(dest, source: Pointer; count: Integer); cdecl;
232
+ begin
233
+ Move(source^, dest^, count);
234
+ end;
235
+
236
+ end.
@@ -0,0 +1,8 @@
1
+ puff: puff.c puff.h
2
+ cc -DTEST -o puff puff.c
3
+
4
+ test: puff
5
+ puff zeros.raw
6
+
7
+ clean:
8
+ rm -f puff puff.o
@@ -0,0 +1,63 @@
1
+ Puff -- A Simple Inflate
2
+ 3 Mar 2003
3
+ Mark Adler
4
+ madler@alumni.caltech.edu
5
+
6
+ What this is --
7
+
8
+ puff.c provides the routine puff() to decompress the deflate data format. It
9
+ does so more slowly than zlib, but the code is about one-fifth the size of the
10
+ inflate code in zlib, and written to be very easy to read.
11
+
12
+ Why I wrote this --
13
+
14
+ puff.c was written to document the deflate format unambiguously, by virtue of
15
+ being working C code. It is meant to supplement RFC 1951, which formally
16
+ describes the deflate format. I have received many questions on details of the
17
+ deflate format, and I hope that reading this code will answer those questions.
18
+ puff.c is heavily commented with details of the deflate format, especially
19
+ those little nooks and cranies of the format that might not be obvious from a
20
+ specification.
21
+
22
+ puff.c may also be useful in applications where code size or memory usage is a
23
+ very limited resource, and speed is not as important.
24
+
25
+ How to use it --
26
+
27
+ Well, most likely you should just be reading puff.c and using zlib for actual
28
+ applications, but if you must ...
29
+
30
+ Include puff.h in your code, which provides this prototype:
31
+
32
+ int puff(unsigned char *dest, /* pointer to destination pointer */
33
+ unsigned long *destlen, /* amount of output space */
34
+ unsigned char *source, /* pointer to source data pointer */
35
+ unsigned long *sourcelen); /* amount of input available */
36
+
37
+ Then you can call puff() to decompress a deflate stream that is in memory in
38
+ its entirety at source, to a sufficiently sized block of memory for the
39
+ decompressed data at dest. puff() is the only external symbol in puff.c The
40
+ only C library functions that puff.c needs are setjmp() and longjmp(), which
41
+ are used to simplify error checking in the code to improve readabilty. puff.c
42
+ does no memory allocation, and uses less than 2K bytes off of the stack.
43
+
44
+ If destlen is not enough space for the uncompressed data, then inflate will
45
+ return an error without writing more than destlen bytes. Note that this means
46
+ that in order to decompress the deflate data successfully, you need to know
47
+ the size of the uncompressed data ahead of time.
48
+
49
+ If needed, puff() can determine the size of the uncompressed data with no
50
+ output space. This is done by passing dest equal to (unsigned char *)0. Then
51
+ the initial value of *destlen is ignored and *destlen is set to the length of
52
+ the uncompressed data. So if the size of the uncompressed data is not known,
53
+ then two passes of puff() can be used--first to determine the size, and second
54
+ to do the actual inflation after allocating the appropriate memory. Not
55
+ pretty, but it works. (This is one of the reasons you should be using zlib.)
56
+
57
+ The deflate format is self-terminating. If the deflate stream does not end
58
+ in *sourcelen bytes, puff() will return an error without reading at or past
59
+ endsource.
60
+
61
+ On return, *sourcelen is updated to the amount of input data consumed, and
62
+ *destlen is updated to the size of the uncompressed data. See the comments
63
+ in puff.c for the possible return codes for puff().