finishm 0.0.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 +1,31 @@
1
+ /* puff.h
2
+ Copyright (C) 2002, 2003 Mark Adler, all rights reserved
3
+ version 1.7, 3 Mar 2002
4
+
5
+ This software is provided 'as-is', without any express or implied
6
+ warranty. In no event will the author be held liable for any damages
7
+ arising from the use of this software.
8
+
9
+ Permission is granted to anyone to use this software for any purpose,
10
+ including commercial applications, and to alter it and redistribute it
11
+ freely, subject to the following restrictions:
12
+
13
+ 1. The origin of this software must not be misrepresented; you must not
14
+ claim that you wrote the original software. If you use this software
15
+ in a product, an acknowledgment in the product documentation would be
16
+ appreciated but is not required.
17
+ 2. Altered source versions must be plainly marked as such, and must not be
18
+ misrepresented as being the original software.
19
+ 3. This notice may not be removed or altered from any source distribution.
20
+
21
+ Mark Adler madler@alumni.caltech.edu
22
+ */
23
+
24
+
25
+ /*
26
+ * See puff.c for purpose and usage.
27
+ */
28
+ int puff(unsigned char *dest, /* pointer to destination pointer */
29
+ unsigned long *destlen, /* amount of output space */
30
+ unsigned char *source, /* pointer to source data pointer */
31
+ unsigned long *sourcelen); /* amount of input available */
@@ -0,0 +1,275 @@
1
+ #include <stdio.h>
2
+ #include <stdlib.h>
3
+ #include <windows.h>
4
+
5
+ #include "zlib.h"
6
+
7
+
8
+ void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
9
+ {
10
+ R->HighPart = A.HighPart - B.HighPart;
11
+ if (A.LowPart >= B.LowPart)
12
+ R->LowPart = A.LowPart - B.LowPart;
13
+ else
14
+ {
15
+ R->LowPart = A.LowPart - B.LowPart;
16
+ R->HighPart --;
17
+ }
18
+ }
19
+
20
+ #ifdef _M_X64
21
+ // see http://msdn2.microsoft.com/library/twchhe95(en-us,vs.80).aspx for __rdtsc
22
+ unsigned __int64 __rdtsc(void);
23
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
24
+ {
25
+ // printf("rdtsc = %I64x\n",__rdtsc());
26
+ pbeginTime64->QuadPart=__rdtsc();
27
+ }
28
+
29
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
30
+ {
31
+ LARGE_INTEGER LIres;
32
+ unsigned _int64 res=__rdtsc()-((unsigned _int64)(beginTime64.QuadPart));
33
+ LIres.QuadPart=res;
34
+ // printf("rdtsc = %I64x\n",__rdtsc());
35
+ return LIres;
36
+ }
37
+ #else
38
+ #ifdef _M_IX86
39
+ void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
40
+ {
41
+ DWORD dwEdx,dwEax;
42
+ _asm
43
+ {
44
+ rdtsc
45
+ mov dwEax,eax
46
+ mov dwEdx,edx
47
+ }
48
+ pbeginTime64->LowPart=dwEax;
49
+ pbeginTime64->HighPart=dwEdx;
50
+ }
51
+
52
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
53
+ {
54
+ myGetRDTSC32(pbeginTime64);
55
+ }
56
+
57
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
58
+ {
59
+ LARGE_INTEGER LIres,endTime64;
60
+ myGetRDTSC32(&endTime64);
61
+
62
+ LIres.LowPart=LIres.HighPart=0;
63
+ MyDoMinus64(&LIres,endTime64,beginTime64);
64
+ return LIres;
65
+ }
66
+ #else
67
+ void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
68
+ {
69
+ }
70
+
71
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
72
+ {
73
+ }
74
+
75
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
76
+ {
77
+ LARGE_INTEGER lr;
78
+ lr.QuadPart=0;
79
+ return lr;
80
+ }
81
+ #endif
82
+ #endif
83
+
84
+ void BeginCountPerfCounter(LARGE_INTEGER * pbeginTime64,BOOL fComputeTimeQueryPerf)
85
+ {
86
+ if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(pbeginTime64)))
87
+ {
88
+ pbeginTime64->LowPart = GetTickCount();
89
+ pbeginTime64->HighPart = 0;
90
+ }
91
+ }
92
+
93
+ DWORD GetMsecSincePerfCounter(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
94
+ {
95
+ LARGE_INTEGER endTime64,ticksPerSecond,ticks;
96
+ DWORDLONG ticksShifted,tickSecShifted;
97
+ DWORD dwLog=16+0;
98
+ DWORD dwRet;
99
+ if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(&endTime64)))
100
+ dwRet = (GetTickCount() - beginTime64.LowPart)*1;
101
+ else
102
+ {
103
+ MyDoMinus64(&ticks,endTime64,beginTime64);
104
+ QueryPerformanceFrequency(&ticksPerSecond);
105
+
106
+
107
+ {
108
+ ticksShifted = Int64ShrlMod32(*(DWORDLONG*)&ticks,dwLog);
109
+ tickSecShifted = Int64ShrlMod32(*(DWORDLONG*)&ticksPerSecond,dwLog);
110
+
111
+ }
112
+
113
+ dwRet = (DWORD)((((DWORD)ticksShifted)*1000)/(DWORD)(tickSecShifted));
114
+ dwRet *=1;
115
+ }
116
+ return dwRet;
117
+ }
118
+
119
+ int ReadFileMemory(const char* filename,long* plFileSize,void** pFilePtr)
120
+ {
121
+ FILE* stream;
122
+ void* ptr;
123
+ int retVal=1;
124
+ stream=fopen(filename, "rb");
125
+ if (stream==NULL)
126
+ return 0;
127
+
128
+ fseek(stream,0,SEEK_END);
129
+
130
+ *plFileSize=ftell(stream);
131
+ fseek(stream,0,SEEK_SET);
132
+ ptr=malloc((*plFileSize)+1);
133
+ if (ptr==NULL)
134
+ retVal=0;
135
+ else
136
+ {
137
+ if (fread(ptr, 1, *plFileSize,stream) != (*plFileSize))
138
+ retVal=0;
139
+ }
140
+ fclose(stream);
141
+ *pFilePtr=ptr;
142
+ return retVal;
143
+ }
144
+
145
+ int main(int argc, char *argv[])
146
+ {
147
+ int BlockSizeCompress=0x8000;
148
+ int BlockSizeUncompress=0x8000;
149
+ int cprLevel=Z_DEFAULT_COMPRESSION ;
150
+ long lFileSize;
151
+ unsigned char* FilePtr;
152
+ long lBufferSizeCpr;
153
+ long lBufferSizeUncpr;
154
+ long lCompressedSize=0;
155
+ unsigned char* CprPtr;
156
+ unsigned char* UncprPtr;
157
+ long lSizeCpr,lSizeUncpr;
158
+ DWORD dwGetTick,dwMsecQP;
159
+ LARGE_INTEGER li_qp,li_rdtsc,dwResRdtsc;
160
+
161
+ if (argc<=1)
162
+ {
163
+ printf("run TestZlib <File> [BlockSizeCompress] [BlockSizeUncompress] [compres. level]\n");
164
+ return 0;
165
+ }
166
+
167
+ if (ReadFileMemory(argv[1],&lFileSize,&FilePtr)==0)
168
+ {
169
+ printf("error reading %s\n",argv[1]);
170
+ return 1;
171
+ }
172
+ else printf("file %s read, %u bytes\n",argv[1],lFileSize);
173
+
174
+ if (argc>=3)
175
+ BlockSizeCompress=atol(argv[2]);
176
+
177
+ if (argc>=4)
178
+ BlockSizeUncompress=atol(argv[3]);
179
+
180
+ if (argc>=5)
181
+ cprLevel=(int)atol(argv[4]);
182
+
183
+ lBufferSizeCpr = lFileSize + (lFileSize/0x10) + 0x200;
184
+ lBufferSizeUncpr = lBufferSizeCpr;
185
+
186
+ CprPtr=(unsigned char*)malloc(lBufferSizeCpr + BlockSizeCompress);
187
+
188
+ BeginCountPerfCounter(&li_qp,TRUE);
189
+ dwGetTick=GetTickCount();
190
+ BeginCountRdtsc(&li_rdtsc);
191
+ {
192
+ z_stream zcpr;
193
+ int ret=Z_OK;
194
+ long lOrigToDo = lFileSize;
195
+ long lOrigDone = 0;
196
+ int step=0;
197
+ memset(&zcpr,0,sizeof(z_stream));
198
+ deflateInit(&zcpr,cprLevel);
199
+
200
+ zcpr.next_in = FilePtr;
201
+ zcpr.next_out = CprPtr;
202
+
203
+
204
+ do
205
+ {
206
+ long all_read_before = zcpr.total_in;
207
+ zcpr.avail_in = min(lOrigToDo,BlockSizeCompress);
208
+ zcpr.avail_out = BlockSizeCompress;
209
+ ret=deflate(&zcpr,(zcpr.avail_in==lOrigToDo) ? Z_FINISH : Z_SYNC_FLUSH);
210
+ lOrigDone += (zcpr.total_in-all_read_before);
211
+ lOrigToDo -= (zcpr.total_in-all_read_before);
212
+ step++;
213
+ } while (ret==Z_OK);
214
+
215
+ lSizeCpr=zcpr.total_out;
216
+ deflateEnd(&zcpr);
217
+ dwGetTick=GetTickCount()-dwGetTick;
218
+ dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
219
+ dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
220
+ printf("total compress size = %u, in %u step\n",lSizeCpr,step);
221
+ printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
222
+ printf("defcpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
223
+ printf("defcpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
224
+ }
225
+
226
+ CprPtr=(unsigned char*)realloc(CprPtr,lSizeCpr);
227
+ UncprPtr=(unsigned char*)malloc(lBufferSizeUncpr + BlockSizeUncompress);
228
+
229
+ BeginCountPerfCounter(&li_qp,TRUE);
230
+ dwGetTick=GetTickCount();
231
+ BeginCountRdtsc(&li_rdtsc);
232
+ {
233
+ z_stream zcpr;
234
+ int ret=Z_OK;
235
+ long lOrigToDo = lSizeCpr;
236
+ long lOrigDone = 0;
237
+ int step=0;
238
+ memset(&zcpr,0,sizeof(z_stream));
239
+ inflateInit(&zcpr);
240
+
241
+ zcpr.next_in = CprPtr;
242
+ zcpr.next_out = UncprPtr;
243
+
244
+
245
+ do
246
+ {
247
+ long all_read_before = zcpr.total_in;
248
+ zcpr.avail_in = min(lOrigToDo,BlockSizeUncompress);
249
+ zcpr.avail_out = BlockSizeUncompress;
250
+ ret=inflate(&zcpr,Z_SYNC_FLUSH);
251
+ lOrigDone += (zcpr.total_in-all_read_before);
252
+ lOrigToDo -= (zcpr.total_in-all_read_before);
253
+ step++;
254
+ } while (ret==Z_OK);
255
+
256
+ lSizeUncpr=zcpr.total_out;
257
+ inflateEnd(&zcpr);
258
+ dwGetTick=GetTickCount()-dwGetTick;
259
+ dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
260
+ dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
261
+ printf("total uncompress size = %u, in %u step\n",lSizeUncpr,step);
262
+ printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
263
+ printf("uncpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
264
+ printf("uncpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
265
+ }
266
+
267
+ if (lSizeUncpr==lFileSize)
268
+ {
269
+ if (memcmp(FilePtr,UncprPtr,lFileSize)==0)
270
+ printf("compare ok\n");
271
+
272
+ }
273
+
274
+ return 0;
275
+ }
@@ -0,0 +1,10 @@
1
+ To build testzLib with Visual Studio 2005:
2
+
3
+ copy to a directory file from :
4
+ - root of zLib tree
5
+ - contrib/testzlib
6
+ - contrib/masmx86
7
+ - contrib/masmx64
8
+ - contrib/vstudio/vc7
9
+
10
+ and open testzlib8.sln
@@ -0,0 +1,14 @@
1
+ CC=cc
2
+ CFLAGS=-g
3
+
4
+ untgz: untgz.o ../../libz.a
5
+ $(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
6
+
7
+ untgz.o: untgz.c ../../zlib.h
8
+ $(CC) $(CFLAGS) -c -I../.. untgz.c
9
+
10
+ ../../libz.a:
11
+ cd ../..; ./configure; make
12
+
13
+ clean:
14
+ rm -f untgz untgz.o *~
@@ -0,0 +1,17 @@
1
+ CC=cl
2
+ CFLAGS=-MD
3
+
4
+ untgz.exe: untgz.obj ..\..\zlib.lib
5
+ $(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
6
+
7
+ untgz.obj: untgz.c ..\..\zlib.h
8
+ $(CC) $(CFLAGS) -c -I..\.. untgz.c
9
+
10
+ ..\..\zlib.lib:
11
+ cd ..\..
12
+ $(MAKE) -f win32\makefile.msc
13
+ cd contrib\untgz
14
+
15
+ clean:
16
+ -del untgz.obj
17
+ -del untgz.exe
@@ -0,0 +1,674 @@
1
+ /*
2
+ * untgz.c -- Display contents and extract files from a gzip'd TAR file
3
+ *
4
+ * written by Pedro A. Aranda Gutierrez <paag@tid.es>
5
+ * adaptation to Unix by Jean-loup Gailly <jloup@gzip.org>
6
+ * various fixes by Cosmin Truta <cosmint@cs.ubbcluj.ro>
7
+ */
8
+
9
+ #include <stdio.h>
10
+ #include <stdlib.h>
11
+ #include <string.h>
12
+ #include <time.h>
13
+ #include <errno.h>
14
+
15
+ #include "zlib.h"
16
+
17
+ #ifdef unix
18
+ # include <unistd.h>
19
+ #else
20
+ # include <direct.h>
21
+ # include <io.h>
22
+ #endif
23
+
24
+ #ifdef WIN32
25
+ #include <windows.h>
26
+ # ifndef F_OK
27
+ # define F_OK 0
28
+ # endif
29
+ # define mkdir(dirname,mode) _mkdir(dirname)
30
+ # ifdef _MSC_VER
31
+ # define access(path,mode) _access(path,mode)
32
+ # define chmod(path,mode) _chmod(path,mode)
33
+ # define strdup(str) _strdup(str)
34
+ # endif
35
+ #else
36
+ # include <utime.h>
37
+ #endif
38
+
39
+
40
+ /* values used in typeflag field */
41
+
42
+ #define REGTYPE '0' /* regular file */
43
+ #define AREGTYPE '\0' /* regular file */
44
+ #define LNKTYPE '1' /* link */
45
+ #define SYMTYPE '2' /* reserved */
46
+ #define CHRTYPE '3' /* character special */
47
+ #define BLKTYPE '4' /* block special */
48
+ #define DIRTYPE '5' /* directory */
49
+ #define FIFOTYPE '6' /* FIFO special */
50
+ #define CONTTYPE '7' /* reserved */
51
+
52
+ /* GNU tar extensions */
53
+
54
+ #define GNUTYPE_DUMPDIR 'D' /* file names from dumped directory */
55
+ #define GNUTYPE_LONGLINK 'K' /* long link name */
56
+ #define GNUTYPE_LONGNAME 'L' /* long file name */
57
+ #define GNUTYPE_MULTIVOL 'M' /* continuation of file from another volume */
58
+ #define GNUTYPE_NAMES 'N' /* file name that does not fit into main hdr */
59
+ #define GNUTYPE_SPARSE 'S' /* sparse file */
60
+ #define GNUTYPE_VOLHDR 'V' /* tape/volume header */
61
+
62
+
63
+ /* tar header */
64
+
65
+ #define BLOCKSIZE 512
66
+ #define SHORTNAMESIZE 100
67
+
68
+ struct tar_header
69
+ { /* byte offset */
70
+ char name[100]; /* 0 */
71
+ char mode[8]; /* 100 */
72
+ char uid[8]; /* 108 */
73
+ char gid[8]; /* 116 */
74
+ char size[12]; /* 124 */
75
+ char mtime[12]; /* 136 */
76
+ char chksum[8]; /* 148 */
77
+ char typeflag; /* 156 */
78
+ char linkname[100]; /* 157 */
79
+ char magic[6]; /* 257 */
80
+ char version[2]; /* 263 */
81
+ char uname[32]; /* 265 */
82
+ char gname[32]; /* 297 */
83
+ char devmajor[8]; /* 329 */
84
+ char devminor[8]; /* 337 */
85
+ char prefix[155]; /* 345 */
86
+ /* 500 */
87
+ };
88
+
89
+ union tar_buffer
90
+ {
91
+ char buffer[BLOCKSIZE];
92
+ struct tar_header header;
93
+ };
94
+
95
+ struct attr_item
96
+ {
97
+ struct attr_item *next;
98
+ char *fname;
99
+ int mode;
100
+ time_t time;
101
+ };
102
+
103
+ enum { TGZ_EXTRACT, TGZ_LIST, TGZ_INVALID };
104
+
105
+ char *TGZfname OF((const char *));
106
+ void TGZnotfound OF((const char *));
107
+
108
+ int getoct OF((char *, int));
109
+ char *strtime OF((time_t *));
110
+ int setfiletime OF((char *, time_t));
111
+ void push_attr OF((struct attr_item **, char *, int, time_t));
112
+ void restore_attr OF((struct attr_item **));
113
+
114
+ int ExprMatch OF((char *, char *));
115
+
116
+ int makedir OF((char *));
117
+ int matchname OF((int, int, char **, char *));
118
+
119
+ void error OF((const char *));
120
+ int tar OF((gzFile, int, int, int, char **));
121
+
122
+ void help OF((int));
123
+ int main OF((int, char **));
124
+
125
+ char *prog;
126
+
127
+ const char *TGZsuffix[] = { "\0", ".tar", ".tar.gz", ".taz", ".tgz", NULL };
128
+
129
+ /* return the file name of the TGZ archive */
130
+ /* or NULL if it does not exist */
131
+
132
+ char *TGZfname (const char *arcname)
133
+ {
134
+ static char buffer[1024];
135
+ int origlen,i;
136
+
137
+ strcpy(buffer,arcname);
138
+ origlen = strlen(buffer);
139
+
140
+ for (i=0; TGZsuffix[i]; i++)
141
+ {
142
+ strcpy(buffer+origlen,TGZsuffix[i]);
143
+ if (access(buffer,F_OK) == 0)
144
+ return buffer;
145
+ }
146
+ return NULL;
147
+ }
148
+
149
+
150
+ /* error message for the filename */
151
+
152
+ void TGZnotfound (const char *arcname)
153
+ {
154
+ int i;
155
+
156
+ fprintf(stderr,"%s: Couldn't find ",prog);
157
+ for (i=0;TGZsuffix[i];i++)
158
+ fprintf(stderr,(TGZsuffix[i+1]) ? "%s%s, " : "or %s%s\n",
159
+ arcname,
160
+ TGZsuffix[i]);
161
+ exit(1);
162
+ }
163
+
164
+
165
+ /* convert octal digits to int */
166
+ /* on error return -1 */
167
+
168
+ int getoct (char *p,int width)
169
+ {
170
+ int result = 0;
171
+ char c;
172
+
173
+ while (width--)
174
+ {
175
+ c = *p++;
176
+ if (c == 0)
177
+ break;
178
+ if (c == ' ')
179
+ continue;
180
+ if (c < '0' || c > '7')
181
+ return -1;
182
+ result = result * 8 + (c - '0');
183
+ }
184
+ return result;
185
+ }
186
+
187
+
188
+ /* convert time_t to string */
189
+ /* use the "YYYY/MM/DD hh:mm:ss" format */
190
+
191
+ char *strtime (time_t *t)
192
+ {
193
+ struct tm *local;
194
+ static char result[32];
195
+
196
+ local = localtime(t);
197
+ sprintf(result,"%4d/%02d/%02d %02d:%02d:%02d",
198
+ local->tm_year+1900, local->tm_mon+1, local->tm_mday,
199
+ local->tm_hour, local->tm_min, local->tm_sec);
200
+ return result;
201
+ }
202
+
203
+
204
+ /* set file time */
205
+
206
+ int setfiletime (char *fname,time_t ftime)
207
+ {
208
+ #ifdef WIN32
209
+ static int isWinNT = -1;
210
+ SYSTEMTIME st;
211
+ FILETIME locft, modft;
212
+ struct tm *loctm;
213
+ HANDLE hFile;
214
+ int result;
215
+
216
+ loctm = localtime(&ftime);
217
+ if (loctm == NULL)
218
+ return -1;
219
+
220
+ st.wYear = (WORD)loctm->tm_year + 1900;
221
+ st.wMonth = (WORD)loctm->tm_mon + 1;
222
+ st.wDayOfWeek = (WORD)loctm->tm_wday;
223
+ st.wDay = (WORD)loctm->tm_mday;
224
+ st.wHour = (WORD)loctm->tm_hour;
225
+ st.wMinute = (WORD)loctm->tm_min;
226
+ st.wSecond = (WORD)loctm->tm_sec;
227
+ st.wMilliseconds = 0;
228
+ if (!SystemTimeToFileTime(&st, &locft) ||
229
+ !LocalFileTimeToFileTime(&locft, &modft))
230
+ return -1;
231
+
232
+ if (isWinNT < 0)
233
+ isWinNT = (GetVersion() < 0x80000000) ? 1 : 0;
234
+ hFile = CreateFile(fname, GENERIC_WRITE, 0, NULL, OPEN_EXISTING,
235
+ (isWinNT ? FILE_FLAG_BACKUP_SEMANTICS : 0),
236
+ NULL);
237
+ if (hFile == INVALID_HANDLE_VALUE)
238
+ return -1;
239
+ result = SetFileTime(hFile, NULL, NULL, &modft) ? 0 : -1;
240
+ CloseHandle(hFile);
241
+ return result;
242
+ #else
243
+ struct utimbuf settime;
244
+
245
+ settime.actime = settime.modtime = ftime;
246
+ return utime(fname,&settime);
247
+ #endif
248
+ }
249
+
250
+
251
+ /* push file attributes */
252
+
253
+ void push_attr(struct attr_item **list,char *fname,int mode,time_t time)
254
+ {
255
+ struct attr_item *item;
256
+
257
+ item = (struct attr_item *)malloc(sizeof(struct attr_item));
258
+ if (item == NULL)
259
+ error("Out of memory");
260
+ item->fname = strdup(fname);
261
+ item->mode = mode;
262
+ item->time = time;
263
+ item->next = *list;
264
+ *list = item;
265
+ }
266
+
267
+
268
+ /* restore file attributes */
269
+
270
+ void restore_attr(struct attr_item **list)
271
+ {
272
+ struct attr_item *item, *prev;
273
+
274
+ for (item = *list; item != NULL; )
275
+ {
276
+ setfiletime(item->fname,item->time);
277
+ chmod(item->fname,item->mode);
278
+ prev = item;
279
+ item = item->next;
280
+ free(prev);
281
+ }
282
+ *list = NULL;
283
+ }
284
+
285
+
286
+ /* match regular expression */
287
+
288
+ #define ISSPECIAL(c) (((c) == '*') || ((c) == '/'))
289
+
290
+ int ExprMatch (char *string,char *expr)
291
+ {
292
+ while (1)
293
+ {
294
+ if (ISSPECIAL(*expr))
295
+ {
296
+ if (*expr == '/')
297
+ {
298
+ if (*string != '\\' && *string != '/')
299
+ return 0;
300
+ string ++; expr++;
301
+ }
302
+ else if (*expr == '*')
303
+ {
304
+ if (*expr ++ == 0)
305
+ return 1;
306
+ while (*++string != *expr)
307
+ if (*string == 0)
308
+ return 0;
309
+ }
310
+ }
311
+ else
312
+ {
313
+ if (*string != *expr)
314
+ return 0;
315
+ if (*expr++ == 0)
316
+ return 1;
317
+ string++;
318
+ }
319
+ }
320
+ }
321
+
322
+
323
+ /* recursive mkdir */
324
+ /* abort on ENOENT; ignore other errors like "directory already exists" */
325
+ /* return 1 if OK */
326
+ /* 0 on error */
327
+
328
+ int makedir (char *newdir)
329
+ {
330
+ char *buffer = strdup(newdir);
331
+ char *p;
332
+ int len = strlen(buffer);
333
+
334
+ if (len <= 0) {
335
+ free(buffer);
336
+ return 0;
337
+ }
338
+ if (buffer[len-1] == '/') {
339
+ buffer[len-1] = '\0';
340
+ }
341
+ if (mkdir(buffer, 0755) == 0)
342
+ {
343
+ free(buffer);
344
+ return 1;
345
+ }
346
+
347
+ p = buffer+1;
348
+ while (1)
349
+ {
350
+ char hold;
351
+
352
+ while(*p && *p != '\\' && *p != '/')
353
+ p++;
354
+ hold = *p;
355
+ *p = 0;
356
+ if ((mkdir(buffer, 0755) == -1) && (errno == ENOENT))
357
+ {
358
+ fprintf(stderr,"%s: Couldn't create directory %s\n",prog,buffer);
359
+ free(buffer);
360
+ return 0;
361
+ }
362
+ if (hold == 0)
363
+ break;
364
+ *p++ = hold;
365
+ }
366
+ free(buffer);
367
+ return 1;
368
+ }
369
+
370
+
371
+ int matchname (int arg,int argc,char **argv,char *fname)
372
+ {
373
+ if (arg == argc) /* no arguments given (untgz tgzarchive) */
374
+ return 1;
375
+
376
+ while (arg < argc)
377
+ if (ExprMatch(fname,argv[arg++]))
378
+ return 1;
379
+
380
+ return 0; /* ignore this for the moment being */
381
+ }
382
+
383
+
384
+ /* tar file list or extract */
385
+
386
+ int tar (gzFile in,int action,int arg,int argc,char **argv)
387
+ {
388
+ union tar_buffer buffer;
389
+ int len;
390
+ int err;
391
+ int getheader = 1;
392
+ int remaining = 0;
393
+ FILE *outfile = NULL;
394
+ char fname[BLOCKSIZE];
395
+ int tarmode;
396
+ time_t tartime;
397
+ struct attr_item *attributes = NULL;
398
+
399
+ if (action == TGZ_LIST)
400
+ printf(" date time size file\n"
401
+ " ---------- -------- --------- -------------------------------------\n");
402
+ while (1)
403
+ {
404
+ len = gzread(in, &buffer, BLOCKSIZE);
405
+ if (len < 0)
406
+ error(gzerror(in, &err));
407
+ /*
408
+ * Always expect complete blocks to process
409
+ * the tar information.
410
+ */
411
+ if (len != BLOCKSIZE)
412
+ {
413
+ action = TGZ_INVALID; /* force error exit */
414
+ remaining = 0; /* force I/O cleanup */
415
+ }
416
+
417
+ /*
418
+ * If we have to get a tar header
419
+ */
420
+ if (getheader >= 1)
421
+ {
422
+ /*
423
+ * if we met the end of the tar
424
+ * or the end-of-tar block,
425
+ * we are done
426
+ */
427
+ if (len == 0 || buffer.header.name[0] == 0)
428
+ break;
429
+
430
+ tarmode = getoct(buffer.header.mode,8);
431
+ tartime = (time_t)getoct(buffer.header.mtime,12);
432
+ if (tarmode == -1 || tartime == (time_t)-1)
433
+ {
434
+ buffer.header.name[0] = 0;
435
+ action = TGZ_INVALID;
436
+ }
437
+
438
+ if (getheader == 1)
439
+ {
440
+ strncpy(fname,buffer.header.name,SHORTNAMESIZE);
441
+ if (fname[SHORTNAMESIZE-1] != 0)
442
+ fname[SHORTNAMESIZE] = 0;
443
+ }
444
+ else
445
+ {
446
+ /*
447
+ * The file name is longer than SHORTNAMESIZE
448
+ */
449
+ if (strncmp(fname,buffer.header.name,SHORTNAMESIZE-1) != 0)
450
+ error("bad long name");
451
+ getheader = 1;
452
+ }
453
+
454
+ /*
455
+ * Act according to the type flag
456
+ */
457
+ switch (buffer.header.typeflag)
458
+ {
459
+ case DIRTYPE:
460
+ if (action == TGZ_LIST)
461
+ printf(" %s <dir> %s\n",strtime(&tartime),fname);
462
+ if (action == TGZ_EXTRACT)
463
+ {
464
+ makedir(fname);
465
+ push_attr(&attributes,fname,tarmode,tartime);
466
+ }
467
+ break;
468
+ case REGTYPE:
469
+ case AREGTYPE:
470
+ remaining = getoct(buffer.header.size,12);
471
+ if (remaining == -1)
472
+ {
473
+ action = TGZ_INVALID;
474
+ break;
475
+ }
476
+ if (action == TGZ_LIST)
477
+ printf(" %s %9d %s\n",strtime(&tartime),remaining,fname);
478
+ else if (action == TGZ_EXTRACT)
479
+ {
480
+ if (matchname(arg,argc,argv,fname))
481
+ {
482
+ outfile = fopen(fname,"wb");
483
+ if (outfile == NULL) {
484
+ /* try creating directory */
485
+ char *p = strrchr(fname, '/');
486
+ if (p != NULL) {
487
+ *p = '\0';
488
+ makedir(fname);
489
+ *p = '/';
490
+ outfile = fopen(fname,"wb");
491
+ }
492
+ }
493
+ if (outfile != NULL)
494
+ printf("Extracting %s\n",fname);
495
+ else
496
+ fprintf(stderr, "%s: Couldn't create %s",prog,fname);
497
+ }
498
+ else
499
+ outfile = NULL;
500
+ }
501
+ getheader = 0;
502
+ break;
503
+ case GNUTYPE_LONGLINK:
504
+ case GNUTYPE_LONGNAME:
505
+ remaining = getoct(buffer.header.size,12);
506
+ if (remaining < 0 || remaining >= BLOCKSIZE)
507
+ {
508
+ action = TGZ_INVALID;
509
+ break;
510
+ }
511
+ len = gzread(in, fname, BLOCKSIZE);
512
+ if (len < 0)
513
+ error(gzerror(in, &err));
514
+ if (fname[BLOCKSIZE-1] != 0 || (int)strlen(fname) > remaining)
515
+ {
516
+ action = TGZ_INVALID;
517
+ break;
518
+ }
519
+ getheader = 2;
520
+ break;
521
+ default:
522
+ if (action == TGZ_LIST)
523
+ printf(" %s <---> %s\n",strtime(&tartime),fname);
524
+ break;
525
+ }
526
+ }
527
+ else
528
+ {
529
+ unsigned int bytes = (remaining > BLOCKSIZE) ? BLOCKSIZE : remaining;
530
+
531
+ if (outfile != NULL)
532
+ {
533
+ if (fwrite(&buffer,sizeof(char),bytes,outfile) != bytes)
534
+ {
535
+ fprintf(stderr,
536
+ "%s: Error writing %s -- skipping\n",prog,fname);
537
+ fclose(outfile);
538
+ outfile = NULL;
539
+ remove(fname);
540
+ }
541
+ }
542
+ remaining -= bytes;
543
+ }
544
+
545
+ if (remaining == 0)
546
+ {
547
+ getheader = 1;
548
+ if (outfile != NULL)
549
+ {
550
+ fclose(outfile);
551
+ outfile = NULL;
552
+ if (action != TGZ_INVALID)
553
+ push_attr(&attributes,fname,tarmode,tartime);
554
+ }
555
+ }
556
+
557
+ /*
558
+ * Abandon if errors are found
559
+ */
560
+ if (action == TGZ_INVALID)
561
+ {
562
+ error("broken archive");
563
+ break;
564
+ }
565
+ }
566
+
567
+ /*
568
+ * Restore file modes and time stamps
569
+ */
570
+ restore_attr(&attributes);
571
+
572
+ if (gzclose(in) != Z_OK)
573
+ error("failed gzclose");
574
+
575
+ return 0;
576
+ }
577
+
578
+
579
+ /* ============================================================ */
580
+
581
+ void help(int exitval)
582
+ {
583
+ printf("untgz version 0.2.1\n"
584
+ " using zlib version %s\n\n",
585
+ zlibVersion());
586
+ printf("Usage: untgz file.tgz extract all files\n"
587
+ " untgz file.tgz fname ... extract selected files\n"
588
+ " untgz -l file.tgz list archive contents\n"
589
+ " untgz -h display this help\n");
590
+ exit(exitval);
591
+ }
592
+
593
+ void error(const char *msg)
594
+ {
595
+ fprintf(stderr, "%s: %s\n", prog, msg);
596
+ exit(1);
597
+ }
598
+
599
+
600
+ /* ============================================================ */
601
+
602
+ #if defined(WIN32) && defined(__GNUC__)
603
+ int _CRT_glob = 0; /* disable argument globbing in MinGW */
604
+ #endif
605
+
606
+ int main(int argc,char **argv)
607
+ {
608
+ int action = TGZ_EXTRACT;
609
+ int arg = 1;
610
+ char *TGZfile;
611
+ gzFile *f;
612
+
613
+ prog = strrchr(argv[0],'\\');
614
+ if (prog == NULL)
615
+ {
616
+ prog = strrchr(argv[0],'/');
617
+ if (prog == NULL)
618
+ {
619
+ prog = strrchr(argv[0],':');
620
+ if (prog == NULL)
621
+ prog = argv[0];
622
+ else
623
+ prog++;
624
+ }
625
+ else
626
+ prog++;
627
+ }
628
+ else
629
+ prog++;
630
+
631
+ if (argc == 1)
632
+ help(0);
633
+
634
+ if (strcmp(argv[arg],"-l") == 0)
635
+ {
636
+ action = TGZ_LIST;
637
+ if (argc == ++arg)
638
+ help(0);
639
+ }
640
+ else if (strcmp(argv[arg],"-h") == 0)
641
+ {
642
+ help(0);
643
+ }
644
+
645
+ if ((TGZfile = TGZfname(argv[arg])) == NULL)
646
+ TGZnotfound(argv[arg]);
647
+
648
+ ++arg;
649
+ if ((action == TGZ_LIST) && (arg != argc))
650
+ help(1);
651
+
652
+ /*
653
+ * Process the TGZ file
654
+ */
655
+ switch(action)
656
+ {
657
+ case TGZ_LIST:
658
+ case TGZ_EXTRACT:
659
+ f = gzopen(TGZfile,"rb");
660
+ if (f == NULL)
661
+ {
662
+ fprintf(stderr,"%s: Couldn't gzopen %s\n",prog,TGZfile);
663
+ return 1;
664
+ }
665
+ exit(tar(f, action, arg, argc, argv));
666
+ break;
667
+
668
+ default:
669
+ error("Unknown option");
670
+ exit(1);
671
+ }
672
+
673
+ return 0;
674
+ }