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 +1,270 @@
1
+ /* iowin32.c -- IO base function header for compress/uncompress .zip
2
+ files using zlib + zip or unzip API
3
+ This IO API version uses the Win32 API (for Microsoft Windows)
4
+
5
+ Version 1.01e, February 12th, 2005
6
+
7
+ Copyright (C) 1998-2005 Gilles Vollant
8
+ */
9
+
10
+ #include <stdlib.h>
11
+
12
+ #include "zlib.h"
13
+ #include "ioapi.h"
14
+ #include "iowin32.h"
15
+
16
+ #ifndef INVALID_HANDLE_VALUE
17
+ #define INVALID_HANDLE_VALUE (0xFFFFFFFF)
18
+ #endif
19
+
20
+ #ifndef INVALID_SET_FILE_POINTER
21
+ #define INVALID_SET_FILE_POINTER ((DWORD)-1)
22
+ #endif
23
+
24
+ voidpf ZCALLBACK win32_open_file_func OF((
25
+ voidpf opaque,
26
+ const char* filename,
27
+ int mode));
28
+
29
+ uLong ZCALLBACK win32_read_file_func OF((
30
+ voidpf opaque,
31
+ voidpf stream,
32
+ void* buf,
33
+ uLong size));
34
+
35
+ uLong ZCALLBACK win32_write_file_func OF((
36
+ voidpf opaque,
37
+ voidpf stream,
38
+ const void* buf,
39
+ uLong size));
40
+
41
+ long ZCALLBACK win32_tell_file_func OF((
42
+ voidpf opaque,
43
+ voidpf stream));
44
+
45
+ long ZCALLBACK win32_seek_file_func OF((
46
+ voidpf opaque,
47
+ voidpf stream,
48
+ uLong offset,
49
+ int origin));
50
+
51
+ int ZCALLBACK win32_close_file_func OF((
52
+ voidpf opaque,
53
+ voidpf stream));
54
+
55
+ int ZCALLBACK win32_error_file_func OF((
56
+ voidpf opaque,
57
+ voidpf stream));
58
+
59
+ typedef struct
60
+ {
61
+ HANDLE hf;
62
+ int error;
63
+ } WIN32FILE_IOWIN;
64
+
65
+ voidpf ZCALLBACK win32_open_file_func (opaque, filename, mode)
66
+ voidpf opaque;
67
+ const char* filename;
68
+ int mode;
69
+ {
70
+ const char* mode_fopen = NULL;
71
+ DWORD dwDesiredAccess,dwCreationDisposition,dwShareMode,dwFlagsAndAttributes ;
72
+ HANDLE hFile = 0;
73
+ voidpf ret=NULL;
74
+
75
+ dwDesiredAccess = dwShareMode = dwFlagsAndAttributes = 0;
76
+
77
+ if ((mode & ZLIB_FILEFUNC_MODE_READWRITEFILTER)==ZLIB_FILEFUNC_MODE_READ)
78
+ {
79
+ dwDesiredAccess = GENERIC_READ;
80
+ dwCreationDisposition = OPEN_EXISTING;
81
+ dwShareMode = FILE_SHARE_READ;
82
+ }
83
+ else
84
+ if (mode & ZLIB_FILEFUNC_MODE_EXISTING)
85
+ {
86
+ dwDesiredAccess = GENERIC_WRITE | GENERIC_READ;
87
+ dwCreationDisposition = OPEN_EXISTING;
88
+ }
89
+ else
90
+ if (mode & ZLIB_FILEFUNC_MODE_CREATE)
91
+ {
92
+ dwDesiredAccess = GENERIC_WRITE | GENERIC_READ;
93
+ dwCreationDisposition = CREATE_ALWAYS;
94
+ }
95
+
96
+ if ((filename!=NULL) && (dwDesiredAccess != 0))
97
+ hFile = CreateFile((LPCTSTR)filename, dwDesiredAccess, dwShareMode, NULL,
98
+ dwCreationDisposition, dwFlagsAndAttributes, NULL);
99
+
100
+ if (hFile == INVALID_HANDLE_VALUE)
101
+ hFile = NULL;
102
+
103
+ if (hFile != NULL)
104
+ {
105
+ WIN32FILE_IOWIN w32fiow;
106
+ w32fiow.hf = hFile;
107
+ w32fiow.error = 0;
108
+ ret = malloc(sizeof(WIN32FILE_IOWIN));
109
+ if (ret==NULL)
110
+ CloseHandle(hFile);
111
+ else *((WIN32FILE_IOWIN*)ret) = w32fiow;
112
+ }
113
+ return ret;
114
+ }
115
+
116
+
117
+ uLong ZCALLBACK win32_read_file_func (opaque, stream, buf, size)
118
+ voidpf opaque;
119
+ voidpf stream;
120
+ void* buf;
121
+ uLong size;
122
+ {
123
+ uLong ret=0;
124
+ HANDLE hFile = NULL;
125
+ if (stream!=NULL)
126
+ hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
127
+ if (hFile != NULL)
128
+ if (!ReadFile(hFile, buf, size, &ret, NULL))
129
+ {
130
+ DWORD dwErr = GetLastError();
131
+ if (dwErr == ERROR_HANDLE_EOF)
132
+ dwErr = 0;
133
+ ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
134
+ }
135
+
136
+ return ret;
137
+ }
138
+
139
+
140
+ uLong ZCALLBACK win32_write_file_func (opaque, stream, buf, size)
141
+ voidpf opaque;
142
+ voidpf stream;
143
+ const void* buf;
144
+ uLong size;
145
+ {
146
+ uLong ret=0;
147
+ HANDLE hFile = NULL;
148
+ if (stream!=NULL)
149
+ hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
150
+
151
+ if (hFile !=NULL)
152
+ if (!WriteFile(hFile, buf, size, &ret, NULL))
153
+ {
154
+ DWORD dwErr = GetLastError();
155
+ if (dwErr == ERROR_HANDLE_EOF)
156
+ dwErr = 0;
157
+ ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
158
+ }
159
+
160
+ return ret;
161
+ }
162
+
163
+ long ZCALLBACK win32_tell_file_func (opaque, stream)
164
+ voidpf opaque;
165
+ voidpf stream;
166
+ {
167
+ long ret=-1;
168
+ HANDLE hFile = NULL;
169
+ if (stream!=NULL)
170
+ hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
171
+ if (hFile != NULL)
172
+ {
173
+ DWORD dwSet = SetFilePointer(hFile, 0, NULL, FILE_CURRENT);
174
+ if (dwSet == INVALID_SET_FILE_POINTER)
175
+ {
176
+ DWORD dwErr = GetLastError();
177
+ ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
178
+ ret = -1;
179
+ }
180
+ else
181
+ ret=(long)dwSet;
182
+ }
183
+ return ret;
184
+ }
185
+
186
+ long ZCALLBACK win32_seek_file_func (opaque, stream, offset, origin)
187
+ voidpf opaque;
188
+ voidpf stream;
189
+ uLong offset;
190
+ int origin;
191
+ {
192
+ DWORD dwMoveMethod=0xFFFFFFFF;
193
+ HANDLE hFile = NULL;
194
+
195
+ long ret=-1;
196
+ if (stream!=NULL)
197
+ hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
198
+ switch (origin)
199
+ {
200
+ case ZLIB_FILEFUNC_SEEK_CUR :
201
+ dwMoveMethod = FILE_CURRENT;
202
+ break;
203
+ case ZLIB_FILEFUNC_SEEK_END :
204
+ dwMoveMethod = FILE_END;
205
+ break;
206
+ case ZLIB_FILEFUNC_SEEK_SET :
207
+ dwMoveMethod = FILE_BEGIN;
208
+ break;
209
+ default: return -1;
210
+ }
211
+
212
+ if (hFile != NULL)
213
+ {
214
+ DWORD dwSet = SetFilePointer(hFile, offset, NULL, dwMoveMethod);
215
+ if (dwSet == INVALID_SET_FILE_POINTER)
216
+ {
217
+ DWORD dwErr = GetLastError();
218
+ ((WIN32FILE_IOWIN*)stream) -> error=(int)dwErr;
219
+ ret = -1;
220
+ }
221
+ else
222
+ ret=0;
223
+ }
224
+ return ret;
225
+ }
226
+
227
+ int ZCALLBACK win32_close_file_func (opaque, stream)
228
+ voidpf opaque;
229
+ voidpf stream;
230
+ {
231
+ int ret=-1;
232
+
233
+ if (stream!=NULL)
234
+ {
235
+ HANDLE hFile;
236
+ hFile = ((WIN32FILE_IOWIN*)stream) -> hf;
237
+ if (hFile != NULL)
238
+ {
239
+ CloseHandle(hFile);
240
+ ret=0;
241
+ }
242
+ free(stream);
243
+ }
244
+ return ret;
245
+ }
246
+
247
+ int ZCALLBACK win32_error_file_func (opaque, stream)
248
+ voidpf opaque;
249
+ voidpf stream;
250
+ {
251
+ int ret=-1;
252
+ if (stream!=NULL)
253
+ {
254
+ ret = ((WIN32FILE_IOWIN*)stream) -> error;
255
+ }
256
+ return ret;
257
+ }
258
+
259
+ void fill_win32_filefunc (pzlib_filefunc_def)
260
+ zlib_filefunc_def* pzlib_filefunc_def;
261
+ {
262
+ pzlib_filefunc_def->zopen_file = win32_open_file_func;
263
+ pzlib_filefunc_def->zread_file = win32_read_file_func;
264
+ pzlib_filefunc_def->zwrite_file = win32_write_file_func;
265
+ pzlib_filefunc_def->ztell_file = win32_tell_file_func;
266
+ pzlib_filefunc_def->zseek_file = win32_seek_file_func;
267
+ pzlib_filefunc_def->zclose_file = win32_close_file_func;
268
+ pzlib_filefunc_def->zerror_file = win32_error_file_func;
269
+ pzlib_filefunc_def->opaque=NULL;
270
+ }
@@ -0,0 +1,21 @@
1
+ /* iowin32.h -- IO base function header for compress/uncompress .zip
2
+ files using zlib + zip or unzip API
3
+ This IO API version uses the Win32 API (for Microsoft Windows)
4
+
5
+ Version 1.01e, February 12th, 2005
6
+
7
+ Copyright (C) 1998-2005 Gilles Vollant
8
+ */
9
+
10
+ #include <windows.h>
11
+
12
+
13
+ #ifdef __cplusplus
14
+ extern "C" {
15
+ #endif
16
+
17
+ void fill_win32_filefunc OF((zlib_filefunc_def* pzlib_filefunc_def));
18
+
19
+ #ifdef __cplusplus
20
+ }
21
+ #endif
@@ -0,0 +1,585 @@
1
+ /*
2
+ miniunz.c
3
+ Version 1.01e, February 12th, 2005
4
+
5
+ Copyright (C) 1998-2005 Gilles Vollant
6
+ */
7
+
8
+
9
+ #include <stdio.h>
10
+ #include <stdlib.h>
11
+ #include <string.h>
12
+ #include <time.h>
13
+ #include <errno.h>
14
+ #include <fcntl.h>
15
+
16
+ #ifdef unix
17
+ # include <unistd.h>
18
+ # include <utime.h>
19
+ #else
20
+ # include <direct.h>
21
+ # include <io.h>
22
+ #endif
23
+
24
+ #include "unzip.h"
25
+
26
+ #define CASESENSITIVITY (0)
27
+ #define WRITEBUFFERSIZE (8192)
28
+ #define MAXFILENAME (256)
29
+
30
+ #ifdef WIN32
31
+ #define USEWIN32IOAPI
32
+ #include "iowin32.h"
33
+ #endif
34
+ /*
35
+ mini unzip, demo of unzip package
36
+
37
+ usage :
38
+ Usage : miniunz [-exvlo] file.zip [file_to_extract] [-d extractdir]
39
+
40
+ list the file in the zipfile, and print the content of FILE_ID.ZIP or README.TXT
41
+ if it exists
42
+ */
43
+
44
+
45
+ /* change_file_date : change the date/time of a file
46
+ filename : the filename of the file where date/time must be modified
47
+ dosdate : the new date at the MSDos format (4 bytes)
48
+ tmu_date : the SAME new date at the tm_unz format */
49
+ void change_file_date(filename,dosdate,tmu_date)
50
+ const char *filename;
51
+ uLong dosdate;
52
+ tm_unz tmu_date;
53
+ {
54
+ #ifdef WIN32
55
+ HANDLE hFile;
56
+ FILETIME ftm,ftLocal,ftCreate,ftLastAcc,ftLastWrite;
57
+
58
+ hFile = CreateFile(filename,GENERIC_READ | GENERIC_WRITE,
59
+ 0,NULL,OPEN_EXISTING,0,NULL);
60
+ GetFileTime(hFile,&ftCreate,&ftLastAcc,&ftLastWrite);
61
+ DosDateTimeToFileTime((WORD)(dosdate>>16),(WORD)dosdate,&ftLocal);
62
+ LocalFileTimeToFileTime(&ftLocal,&ftm);
63
+ SetFileTime(hFile,&ftm,&ftLastAcc,&ftm);
64
+ CloseHandle(hFile);
65
+ #else
66
+ #ifdef unix
67
+ struct utimbuf ut;
68
+ struct tm newdate;
69
+ newdate.tm_sec = tmu_date.tm_sec;
70
+ newdate.tm_min=tmu_date.tm_min;
71
+ newdate.tm_hour=tmu_date.tm_hour;
72
+ newdate.tm_mday=tmu_date.tm_mday;
73
+ newdate.tm_mon=tmu_date.tm_mon;
74
+ if (tmu_date.tm_year > 1900)
75
+ newdate.tm_year=tmu_date.tm_year - 1900;
76
+ else
77
+ newdate.tm_year=tmu_date.tm_year ;
78
+ newdate.tm_isdst=-1;
79
+
80
+ ut.actime=ut.modtime=mktime(&newdate);
81
+ utime(filename,&ut);
82
+ #endif
83
+ #endif
84
+ }
85
+
86
+
87
+ /* mymkdir and change_file_date are not 100 % portable
88
+ As I don't know well Unix, I wait feedback for the unix portion */
89
+
90
+ int mymkdir(dirname)
91
+ const char* dirname;
92
+ {
93
+ int ret=0;
94
+ #ifdef WIN32
95
+ ret = mkdir(dirname);
96
+ #else
97
+ #ifdef unix
98
+ ret = mkdir (dirname,0775);
99
+ #endif
100
+ #endif
101
+ return ret;
102
+ }
103
+
104
+ int makedir (newdir)
105
+ char *newdir;
106
+ {
107
+ char *buffer ;
108
+ char *p;
109
+ int len = (int)strlen(newdir);
110
+
111
+ if (len <= 0)
112
+ return 0;
113
+
114
+ buffer = (char*)malloc(len+1);
115
+ strcpy(buffer,newdir);
116
+
117
+ if (buffer[len-1] == '/') {
118
+ buffer[len-1] = '\0';
119
+ }
120
+ if (mymkdir(buffer) == 0)
121
+ {
122
+ free(buffer);
123
+ return 1;
124
+ }
125
+
126
+ p = buffer+1;
127
+ while (1)
128
+ {
129
+ char hold;
130
+
131
+ while(*p && *p != '\\' && *p != '/')
132
+ p++;
133
+ hold = *p;
134
+ *p = 0;
135
+ if ((mymkdir(buffer) == -1) && (errno == ENOENT))
136
+ {
137
+ printf("couldn't create directory %s\n",buffer);
138
+ free(buffer);
139
+ return 0;
140
+ }
141
+ if (hold == 0)
142
+ break;
143
+ *p++ = hold;
144
+ }
145
+ free(buffer);
146
+ return 1;
147
+ }
148
+
149
+ void do_banner()
150
+ {
151
+ printf("MiniUnz 1.01b, demo of zLib + Unz package written by Gilles Vollant\n");
152
+ printf("more info at http://www.winimage.com/zLibDll/unzip.html\n\n");
153
+ }
154
+
155
+ void do_help()
156
+ {
157
+ printf("Usage : miniunz [-e] [-x] [-v] [-l] [-o] [-p password] file.zip [file_to_extr.] [-d extractdir]\n\n" \
158
+ " -e Extract without pathname (junk paths)\n" \
159
+ " -x Extract with pathname\n" \
160
+ " -v list files\n" \
161
+ " -l list files\n" \
162
+ " -d directory to extract into\n" \
163
+ " -o overwrite files without prompting\n" \
164
+ " -p extract crypted file using password\n\n");
165
+ }
166
+
167
+
168
+ int do_list(uf)
169
+ unzFile uf;
170
+ {
171
+ uLong i;
172
+ unz_global_info gi;
173
+ int err;
174
+
175
+ err = unzGetGlobalInfo (uf,&gi);
176
+ if (err!=UNZ_OK)
177
+ printf("error %d with zipfile in unzGetGlobalInfo \n",err);
178
+ printf(" Length Method Size Ratio Date Time CRC-32 Name\n");
179
+ printf(" ------ ------ ---- ----- ---- ---- ------ ----\n");
180
+ for (i=0;i<gi.number_entry;i++)
181
+ {
182
+ char filename_inzip[256];
183
+ unz_file_info file_info;
184
+ uLong ratio=0;
185
+ const char *string_method;
186
+ char charCrypt=' ';
187
+ err = unzGetCurrentFileInfo(uf,&file_info,filename_inzip,sizeof(filename_inzip),NULL,0,NULL,0);
188
+ if (err!=UNZ_OK)
189
+ {
190
+ printf("error %d with zipfile in unzGetCurrentFileInfo\n",err);
191
+ break;
192
+ }
193
+ if (file_info.uncompressed_size>0)
194
+ ratio = (file_info.compressed_size*100)/file_info.uncompressed_size;
195
+
196
+ /* display a '*' if the file is crypted */
197
+ if ((file_info.flag & 1) != 0)
198
+ charCrypt='*';
199
+
200
+ if (file_info.compression_method==0)
201
+ string_method="Stored";
202
+ else
203
+ if (file_info.compression_method==Z_DEFLATED)
204
+ {
205
+ uInt iLevel=(uInt)((file_info.flag & 0x6)/2);
206
+ if (iLevel==0)
207
+ string_method="Defl:N";
208
+ else if (iLevel==1)
209
+ string_method="Defl:X";
210
+ else if ((iLevel==2) || (iLevel==3))
211
+ string_method="Defl:F"; /* 2:fast , 3 : extra fast*/
212
+ }
213
+ else
214
+ string_method="Unkn. ";
215
+
216
+ printf("%7lu %6s%c%7lu %3lu%% %2.2lu-%2.2lu-%2.2lu %2.2lu:%2.2lu %8.8lx %s\n",
217
+ file_info.uncompressed_size,string_method,
218
+ charCrypt,
219
+ file_info.compressed_size,
220
+ ratio,
221
+ (uLong)file_info.tmu_date.tm_mon + 1,
222
+ (uLong)file_info.tmu_date.tm_mday,
223
+ (uLong)file_info.tmu_date.tm_year % 100,
224
+ (uLong)file_info.tmu_date.tm_hour,(uLong)file_info.tmu_date.tm_min,
225
+ (uLong)file_info.crc,filename_inzip);
226
+ if ((i+1)<gi.number_entry)
227
+ {
228
+ err = unzGoToNextFile(uf);
229
+ if (err!=UNZ_OK)
230
+ {
231
+ printf("error %d with zipfile in unzGoToNextFile\n",err);
232
+ break;
233
+ }
234
+ }
235
+ }
236
+
237
+ return 0;
238
+ }
239
+
240
+
241
+ int do_extract_currentfile(uf,popt_extract_without_path,popt_overwrite,password)
242
+ unzFile uf;
243
+ const int* popt_extract_without_path;
244
+ int* popt_overwrite;
245
+ const char* password;
246
+ {
247
+ char filename_inzip[256];
248
+ char* filename_withoutpath;
249
+ char* p;
250
+ int err=UNZ_OK;
251
+ FILE *fout=NULL;
252
+ void* buf;
253
+ uInt size_buf;
254
+
255
+ unz_file_info file_info;
256
+ uLong ratio=0;
257
+ err = unzGetCurrentFileInfo(uf,&file_info,filename_inzip,sizeof(filename_inzip),NULL,0,NULL,0);
258
+
259
+ if (err!=UNZ_OK)
260
+ {
261
+ printf("error %d with zipfile in unzGetCurrentFileInfo\n",err);
262
+ return err;
263
+ }
264
+
265
+ size_buf = WRITEBUFFERSIZE;
266
+ buf = (void*)malloc(size_buf);
267
+ if (buf==NULL)
268
+ {
269
+ printf("Error allocating memory\n");
270
+ return UNZ_INTERNALERROR;
271
+ }
272
+
273
+ p = filename_withoutpath = filename_inzip;
274
+ while ((*p) != '\0')
275
+ {
276
+ if (((*p)=='/') || ((*p)=='\\'))
277
+ filename_withoutpath = p+1;
278
+ p++;
279
+ }
280
+
281
+ if ((*filename_withoutpath)=='\0')
282
+ {
283
+ if ((*popt_extract_without_path)==0)
284
+ {
285
+ printf("creating directory: %s\n",filename_inzip);
286
+ mymkdir(filename_inzip);
287
+ }
288
+ }
289
+ else
290
+ {
291
+ const char* write_filename;
292
+ int skip=0;
293
+
294
+ if ((*popt_extract_without_path)==0)
295
+ write_filename = filename_inzip;
296
+ else
297
+ write_filename = filename_withoutpath;
298
+
299
+ err = unzOpenCurrentFilePassword(uf,password);
300
+ if (err!=UNZ_OK)
301
+ {
302
+ printf("error %d with zipfile in unzOpenCurrentFilePassword\n",err);
303
+ }
304
+
305
+ if (((*popt_overwrite)==0) && (err==UNZ_OK))
306
+ {
307
+ char rep=0;
308
+ FILE* ftestexist;
309
+ ftestexist = fopen(write_filename,"rb");
310
+ if (ftestexist!=NULL)
311
+ {
312
+ fclose(ftestexist);
313
+ do
314
+ {
315
+ char answer[128];
316
+ int ret;
317
+
318
+ printf("The file %s exists. Overwrite ? [y]es, [n]o, [A]ll: ",write_filename);
319
+ ret = scanf("%1s",answer);
320
+ if (ret != 1)
321
+ {
322
+ exit(EXIT_FAILURE);
323
+ }
324
+ rep = answer[0] ;
325
+ if ((rep>='a') && (rep<='z'))
326
+ rep -= 0x20;
327
+ }
328
+ while ((rep!='Y') && (rep!='N') && (rep!='A'));
329
+ }
330
+
331
+ if (rep == 'N')
332
+ skip = 1;
333
+
334
+ if (rep == 'A')
335
+ *popt_overwrite=1;
336
+ }
337
+
338
+ if ((skip==0) && (err==UNZ_OK))
339
+ {
340
+ fout=fopen(write_filename,"wb");
341
+
342
+ /* some zipfile don't contain directory alone before file */
343
+ if ((fout==NULL) && ((*popt_extract_without_path)==0) &&
344
+ (filename_withoutpath!=(char*)filename_inzip))
345
+ {
346
+ char c=*(filename_withoutpath-1);
347
+ *(filename_withoutpath-1)='\0';
348
+ makedir(write_filename);
349
+ *(filename_withoutpath-1)=c;
350
+ fout=fopen(write_filename,"wb");
351
+ }
352
+
353
+ if (fout==NULL)
354
+ {
355
+ printf("error opening %s\n",write_filename);
356
+ }
357
+ }
358
+
359
+ if (fout!=NULL)
360
+ {
361
+ printf(" extracting: %s\n",write_filename);
362
+
363
+ do
364
+ {
365
+ err = unzReadCurrentFile(uf,buf,size_buf);
366
+ if (err<0)
367
+ {
368
+ printf("error %d with zipfile in unzReadCurrentFile\n",err);
369
+ break;
370
+ }
371
+ if (err>0)
372
+ if (fwrite(buf,err,1,fout)!=1)
373
+ {
374
+ printf("error in writing extracted file\n");
375
+ err=UNZ_ERRNO;
376
+ break;
377
+ }
378
+ }
379
+ while (err>0);
380
+ if (fout)
381
+ fclose(fout);
382
+
383
+ if (err==0)
384
+ change_file_date(write_filename,file_info.dosDate,
385
+ file_info.tmu_date);
386
+ }
387
+
388
+ if (err==UNZ_OK)
389
+ {
390
+ err = unzCloseCurrentFile (uf);
391
+ if (err!=UNZ_OK)
392
+ {
393
+ printf("error %d with zipfile in unzCloseCurrentFile\n",err);
394
+ }
395
+ }
396
+ else
397
+ unzCloseCurrentFile(uf); /* don't lose the error */
398
+ }
399
+
400
+ free(buf);
401
+ return err;
402
+ }
403
+
404
+
405
+ int do_extract(uf,opt_extract_without_path,opt_overwrite,password)
406
+ unzFile uf;
407
+ int opt_extract_without_path;
408
+ int opt_overwrite;
409
+ const char* password;
410
+ {
411
+ uLong i;
412
+ unz_global_info gi;
413
+ int err;
414
+ FILE* fout=NULL;
415
+
416
+ err = unzGetGlobalInfo (uf,&gi);
417
+ if (err!=UNZ_OK)
418
+ printf("error %d with zipfile in unzGetGlobalInfo \n",err);
419
+
420
+ for (i=0;i<gi.number_entry;i++)
421
+ {
422
+ if (do_extract_currentfile(uf,&opt_extract_without_path,
423
+ &opt_overwrite,
424
+ password) != UNZ_OK)
425
+ break;
426
+
427
+ if ((i+1)<gi.number_entry)
428
+ {
429
+ err = unzGoToNextFile(uf);
430
+ if (err!=UNZ_OK)
431
+ {
432
+ printf("error %d with zipfile in unzGoToNextFile\n",err);
433
+ break;
434
+ }
435
+ }
436
+ }
437
+
438
+ return 0;
439
+ }
440
+
441
+ int do_extract_onefile(uf,filename,opt_extract_without_path,opt_overwrite,password)
442
+ unzFile uf;
443
+ const char* filename;
444
+ int opt_extract_without_path;
445
+ int opt_overwrite;
446
+ const char* password;
447
+ {
448
+ int err = UNZ_OK;
449
+ if (unzLocateFile(uf,filename,CASESENSITIVITY)!=UNZ_OK)
450
+ {
451
+ printf("file %s not found in the zipfile\n",filename);
452
+ return 2;
453
+ }
454
+
455
+ if (do_extract_currentfile(uf,&opt_extract_without_path,
456
+ &opt_overwrite,
457
+ password) == UNZ_OK)
458
+ return 0;
459
+ else
460
+ return 1;
461
+ }
462
+
463
+
464
+ int main(argc,argv)
465
+ int argc;
466
+ char *argv[];
467
+ {
468
+ const char *zipfilename=NULL;
469
+ const char *filename_to_extract=NULL;
470
+ const char *password=NULL;
471
+ char filename_try[MAXFILENAME+16] = "";
472
+ int i;
473
+ int opt_do_list=0;
474
+ int opt_do_extract=1;
475
+ int opt_do_extract_withoutpath=0;
476
+ int opt_overwrite=0;
477
+ int opt_extractdir=0;
478
+ const char *dirname=NULL;
479
+ unzFile uf=NULL;
480
+
481
+ do_banner();
482
+ if (argc==1)
483
+ {
484
+ do_help();
485
+ return 0;
486
+ }
487
+ else
488
+ {
489
+ for (i=1;i<argc;i++)
490
+ {
491
+ if ((*argv[i])=='-')
492
+ {
493
+ const char *p=argv[i]+1;
494
+
495
+ while ((*p)!='\0')
496
+ {
497
+ char c=*(p++);;
498
+ if ((c=='l') || (c=='L'))
499
+ opt_do_list = 1;
500
+ if ((c=='v') || (c=='V'))
501
+ opt_do_list = 1;
502
+ if ((c=='x') || (c=='X'))
503
+ opt_do_extract = 1;
504
+ if ((c=='e') || (c=='E'))
505
+ opt_do_extract = opt_do_extract_withoutpath = 1;
506
+ if ((c=='o') || (c=='O'))
507
+ opt_overwrite=1;
508
+ if ((c=='d') || (c=='D'))
509
+ {
510
+ opt_extractdir=1;
511
+ dirname=argv[i+1];
512
+ }
513
+
514
+ if (((c=='p') || (c=='P')) && (i+1<argc))
515
+ {
516
+ password=argv[i+1];
517
+ i++;
518
+ }
519
+ }
520
+ }
521
+ else
522
+ {
523
+ if (zipfilename == NULL)
524
+ zipfilename = argv[i];
525
+ else if ((filename_to_extract==NULL) && (!opt_extractdir))
526
+ filename_to_extract = argv[i] ;
527
+ }
528
+ }
529
+ }
530
+
531
+ if (zipfilename!=NULL)
532
+ {
533
+
534
+ # ifdef USEWIN32IOAPI
535
+ zlib_filefunc_def ffunc;
536
+ # endif
537
+
538
+ strncpy(filename_try, zipfilename,MAXFILENAME-1);
539
+ /* strncpy doesnt append the trailing NULL, of the string is too long. */
540
+ filename_try[ MAXFILENAME ] = '\0';
541
+
542
+ # ifdef USEWIN32IOAPI
543
+ fill_win32_filefunc(&ffunc);
544
+ uf = unzOpen2(zipfilename,&ffunc);
545
+ # else
546
+ uf = unzOpen(zipfilename);
547
+ # endif
548
+ if (uf==NULL)
549
+ {
550
+ strcat(filename_try,".zip");
551
+ # ifdef USEWIN32IOAPI
552
+ uf = unzOpen2(filename_try,&ffunc);
553
+ # else
554
+ uf = unzOpen(filename_try);
555
+ # endif
556
+ }
557
+ }
558
+
559
+ if (uf==NULL)
560
+ {
561
+ printf("Cannot open %s or %s.zip\n",zipfilename,zipfilename);
562
+ return 1;
563
+ }
564
+ printf("%s opened\n",filename_try);
565
+
566
+ if (opt_do_list==1)
567
+ return do_list(uf);
568
+ else if (opt_do_extract==1)
569
+ {
570
+ if (opt_extractdir && chdir(dirname))
571
+ {
572
+ printf("Error changing into %s, aborting\n", dirname);
573
+ exit(-1);
574
+ }
575
+
576
+ if (filename_to_extract == NULL)
577
+ return do_extract(uf,opt_do_extract_withoutpath,opt_overwrite,password);
578
+ else
579
+ return do_extract_onefile(uf,filename_to_extract,
580
+ opt_do_extract_withoutpath,opt_overwrite,password);
581
+ }
582
+ unzCloseCurrentFile(uf);
583
+
584
+ return 0;
585
+ }