finishm 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
  192. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
  195. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
  216. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
  225. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
  229. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  230. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  231. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  232. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  233. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
  234. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
  235. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
  236. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  237. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  238. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  239. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  240. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  241. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  242. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  243. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  244. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  246. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  247. data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  249. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  250. data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
  252. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
  259. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
  262. data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
  263. data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
  264. data/ext/src/third-party/zlib-1.2.3/gzio.o +0 -0
  265. data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
  266. data/ext/src/third-party/zlib-1.2.3/infback.o +0 -0
  267. data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
  268. data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
  269. data/ext/src/third-party/zlib-1.2.3/inffast.o +0 -0
  270. data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
  271. data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
  272. data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
  273. data/ext/src/third-party/zlib-1.2.3/inflate.o +0 -0
  274. data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
  275. data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
  276. data/ext/src/third-party/zlib-1.2.3/inftrees.o +0 -0
  277. data/ext/src/third-party/zlib-1.2.3/libz.a +0 -0
  278. data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
  279. data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
  280. data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
  281. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
  282. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
  283. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
  284. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
  285. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
  286. data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
  287. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  288. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  289. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  290. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  291. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  292. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  293. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  294. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  295. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  296. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  297. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  298. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  299. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  300. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  301. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  302. data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
  303. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  304. data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
  305. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  306. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  307. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  308. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  309. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  310. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  311. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  312. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  313. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  314. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  315. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  316. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  317. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  318. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  319. data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
  320. data/lib/assembly/a_b_visualiser.rb +169 -0
  321. data/lib/assembly/acyclic_connection_finder.rb +81 -0
  322. data/lib/assembly/all_orfs.rb +615 -0
  323. data/lib/assembly/bad_format_writer.rb +46 -0
  324. data/lib/assembly/bam_probe_read_selector.rb +48 -0
  325. data/lib/assembly/bubbly_assembler.rb +842 -0
  326. data/lib/assembly/c_probe_node_finder.rb +38 -0
  327. data/lib/assembly/connection_interpreter.rb +350 -0
  328. data/lib/assembly/contig_printer.rb +400 -0
  329. data/lib/assembly/coverage_based_graph_filter.rb +68 -0
  330. data/lib/assembly/depth_first_search.rb +63 -0
  331. data/lib/assembly/dijkstra.rb +216 -0
  332. data/lib/assembly/fluffer.rb +253 -0
  333. data/lib/assembly/graph_explorer.rb +85 -0
  334. data/lib/assembly/graph_generator.rb +315 -0
  335. data/lib/assembly/height_finder.rb +355 -0
  336. data/lib/assembly/hybrid_velvet_graph.rb +70 -0
  337. data/lib/assembly/input_genome.rb +182 -0
  338. data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
  339. data/lib/assembly/node_finder.rb +171 -0
  340. data/lib/assembly/oriented_node_trail.rb +507 -0
  341. data/lib/assembly/paired_end_assembler.rb +53 -0
  342. data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
  343. data/lib/assembly/probed_graph.rb +105 -0
  344. data/lib/assembly/read_input.rb +79 -0
  345. data/lib/assembly/read_to_node.rb +37 -0
  346. data/lib/assembly/scaffold_breaker.rb +126 -0
  347. data/lib/assembly/sequence_hasher.rb +71 -0
  348. data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
  349. data/lib/assembly/single_coherent_wanderer.rb +261 -0
  350. data/lib/assembly/single_ended_assembler.rb +441 -0
  351. data/lib/assembly/velvet_c_binding.rb +54 -0
  352. data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
  353. data/lib/external/VERSION +1 -0
  354. data/lib/finishm/assemble.rb +224 -0
  355. data/lib/finishm/explore.rb +217 -0
  356. data/lib/finishm/finisher.rb +303 -0
  357. data/lib/finishm/fluff.rb +122 -0
  358. data/lib/finishm/gapfiller.rb +325 -0
  359. data/lib/finishm/orfs_finder.rb +88 -0
  360. data/lib/finishm/path_counter.rb +90 -0
  361. data/lib/finishm/primers.rb +425 -0
  362. data/lib/finishm/primers_check.rb +176 -0
  363. data/lib/finishm/roundup.rb +344 -0
  364. data/lib/finishm/sequence.rb +142 -0
  365. data/lib/finishm/visualise.rb +430 -0
  366. data/lib/finishm/wander.rb +270 -0
  367. data/lib/kmer_abundance_pattern.rb +79 -0
  368. data/lib/kmer_multi_abundance_file.rb +48 -0
  369. data/lib/oligo_designer.rb +88 -0
  370. data/lib/priner.rb +66 -0
  371. data/spec/acyclic_connection_finder_spec.rb +551 -0
  372. data/spec/all_orfs_spec.rb +443 -0
  373. data/spec/assemble_spec.rb +186 -0
  374. data/spec/bubbly_assembler_spec.rb +707 -0
  375. data/spec/c_node_finder_spec.rb +58 -0
  376. data/spec/connection_interpreter_spec.rb +284 -0
  377. data/spec/contig_printer_spec.rb +291 -0
  378. data/spec/coverage_based_graph_filter_spec.rb +102 -0
  379. data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
  380. data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
  381. data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
  382. data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
  383. data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
  384. data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
  385. data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
  386. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
  387. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
  388. data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
  389. data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
  390. data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
  391. data/spec/data/assembly_visualiser/Graph +46 -0
  392. data/spec/data/assembly_visualiser/start_kmers1 +2 -0
  393. data/spec/data/bands.csv +1 -0
  394. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
  395. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
  396. data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
  397. data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
  398. data/spec/data/c_probe_node_finder/1/Log +756 -0
  399. data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
  400. data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
  401. data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
  402. data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
  403. data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
  404. data/spec/data/contig_printer/1/contigs.fa +4 -0
  405. data/spec/data/contig_printer/1/seq.fa +2408 -0
  406. data/spec/data/contig_printer/1/seq.fa.svg +153 -0
  407. data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
  408. data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
  409. data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
  410. data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
  411. data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
  412. data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
  413. data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
  414. data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
  415. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
  416. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
  417. data/spec/data/contig_printer/1/seq.node12.fa +4 -0
  418. data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
  419. data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
  420. data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
  421. data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
  422. data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
  423. data/spec/data/explore/1/a.fa +2 -0
  424. data/spec/data/explore/1/seq1_and_a.fa +3 -0
  425. data/spec/data/explore/1/seq2.fa +2 -0
  426. data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
  427. data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
  428. data/spec/data/fluff/1/seq1.fa +2 -0
  429. data/spec/data/fluff/1/seq2.fa +2 -0
  430. data/spec/data/gapfilling/1/reads.fa +171 -0
  431. data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
  432. data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
  433. data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
  434. data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
  435. data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
  436. data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
  437. data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
  438. data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
  439. data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
  440. data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
  441. data/spec/data/gapfilling/2/reference.fa +2 -0
  442. data/spec/data/gapfilling/2/reference_part1.fa +4 -0
  443. data/spec/data/gapfilling/2/reference_part2.fa +4 -0
  444. data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
  445. data/spec/data/gapfilling/2/with_gaps.fa +4 -0
  446. data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
  447. data/spec/data/gapfilling/3/reads.fa.gz +0 -0
  448. data/spec/data/gapfilling/3/reference_part1.fa +4 -0
  449. data/spec/data/gapfilling/3/reference_part2.fa +4 -0
  450. data/spec/data/gapfilling/3/with_gaps.fa +4 -0
  451. data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
  452. data/spec/data/gapfilling/4/reads.fa.gz +0 -0
  453. data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
  454. data/spec/data/gapfilling/5/answer.fna +2 -0
  455. data/spec/data/gapfilling/5/gappy.fna +2 -0
  456. data/spec/data/gapfilling/5/reads.fa +17961 -0
  457. data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
  458. data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
  459. data/spec/data/gapfilling/6/random1.fa +28 -0
  460. data/spec/data/gapfilling/6/random2.fa +28 -0
  461. data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
  462. data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
  463. data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
  464. data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
  465. data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
  466. data/spec/data/kmers_count1.csv +2 -0
  467. data/spec/data/kmers_count2.csv +3 -0
  468. data/spec/data/out +3 -0
  469. data/spec/data/positive_latching_pair.fa +2 -0
  470. data/spec/data/primers.csv +4 -0
  471. data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
  472. data/spec/data/read_selection_by_kmer/input.fasta +6 -0
  473. data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
  474. data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
  475. data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
  476. data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
  477. data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
  478. data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
  479. data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
  480. data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
  481. data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
  482. data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
  483. data/spec/data/t/details.txt +5 -0
  484. data/spec/data/t/details.txt.srt +5 -0
  485. data/spec/data/t/location.txt +3 -0
  486. data/spec/data/t/location.txt.srt +3 -0
  487. data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
  488. data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
  489. data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
  490. data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
  491. data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
  492. data/spec/data/tweak/3_variant/answer.fa +2 -0
  493. data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
  494. data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
  495. data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
  496. data/spec/data/velvet_test_trails/Assem/Graph +17 -0
  497. data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
  498. data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
  499. data/spec/data/velvet_test_trails/Assem/Log +35 -0
  500. data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
  501. data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
  502. data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
  503. data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
  504. data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
  505. data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
  506. data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
  507. data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
  508. data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
  509. data/spec/data/velvet_test_trails/read1.fa +2 -0
  510. data/spec/data/velvet_test_trails/reads.fa +50 -0
  511. data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
  512. data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
  513. data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
  514. data/spec/data/visualise/1/LastGraph +6695 -0
  515. data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
  516. data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
  517. data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
  518. data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
  519. data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
  520. data/spec/data/wander/1/random1.fa +2 -0
  521. data/spec/data/wander/1/random1.sammy.fa +804 -0
  522. data/spec/depth_first_search_spec.rb +190 -0
  523. data/spec/dijkstra_spec.rb +143 -0
  524. data/spec/explore_spec.rb +29 -0
  525. data/spec/fluffer_spec.rb +155 -0
  526. data/spec/gapfiller_spec.rb +107 -0
  527. data/spec/graph_explorer_spec.rb +475 -0
  528. data/spec/graph_generator_spec.rb +99 -0
  529. data/spec/height_finder_spec.rb +306 -0
  530. data/spec/kmer_abundance_pattern_spec.rb +56 -0
  531. data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
  532. data/spec/kmer_profile_finder_spec.rb +38 -0
  533. data/spec/kmers_count_tabulate_spec.rb +120 -0
  534. data/spec/oriented_node_trail_spec.rb +221 -0
  535. data/spec/paired_end_neighbours_spec.rb +126 -0
  536. data/spec/paths_between_nodes_spec.rb +349 -0
  537. data/spec/priner_spec.rb +7 -0
  538. data/spec/read_input_spec.rb +23 -0
  539. data/spec/read_selection_by_kmer_spec.rb +166 -0
  540. data/spec/read_to_node_spec.rb +35 -0
  541. data/spec/roundup_spec.rb +366 -0
  542. data/spec/scaffold_breaker_spec.rb +144 -0
  543. data/spec/sequence_spec.rb +43 -0
  544. data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
  545. data/spec/single_coherent_wanderer_spec.rb +120 -0
  546. data/spec/single_ended_assembler_spec.rb +398 -0
  547. data/spec/spec_helper.rb +310 -0
  548. data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
  549. data/spec/visualise_spec.rb +105 -0
  550. data/spec/wander_spec.rb +119 -0
  551. data/spec/watch_for_changes.sh +16 -0
  552. data/validation/fasta_compare.rb +72 -0
  553. data/validation/gapfill_simulate_perfect.rb +108 -0
  554. metadata +899 -0
@@ -0,0 +1,115 @@
1
+ /* inflate.h -- internal inflate state definition
2
+ * Copyright (C) 1995-2004 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* WARNING: this file should *not* be used by applications. It is
7
+ part of the implementation of the compression library and is
8
+ subject to change. Applications should only use zlib.h.
9
+ */
10
+
11
+ /* define NO_GZIP when compiling if you want to disable gzip header and
12
+ trailer decoding by inflate(). NO_GZIP would be used to avoid linking in
13
+ the crc code when it is not needed. For shared libraries, gzip decoding
14
+ should be left enabled. */
15
+ #ifndef NO_GZIP
16
+ # define GUNZIP
17
+ #endif
18
+
19
+ /* Possible inflate modes between inflate() calls */
20
+ typedef enum {
21
+ HEAD, /* i: waiting for magic header */
22
+ FLAGS, /* i: waiting for method and flags (gzip) */
23
+ TIME, /* i: waiting for modification time (gzip) */
24
+ OS, /* i: waiting for extra flags and operating system (gzip) */
25
+ EXLEN, /* i: waiting for extra length (gzip) */
26
+ EXTRA, /* i: waiting for extra bytes (gzip) */
27
+ NAME, /* i: waiting for end of file name (gzip) */
28
+ COMMENT, /* i: waiting for end of comment (gzip) */
29
+ HCRC, /* i: waiting for header crc (gzip) */
30
+ DICTID, /* i: waiting for dictionary check value */
31
+ DICT, /* waiting for inflateSetDictionary() call */
32
+ TYPE, /* i: waiting for type bits, including last-flag bit */
33
+ TYPEDO, /* i: same, but skip check to exit inflate on new block */
34
+ STORED, /* i: waiting for stored size (length and complement) */
35
+ COPY, /* i/o: waiting for input or output to copy stored block */
36
+ TABLE, /* i: waiting for dynamic block table lengths */
37
+ LENLENS, /* i: waiting for code length code lengths */
38
+ CODELENS, /* i: waiting for length/lit and distance code lengths */
39
+ LEN, /* i: waiting for length/lit code */
40
+ LENEXT, /* i: waiting for length extra bits */
41
+ DIST, /* i: waiting for distance code */
42
+ DISTEXT, /* i: waiting for distance extra bits */
43
+ MATCH, /* o: waiting for output space to copy string */
44
+ LIT, /* o: waiting for output space to write literal */
45
+ CHECK, /* i: waiting for 32-bit check value */
46
+ LENGTH, /* i: waiting for 32-bit length (gzip) */
47
+ DONE, /* finished check, done -- remain here until reset */
48
+ BAD, /* got a data error -- remain here until reset */
49
+ MEM, /* got an inflate() memory error -- remain here until reset */
50
+ SYNC /* looking for synchronization bytes to restart inflate() */
51
+ } inflate_mode;
52
+
53
+ /*
54
+ State transitions between above modes -
55
+
56
+ (most modes can go to the BAD or MEM mode -- not shown for clarity)
57
+
58
+ Process header:
59
+ HEAD -> (gzip) or (zlib)
60
+ (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME
61
+ NAME -> COMMENT -> HCRC -> TYPE
62
+ (zlib) -> DICTID or TYPE
63
+ DICTID -> DICT -> TYPE
64
+ Read deflate blocks:
65
+ TYPE -> STORED or TABLE or LEN or CHECK
66
+ STORED -> COPY -> TYPE
67
+ TABLE -> LENLENS -> CODELENS -> LEN
68
+ Read deflate codes:
69
+ LEN -> LENEXT or LIT or TYPE
70
+ LENEXT -> DIST -> DISTEXT -> MATCH -> LEN
71
+ LIT -> LEN
72
+ Process trailer:
73
+ CHECK -> LENGTH -> DONE
74
+ */
75
+
76
+ /* state maintained between inflate() calls. Approximately 7K bytes. */
77
+ struct inflate_state {
78
+ inflate_mode mode; /* current inflate mode */
79
+ int last; /* true if processing last block */
80
+ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
81
+ int havedict; /* true if dictionary provided */
82
+ int flags; /* gzip header method and flags (0 if zlib) */
83
+ unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */
84
+ unsigned long check; /* protected copy of check value */
85
+ unsigned long total; /* protected copy of output count */
86
+ gz_headerp head; /* where to save gzip header information */
87
+ /* sliding window */
88
+ unsigned wbits; /* log base 2 of requested window size */
89
+ unsigned wsize; /* window size or zero if not using window */
90
+ unsigned whave; /* valid bytes in the window */
91
+ unsigned write; /* window write index */
92
+ unsigned char FAR *window; /* allocated sliding window, if needed */
93
+ /* bit accumulator */
94
+ unsigned long hold; /* input bit accumulator */
95
+ unsigned bits; /* number of bits in "in" */
96
+ /* for string and stored block copying */
97
+ unsigned length; /* literal or length of data to copy */
98
+ unsigned offset; /* distance back to copy string from */
99
+ /* for table and code decoding */
100
+ unsigned extra; /* extra bits needed */
101
+ /* fixed and dynamic code tables */
102
+ code const FAR *lencode; /* starting table for length/literal codes */
103
+ code const FAR *distcode; /* starting table for distance codes */
104
+ unsigned lenbits; /* index bits for lencode */
105
+ unsigned distbits; /* index bits for distcode */
106
+ /* dynamic table building */
107
+ unsigned ncode; /* number of code length code lengths */
108
+ unsigned nlen; /* number of length code lengths */
109
+ unsigned ndist; /* number of distance code lengths */
110
+ unsigned have; /* number of code lengths in lens[] */
111
+ code FAR *next; /* next available space in codes[] */
112
+ unsigned short lens[320]; /* temporary storage for code lengths */
113
+ unsigned short work[288]; /* work area for code table building */
114
+ code codes[ENOUGH]; /* space for code tables */
115
+ };
@@ -0,0 +1,329 @@
1
+ /* inftrees.c -- generate Huffman trees for efficient decoding
2
+ * Copyright (C) 1995-2005 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ #include "zutil.h"
7
+ #include "inftrees.h"
8
+
9
+ #define MAXBITS 15
10
+
11
+ const char inflate_copyright[] =
12
+ " inflate 1.2.3 Copyright 1995-2005 Mark Adler ";
13
+ /*
14
+ If you use the zlib library in a product, an acknowledgment is welcome
15
+ in the documentation of your product. If for some reason you cannot
16
+ include such an acknowledgment, I would appreciate that you keep this
17
+ copyright string in the executable of your product.
18
+ */
19
+
20
+ /*
21
+ Build a set of tables to decode the provided canonical Huffman code.
22
+ The code lengths are lens[0..codes-1]. The result starts at *table,
23
+ whose indices are 0..2^bits-1. work is a writable array of at least
24
+ lens shorts, which is used as a work area. type is the type of code
25
+ to be generated, CODES, LENS, or DISTS. On return, zero is success,
26
+ -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
27
+ on return points to the next available entry's address. bits is the
28
+ requested root table index bits, and on return it is the actual root
29
+ table index bits. It will differ if the request is greater than the
30
+ longest code or if it is less than the shortest code.
31
+ */
32
+ int inflate_table(type, lens, codes, table, bits, work)
33
+ codetype type;
34
+ unsigned short FAR *lens;
35
+ unsigned codes;
36
+ code FAR * FAR *table;
37
+ unsigned FAR *bits;
38
+ unsigned short FAR *work;
39
+ {
40
+ unsigned len; /* a code's length in bits */
41
+ unsigned sym; /* index of code symbols */
42
+ unsigned min, max; /* minimum and maximum code lengths */
43
+ unsigned root; /* number of index bits for root table */
44
+ unsigned curr; /* number of index bits for current table */
45
+ unsigned drop; /* code bits to drop for sub-table */
46
+ int left; /* number of prefix codes available */
47
+ unsigned used; /* code entries in table used */
48
+ unsigned huff; /* Huffman code */
49
+ unsigned incr; /* for incrementing code, index */
50
+ unsigned fill; /* index for replicating entries */
51
+ unsigned low; /* low bits for current root entry */
52
+ unsigned mask; /* mask for low root bits */
53
+ code this; /* table entry for duplication */
54
+ code FAR *next; /* next available space in table */
55
+ const unsigned short FAR *base; /* base value table to use */
56
+ const unsigned short FAR *extra; /* extra bits table to use */
57
+ int end; /* use base and extra for symbol > end */
58
+ unsigned short count[MAXBITS+1]; /* number of codes of each length */
59
+ unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
60
+ static const unsigned short lbase[31] = { /* Length codes 257..285 base */
61
+ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
62
+ 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0};
63
+ static const unsigned short lext[31] = { /* Length codes 257..285 extra */
64
+ 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
65
+ 19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 201, 196};
66
+ static const unsigned short dbase[32] = { /* Distance codes 0..29 base */
67
+ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
68
+ 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
69
+ 8193, 12289, 16385, 24577, 0, 0};
70
+ static const unsigned short dext[32] = { /* Distance codes 0..29 extra */
71
+ 16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
72
+ 23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
73
+ 28, 28, 29, 29, 64, 64};
74
+
75
+ /*
76
+ Process a set of code lengths to create a canonical Huffman code. The
77
+ code lengths are lens[0..codes-1]. Each length corresponds to the
78
+ symbols 0..codes-1. The Huffman code is generated by first sorting the
79
+ symbols by length from short to long, and retaining the symbol order
80
+ for codes with equal lengths. Then the code starts with all zero bits
81
+ for the first code of the shortest length, and the codes are integer
82
+ increments for the same length, and zeros are appended as the length
83
+ increases. For the deflate format, these bits are stored backwards
84
+ from their more natural integer increment ordering, and so when the
85
+ decoding tables are built in the large loop below, the integer codes
86
+ are incremented backwards.
87
+
88
+ This routine assumes, but does not check, that all of the entries in
89
+ lens[] are in the range 0..MAXBITS. The caller must assure this.
90
+ 1..MAXBITS is interpreted as that code length. zero means that that
91
+ symbol does not occur in this code.
92
+
93
+ The codes are sorted by computing a count of codes for each length,
94
+ creating from that a table of starting indices for each length in the
95
+ sorted table, and then entering the symbols in order in the sorted
96
+ table. The sorted table is work[], with that space being provided by
97
+ the caller.
98
+
99
+ The length counts are used for other purposes as well, i.e. finding
100
+ the minimum and maximum length codes, determining if there are any
101
+ codes at all, checking for a valid set of lengths, and looking ahead
102
+ at length counts to determine sub-table sizes when building the
103
+ decoding tables.
104
+ */
105
+
106
+ /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
107
+ for (len = 0; len <= MAXBITS; len++)
108
+ count[len] = 0;
109
+ for (sym = 0; sym < codes; sym++)
110
+ count[lens[sym]]++;
111
+
112
+ /* bound code lengths, force root to be within code lengths */
113
+ root = *bits;
114
+ for (max = MAXBITS; max >= 1; max--)
115
+ if (count[max] != 0) break;
116
+ if (root > max) root = max;
117
+ if (max == 0) { /* no symbols to code at all */
118
+ this.op = (unsigned char)64; /* invalid code marker */
119
+ this.bits = (unsigned char)1;
120
+ this.val = (unsigned short)0;
121
+ *(*table)++ = this; /* make a table to force an error */
122
+ *(*table)++ = this;
123
+ *bits = 1;
124
+ return 0; /* no symbols, but wait for decoding to report error */
125
+ }
126
+ for (min = 1; min <= MAXBITS; min++)
127
+ if (count[min] != 0) break;
128
+ if (root < min) root = min;
129
+
130
+ /* check for an over-subscribed or incomplete set of lengths */
131
+ left = 1;
132
+ for (len = 1; len <= MAXBITS; len++) {
133
+ left <<= 1;
134
+ left -= count[len];
135
+ if (left < 0) return -1; /* over-subscribed */
136
+ }
137
+ if (left > 0 && (type == CODES || max != 1))
138
+ return -1; /* incomplete set */
139
+
140
+ /* generate offsets into symbol table for each length for sorting */
141
+ offs[1] = 0;
142
+ for (len = 1; len < MAXBITS; len++)
143
+ offs[len + 1] = offs[len] + count[len];
144
+
145
+ /* sort symbols by length, by symbol order within each length */
146
+ for (sym = 0; sym < codes; sym++)
147
+ if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
148
+
149
+ /*
150
+ Create and fill in decoding tables. In this loop, the table being
151
+ filled is at next and has curr index bits. The code being used is huff
152
+ with length len. That code is converted to an index by dropping drop
153
+ bits off of the bottom. For codes where len is less than drop + curr,
154
+ those top drop + curr - len bits are incremented through all values to
155
+ fill the table with replicated entries.
156
+
157
+ root is the number of index bits for the root table. When len exceeds
158
+ root, sub-tables are created pointed to by the root entry with an index
159
+ of the low root bits of huff. This is saved in low to check for when a
160
+ new sub-table should be started. drop is zero when the root table is
161
+ being filled, and drop is root when sub-tables are being filled.
162
+
163
+ When a new sub-table is needed, it is necessary to look ahead in the
164
+ code lengths to determine what size sub-table is needed. The length
165
+ counts are used for this, and so count[] is decremented as codes are
166
+ entered in the tables.
167
+
168
+ used keeps track of how many table entries have been allocated from the
169
+ provided *table space. It is checked when a LENS table is being made
170
+ against the space in *table, ENOUGH, minus the maximum space needed by
171
+ the worst case distance code, MAXD. This should never happen, but the
172
+ sufficiency of ENOUGH has not been proven exhaustively, hence the check.
173
+ This assumes that when type == LENS, bits == 9.
174
+
175
+ sym increments through all symbols, and the loop terminates when
176
+ all codes of length max, i.e. all codes, have been processed. This
177
+ routine permits incomplete codes, so another loop after this one fills
178
+ in the rest of the decoding tables with invalid code markers.
179
+ */
180
+
181
+ /* set up for code type */
182
+ switch (type) {
183
+ case CODES:
184
+ base = extra = work; /* dummy value--not used */
185
+ end = 19;
186
+ break;
187
+ case LENS:
188
+ base = lbase;
189
+ base -= 257;
190
+ extra = lext;
191
+ extra -= 257;
192
+ end = 256;
193
+ break;
194
+ default: /* DISTS */
195
+ base = dbase;
196
+ extra = dext;
197
+ end = -1;
198
+ }
199
+
200
+ /* initialize state for loop */
201
+ huff = 0; /* starting code */
202
+ sym = 0; /* starting code symbol */
203
+ len = min; /* starting code length */
204
+ next = *table; /* current table to fill in */
205
+ curr = root; /* current table index bits */
206
+ drop = 0; /* current bits to drop from code for index */
207
+ low = (unsigned)(-1); /* trigger new sub-table when len > root */
208
+ used = 1U << root; /* use root table entries */
209
+ mask = used - 1; /* mask for comparing low */
210
+
211
+ /* check available table space */
212
+ if (type == LENS && used >= ENOUGH - MAXD)
213
+ return 1;
214
+
215
+ /* process all codes and make table entries */
216
+ for (;;) {
217
+ /* create table entry */
218
+ this.bits = (unsigned char)(len - drop);
219
+ if ((int)(work[sym]) < end) {
220
+ this.op = (unsigned char)0;
221
+ this.val = work[sym];
222
+ }
223
+ else if ((int)(work[sym]) > end) {
224
+ this.op = (unsigned char)(extra[work[sym]]);
225
+ this.val = base[work[sym]];
226
+ }
227
+ else {
228
+ this.op = (unsigned char)(32 + 64); /* end of block */
229
+ this.val = 0;
230
+ }
231
+
232
+ /* replicate for those indices with low len bits equal to huff */
233
+ incr = 1U << (len - drop);
234
+ fill = 1U << curr;
235
+ min = fill; /* save offset to next table */
236
+ do {
237
+ fill -= incr;
238
+ next[(huff >> drop) + fill] = this;
239
+ } while (fill != 0);
240
+
241
+ /* backwards increment the len-bit code huff */
242
+ incr = 1U << (len - 1);
243
+ while (huff & incr)
244
+ incr >>= 1;
245
+ if (incr != 0) {
246
+ huff &= incr - 1;
247
+ huff += incr;
248
+ }
249
+ else
250
+ huff = 0;
251
+
252
+ /* go to next symbol, update count, len */
253
+ sym++;
254
+ if (--(count[len]) == 0) {
255
+ if (len == max) break;
256
+ len = lens[work[sym]];
257
+ }
258
+
259
+ /* create new sub-table if needed */
260
+ if (len > root && (huff & mask) != low) {
261
+ /* if first time, transition to sub-tables */
262
+ if (drop == 0)
263
+ drop = root;
264
+
265
+ /* increment past last table */
266
+ next += min; /* here min is 1 << curr */
267
+
268
+ /* determine length of next table */
269
+ curr = len - drop;
270
+ left = (int)(1 << curr);
271
+ while (curr + drop < max) {
272
+ left -= count[curr + drop];
273
+ if (left <= 0) break;
274
+ curr++;
275
+ left <<= 1;
276
+ }
277
+
278
+ /* check for enough space */
279
+ used += 1U << curr;
280
+ if (type == LENS && used >= ENOUGH - MAXD)
281
+ return 1;
282
+
283
+ /* point entry in root table to sub-table */
284
+ low = huff & mask;
285
+ (*table)[low].op = (unsigned char)curr;
286
+ (*table)[low].bits = (unsigned char)root;
287
+ (*table)[low].val = (unsigned short)(next - *table);
288
+ }
289
+ }
290
+
291
+ /*
292
+ Fill in rest of table for incomplete codes. This loop is similar to the
293
+ loop above in incrementing huff for table indices. It is assumed that
294
+ len is equal to curr + drop, so there is no loop needed to increment
295
+ through high index bits. When the current sub-table is filled, the loop
296
+ drops back to the root table to fill in any remaining entries there.
297
+ */
298
+ this.op = (unsigned char)64; /* invalid code marker */
299
+ this.bits = (unsigned char)(len - drop);
300
+ this.val = (unsigned short)0;
301
+ while (huff != 0) {
302
+ /* when done with sub-table, drop back to root table */
303
+ if (drop != 0 && (huff & mask) != low) {
304
+ drop = 0;
305
+ len = root;
306
+ next = *table;
307
+ this.bits = (unsigned char)len;
308
+ }
309
+
310
+ /* put invalid code marker in table */
311
+ next[huff >> drop] = this;
312
+
313
+ /* backwards increment the len-bit code huff */
314
+ incr = 1U << (len - 1);
315
+ while (huff & incr)
316
+ incr >>= 1;
317
+ if (incr != 0) {
318
+ huff &= incr - 1;
319
+ huff += incr;
320
+ }
321
+ else
322
+ huff = 0;
323
+ }
324
+
325
+ /* set return parameters */
326
+ *table += used;
327
+ *bits = root;
328
+ return 0;
329
+ }
@@ -0,0 +1,55 @@
1
+ /* inftrees.h -- header to use inftrees.c
2
+ * Copyright (C) 1995-2005 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /* WARNING: this file should *not* be used by applications. It is
7
+ part of the implementation of the compression library and is
8
+ subject to change. Applications should only use zlib.h.
9
+ */
10
+
11
+ /* Structure for decoding tables. Each entry provides either the
12
+ information needed to do the operation requested by the code that
13
+ indexed that table entry, or it provides a pointer to another
14
+ table that indexes more bits of the code. op indicates whether
15
+ the entry is a pointer to another table, a literal, a length or
16
+ distance, an end-of-block, or an invalid code. For a table
17
+ pointer, the low four bits of op is the number of index bits of
18
+ that table. For a length or distance, the low four bits of op
19
+ is the number of extra bits to get after the code. bits is
20
+ the number of bits in this code or part of the code to drop off
21
+ of the bit buffer. val is the actual byte to output in the case
22
+ of a literal, the base length or distance, or the offset from
23
+ the current table to the next table. Each entry is four bytes. */
24
+ typedef struct {
25
+ unsigned char op; /* operation, extra bits, table bits */
26
+ unsigned char bits; /* bits in this part of the code */
27
+ unsigned short val; /* offset in table or code value */
28
+ } code;
29
+
30
+ /* op values as set by inflate_table():
31
+ 00000000 - literal
32
+ 0000tttt - table link, tttt != 0 is the number of table index bits
33
+ 0001eeee - length or distance, eeee is the number of extra bits
34
+ 01100000 - end of block
35
+ 01000000 - invalid code
36
+ */
37
+
38
+ /* Maximum size of dynamic tree. The maximum found in a long but non-
39
+ exhaustive search was 1444 code structures (852 for length/literals
40
+ and 592 for distances, the latter actually the result of an
41
+ exhaustive search). The true maximum is not known, but the value
42
+ below is more than safe. */
43
+ #define ENOUGH 2048
44
+ #define MAXD 592
45
+
46
+ /* Type of code to build for inftable() */
47
+ typedef enum {
48
+ CODES,
49
+ LENS,
50
+ DISTS
51
+ } codetype;
52
+
53
+ extern int inflate_table OF((codetype type, unsigned short FAR *lens,
54
+ unsigned codes, code FAR * FAR *table,
55
+ unsigned FAR *bits, unsigned short FAR *work));