finishm 0.0.1

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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
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  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
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  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
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  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
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  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
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  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
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@@ -0,0 +1,420 @@
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+ /*
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+ minizip.c
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+ Version 1.01e, February 12th, 2005
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+
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+ Copyright (C) 1998-2005 Gilles Vollant
6
+ */
7
+
8
+ #include <stdio.h>
9
+ #include <stdlib.h>
10
+ #include <string.h>
11
+ #include <time.h>
12
+ #include <errno.h>
13
+ #include <fcntl.h>
14
+
15
+ #ifdef unix
16
+ # include <unistd.h>
17
+ # include <utime.h>
18
+ # include <sys/types.h>
19
+ # include <sys/stat.h>
20
+ #else
21
+ # include <direct.h>
22
+ # include <io.h>
23
+ #endif
24
+
25
+ #include "zip.h"
26
+
27
+ #ifdef WIN32
28
+ #define USEWIN32IOAPI
29
+ #include "iowin32.h"
30
+ #endif
31
+
32
+
33
+
34
+ #define WRITEBUFFERSIZE (16384)
35
+ #define MAXFILENAME (256)
36
+
37
+ #ifdef WIN32
38
+ uLong filetime(f, tmzip, dt)
39
+ char *f; /* name of file to get info on */
40
+ tm_zip *tmzip; /* return value: access, modific. and creation times */
41
+ uLong *dt; /* dostime */
42
+ {
43
+ int ret = 0;
44
+ {
45
+ FILETIME ftLocal;
46
+ HANDLE hFind;
47
+ WIN32_FIND_DATA ff32;
48
+
49
+ hFind = FindFirstFile(f,&ff32);
50
+ if (hFind != INVALID_HANDLE_VALUE)
51
+ {
52
+ FileTimeToLocalFileTime(&(ff32.ftLastWriteTime),&ftLocal);
53
+ FileTimeToDosDateTime(&ftLocal,((LPWORD)dt)+1,((LPWORD)dt)+0);
54
+ FindClose(hFind);
55
+ ret = 1;
56
+ }
57
+ }
58
+ return ret;
59
+ }
60
+ #else
61
+ #ifdef unix
62
+ uLong filetime(f, tmzip, dt)
63
+ char *f; /* name of file to get info on */
64
+ tm_zip *tmzip; /* return value: access, modific. and creation times */
65
+ uLong *dt; /* dostime */
66
+ {
67
+ int ret=0;
68
+ struct stat s; /* results of stat() */
69
+ struct tm* filedate;
70
+ time_t tm_t=0;
71
+
72
+ if (strcmp(f,"-")!=0)
73
+ {
74
+ char name[MAXFILENAME+1];
75
+ int len = strlen(f);
76
+ if (len > MAXFILENAME)
77
+ len = MAXFILENAME;
78
+
79
+ strncpy(name, f,MAXFILENAME-1);
80
+ /* strncpy doesnt append the trailing NULL, of the string is too long. */
81
+ name[ MAXFILENAME ] = '\0';
82
+
83
+ if (name[len - 1] == '/')
84
+ name[len - 1] = '\0';
85
+ /* not all systems allow stat'ing a file with / appended */
86
+ if (stat(name,&s)==0)
87
+ {
88
+ tm_t = s.st_mtime;
89
+ ret = 1;
90
+ }
91
+ }
92
+ filedate = localtime(&tm_t);
93
+
94
+ tmzip->tm_sec = filedate->tm_sec;
95
+ tmzip->tm_min = filedate->tm_min;
96
+ tmzip->tm_hour = filedate->tm_hour;
97
+ tmzip->tm_mday = filedate->tm_mday;
98
+ tmzip->tm_mon = filedate->tm_mon ;
99
+ tmzip->tm_year = filedate->tm_year;
100
+
101
+ return ret;
102
+ }
103
+ #else
104
+ uLong filetime(f, tmzip, dt)
105
+ char *f; /* name of file to get info on */
106
+ tm_zip *tmzip; /* return value: access, modific. and creation times */
107
+ uLong *dt; /* dostime */
108
+ {
109
+ return 0;
110
+ }
111
+ #endif
112
+ #endif
113
+
114
+
115
+
116
+
117
+ int check_exist_file(filename)
118
+ const char* filename;
119
+ {
120
+ FILE* ftestexist;
121
+ int ret = 1;
122
+ ftestexist = fopen(filename,"rb");
123
+ if (ftestexist==NULL)
124
+ ret = 0;
125
+ else
126
+ fclose(ftestexist);
127
+ return ret;
128
+ }
129
+
130
+ void do_banner()
131
+ {
132
+ printf("MiniZip 1.01b, demo of zLib + Zip package written by Gilles Vollant\n");
133
+ printf("more info at http://www.winimage.com/zLibDll/unzip.html\n\n");
134
+ }
135
+
136
+ void do_help()
137
+ {
138
+ printf("Usage : minizip [-o] [-a] [-0 to -9] [-p password] file.zip [files_to_add]\n\n" \
139
+ " -o Overwrite existing file.zip\n" \
140
+ " -a Append to existing file.zip\n" \
141
+ " -0 Store only\n" \
142
+ " -1 Compress faster\n" \
143
+ " -9 Compress better\n\n");
144
+ }
145
+
146
+ /* calculate the CRC32 of a file,
147
+ because to encrypt a file, we need known the CRC32 of the file before */
148
+ int getFileCrc(const char* filenameinzip,void*buf,unsigned long size_buf,unsigned long* result_crc)
149
+ {
150
+ unsigned long calculate_crc=0;
151
+ int err=ZIP_OK;
152
+ FILE * fin = fopen(filenameinzip,"rb");
153
+ unsigned long size_read = 0;
154
+ unsigned long total_read = 0;
155
+ if (fin==NULL)
156
+ {
157
+ err = ZIP_ERRNO;
158
+ }
159
+
160
+ if (err == ZIP_OK)
161
+ do
162
+ {
163
+ err = ZIP_OK;
164
+ size_read = (int)fread(buf,1,size_buf,fin);
165
+ if (size_read < size_buf)
166
+ if (feof(fin)==0)
167
+ {
168
+ printf("error in reading %s\n",filenameinzip);
169
+ err = ZIP_ERRNO;
170
+ }
171
+
172
+ if (size_read>0)
173
+ calculate_crc = crc32(calculate_crc,buf,size_read);
174
+ total_read += size_read;
175
+
176
+ } while ((err == ZIP_OK) && (size_read>0));
177
+
178
+ if (fin)
179
+ fclose(fin);
180
+
181
+ *result_crc=calculate_crc;
182
+ printf("file %s crc %x\n",filenameinzip,calculate_crc);
183
+ return err;
184
+ }
185
+
186
+ int main(argc,argv)
187
+ int argc;
188
+ char *argv[];
189
+ {
190
+ int i;
191
+ int opt_overwrite=0;
192
+ int opt_compress_level=Z_DEFAULT_COMPRESSION;
193
+ int zipfilenamearg = 0;
194
+ char filename_try[MAXFILENAME+16];
195
+ int zipok;
196
+ int err=0;
197
+ int size_buf=0;
198
+ void* buf=NULL;
199
+ const char* password=NULL;
200
+
201
+
202
+ do_banner();
203
+ if (argc==1)
204
+ {
205
+ do_help();
206
+ return 0;
207
+ }
208
+ else
209
+ {
210
+ for (i=1;i<argc;i++)
211
+ {
212
+ if ((*argv[i])=='-')
213
+ {
214
+ const char *p=argv[i]+1;
215
+
216
+ while ((*p)!='\0')
217
+ {
218
+ char c=*(p++);;
219
+ if ((c=='o') || (c=='O'))
220
+ opt_overwrite = 1;
221
+ if ((c=='a') || (c=='A'))
222
+ opt_overwrite = 2;
223
+ if ((c>='0') && (c<='9'))
224
+ opt_compress_level = c-'0';
225
+
226
+ if (((c=='p') || (c=='P')) && (i+1<argc))
227
+ {
228
+ password=argv[i+1];
229
+ i++;
230
+ }
231
+ }
232
+ }
233
+ else
234
+ if (zipfilenamearg == 0)
235
+ zipfilenamearg = i ;
236
+ }
237
+ }
238
+
239
+ size_buf = WRITEBUFFERSIZE;
240
+ buf = (void*)malloc(size_buf);
241
+ if (buf==NULL)
242
+ {
243
+ printf("Error allocating memory\n");
244
+ return ZIP_INTERNALERROR;
245
+ }
246
+
247
+ if (zipfilenamearg==0)
248
+ zipok=0;
249
+ else
250
+ {
251
+ int i,len;
252
+ int dot_found=0;
253
+
254
+ zipok = 1 ;
255
+ strncpy(filename_try, argv[zipfilenamearg],MAXFILENAME-1);
256
+ /* strncpy doesnt append the trailing NULL, of the string is too long. */
257
+ filename_try[ MAXFILENAME ] = '\0';
258
+
259
+ len=(int)strlen(filename_try);
260
+ for (i=0;i<len;i++)
261
+ if (filename_try[i]=='.')
262
+ dot_found=1;
263
+
264
+ if (dot_found==0)
265
+ strcat(filename_try,".zip");
266
+
267
+ if (opt_overwrite==2)
268
+ {
269
+ /* if the file don't exist, we not append file */
270
+ if (check_exist_file(filename_try)==0)
271
+ opt_overwrite=1;
272
+ }
273
+ else
274
+ if (opt_overwrite==0)
275
+ if (check_exist_file(filename_try)!=0)
276
+ {
277
+ char rep=0;
278
+ do
279
+ {
280
+ char answer[128];
281
+ int ret;
282
+ printf("The file %s exists. Overwrite ? [y]es, [n]o, [a]ppend : ",filename_try);
283
+ ret = scanf("%1s",answer);
284
+ if (ret != 1)
285
+ {
286
+ exit(EXIT_FAILURE);
287
+ }
288
+ rep = answer[0] ;
289
+ if ((rep>='a') && (rep<='z'))
290
+ rep -= 0x20;
291
+ }
292
+ while ((rep!='Y') && (rep!='N') && (rep!='A'));
293
+ if (rep=='N')
294
+ zipok = 0;
295
+ if (rep=='A')
296
+ opt_overwrite = 2;
297
+ }
298
+ }
299
+
300
+ if (zipok==1)
301
+ {
302
+ zipFile zf;
303
+ int errclose;
304
+ # ifdef USEWIN32IOAPI
305
+ zlib_filefunc_def ffunc;
306
+ fill_win32_filefunc(&ffunc);
307
+ zf = zipOpen2(filename_try,(opt_overwrite==2) ? 2 : 0,NULL,&ffunc);
308
+ # else
309
+ zf = zipOpen(filename_try,(opt_overwrite==2) ? 2 : 0);
310
+ # endif
311
+
312
+ if (zf == NULL)
313
+ {
314
+ printf("error opening %s\n",filename_try);
315
+ err= ZIP_ERRNO;
316
+ }
317
+ else
318
+ printf("creating %s\n",filename_try);
319
+
320
+ for (i=zipfilenamearg+1;(i<argc) && (err==ZIP_OK);i++)
321
+ {
322
+ if (!((((*(argv[i]))=='-') || ((*(argv[i]))=='/')) &&
323
+ ((argv[i][1]=='o') || (argv[i][1]=='O') ||
324
+ (argv[i][1]=='a') || (argv[i][1]=='A') ||
325
+ (argv[i][1]=='p') || (argv[i][1]=='P') ||
326
+ ((argv[i][1]>='0') || (argv[i][1]<='9'))) &&
327
+ (strlen(argv[i]) == 2)))
328
+ {
329
+ FILE * fin;
330
+ int size_read;
331
+ const char* filenameinzip = argv[i];
332
+ zip_fileinfo zi;
333
+ unsigned long crcFile=0;
334
+
335
+ zi.tmz_date.tm_sec = zi.tmz_date.tm_min = zi.tmz_date.tm_hour =
336
+ zi.tmz_date.tm_mday = zi.tmz_date.tm_mon = zi.tmz_date.tm_year = 0;
337
+ zi.dosDate = 0;
338
+ zi.internal_fa = 0;
339
+ zi.external_fa = 0;
340
+ filetime(filenameinzip,&zi.tmz_date,&zi.dosDate);
341
+
342
+ /*
343
+ err = zipOpenNewFileInZip(zf,filenameinzip,&zi,
344
+ NULL,0,NULL,0,NULL / * comment * /,
345
+ (opt_compress_level != 0) ? Z_DEFLATED : 0,
346
+ opt_compress_level);
347
+ */
348
+ if ((password != NULL) && (err==ZIP_OK))
349
+ err = getFileCrc(filenameinzip,buf,size_buf,&crcFile);
350
+
351
+ err = zipOpenNewFileInZip3(zf,filenameinzip,&zi,
352
+ NULL,0,NULL,0,NULL /* comment*/,
353
+ (opt_compress_level != 0) ? Z_DEFLATED : 0,
354
+ opt_compress_level,0,
355
+ /* -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY, */
356
+ -MAX_WBITS, DEF_MEM_LEVEL, Z_DEFAULT_STRATEGY,
357
+ password,crcFile);
358
+
359
+ if (err != ZIP_OK)
360
+ printf("error in opening %s in zipfile\n",filenameinzip);
361
+ else
362
+ {
363
+ fin = fopen(filenameinzip,"rb");
364
+ if (fin==NULL)
365
+ {
366
+ err=ZIP_ERRNO;
367
+ printf("error in opening %s for reading\n",filenameinzip);
368
+ }
369
+ }
370
+
371
+ if (err == ZIP_OK)
372
+ do
373
+ {
374
+ err = ZIP_OK;
375
+ size_read = (int)fread(buf,1,size_buf,fin);
376
+ if (size_read < size_buf)
377
+ if (feof(fin)==0)
378
+ {
379
+ printf("error in reading %s\n",filenameinzip);
380
+ err = ZIP_ERRNO;
381
+ }
382
+
383
+ if (size_read>0)
384
+ {
385
+ err = zipWriteInFileInZip (zf,buf,size_read);
386
+ if (err<0)
387
+ {
388
+ printf("error in writing %s in the zipfile\n",
389
+ filenameinzip);
390
+ }
391
+
392
+ }
393
+ } while ((err == ZIP_OK) && (size_read>0));
394
+
395
+ if (fin)
396
+ fclose(fin);
397
+
398
+ if (err<0)
399
+ err=ZIP_ERRNO;
400
+ else
401
+ {
402
+ err = zipCloseFileInZip(zf);
403
+ if (err!=ZIP_OK)
404
+ printf("error in closing %s in the zipfile\n",
405
+ filenameinzip);
406
+ }
407
+ }
408
+ }
409
+ errclose = zipClose(zf,NULL);
410
+ if (errclose != ZIP_OK)
411
+ printf("error in closing %s\n",filename_try);
412
+ }
413
+ else
414
+ {
415
+ do_help();
416
+ }
417
+
418
+ free(buf);
419
+ return 0;
420
+ }
@@ -0,0 +1,281 @@
1
+ /*
2
+ Additional tools for Minizip
3
+ Code: Xavier Roche '2004
4
+ License: Same as ZLIB (www.gzip.org)
5
+ */
6
+
7
+ /* Code */
8
+ #include <stdio.h>
9
+ #include <stdlib.h>
10
+ #include <string.h>
11
+ #include "zlib.h"
12
+ #include "unzip.h"
13
+
14
+ #define READ_8(adr) ((unsigned char)*(adr))
15
+ #define READ_16(adr) ( READ_8(adr) | (READ_8(adr+1) << 8) )
16
+ #define READ_32(adr) ( READ_16(adr) | (READ_16((adr)+2) << 16) )
17
+
18
+ #define WRITE_8(buff, n) do { \
19
+ *((unsigned char*)(buff)) = (unsigned char) ((n) & 0xff); \
20
+ } while(0)
21
+ #define WRITE_16(buff, n) do { \
22
+ WRITE_8((unsigned char*)(buff), n); \
23
+ WRITE_8(((unsigned char*)(buff)) + 1, (n) >> 8); \
24
+ } while(0)
25
+ #define WRITE_32(buff, n) do { \
26
+ WRITE_16((unsigned char*)(buff), (n) & 0xffff); \
27
+ WRITE_16((unsigned char*)(buff) + 2, (n) >> 16); \
28
+ } while(0)
29
+
30
+ extern int ZEXPORT unzRepair(file, fileOut, fileOutTmp, nRecovered, bytesRecovered)
31
+ const char* file;
32
+ const char* fileOut;
33
+ const char* fileOutTmp;
34
+ uLong* nRecovered;
35
+ uLong* bytesRecovered;
36
+ {
37
+ int err = Z_OK;
38
+ FILE* fpZip = fopen(file, "rb");
39
+ FILE* fpOut = fopen(fileOut, "wb");
40
+ FILE* fpOutCD = fopen(fileOutTmp, "wb");
41
+ if (fpZip != NULL && fpOut != NULL) {
42
+ int entries = 0;
43
+ uLong totalBytes = 0;
44
+ char header[30];
45
+ char filename[256];
46
+ char extra[1024];
47
+ int offset = 0;
48
+ int offsetCD = 0;
49
+ while ( fread(header, 1, 30, fpZip) == 30 ) {
50
+ int currentOffset = offset;
51
+
52
+ /* File entry */
53
+ if (READ_32(header) == 0x04034b50) {
54
+ unsigned int version = READ_16(header + 4);
55
+ unsigned int gpflag = READ_16(header + 6);
56
+ unsigned int method = READ_16(header + 8);
57
+ unsigned int filetime = READ_16(header + 10);
58
+ unsigned int filedate = READ_16(header + 12);
59
+ unsigned int crc = READ_32(header + 14); /* crc */
60
+ unsigned int cpsize = READ_32(header + 18); /* compressed size */
61
+ unsigned int uncpsize = READ_32(header + 22); /* uncompressed sz */
62
+ unsigned int fnsize = READ_16(header + 26); /* file name length */
63
+ unsigned int extsize = READ_16(header + 28); /* extra field length */
64
+ filename[0] = extra[0] = '\0';
65
+
66
+ /* Header */
67
+ if (fwrite(header, 1, 30, fpOut) == 30) {
68
+ offset += 30;
69
+ } else {
70
+ err = Z_ERRNO;
71
+ break;
72
+ }
73
+
74
+ /* Filename */
75
+ if (fnsize > 0) {
76
+ if (fread(filename, 1, fnsize, fpZip) == fnsize) {
77
+ if (fwrite(filename, 1, fnsize, fpOut) == fnsize) {
78
+ offset += fnsize;
79
+ } else {
80
+ err = Z_ERRNO;
81
+ break;
82
+ }
83
+ } else {
84
+ err = Z_ERRNO;
85
+ break;
86
+ }
87
+ } else {
88
+ err = Z_STREAM_ERROR;
89
+ break;
90
+ }
91
+
92
+ /* Extra field */
93
+ if (extsize > 0) {
94
+ if (fread(extra, 1, extsize, fpZip) == extsize) {
95
+ if (fwrite(extra, 1, extsize, fpOut) == extsize) {
96
+ offset += extsize;
97
+ } else {
98
+ err = Z_ERRNO;
99
+ break;
100
+ }
101
+ } else {
102
+ err = Z_ERRNO;
103
+ break;
104
+ }
105
+ }
106
+
107
+ /* Data */
108
+ {
109
+ int dataSize = cpsize;
110
+ if (dataSize == 0) {
111
+ dataSize = uncpsize;
112
+ }
113
+ if (dataSize > 0) {
114
+ char* data = malloc(dataSize);
115
+ if (data != NULL) {
116
+ if ((int)fread(data, 1, dataSize, fpZip) == dataSize) {
117
+ if ((int)fwrite(data, 1, dataSize, fpOut) == dataSize) {
118
+ offset += dataSize;
119
+ totalBytes += dataSize;
120
+ } else {
121
+ err = Z_ERRNO;
122
+ }
123
+ } else {
124
+ err = Z_ERRNO;
125
+ }
126
+ free(data);
127
+ if (err != Z_OK) {
128
+ break;
129
+ }
130
+ } else {
131
+ err = Z_MEM_ERROR;
132
+ break;
133
+ }
134
+ }
135
+ }
136
+
137
+ /* Central directory entry */
138
+ {
139
+ char header[46];
140
+ char* comment = "";
141
+ int comsize = (int) strlen(comment);
142
+ WRITE_32(header, 0x02014b50);
143
+ WRITE_16(header + 4, version);
144
+ WRITE_16(header + 6, version);
145
+ WRITE_16(header + 8, gpflag);
146
+ WRITE_16(header + 10, method);
147
+ WRITE_16(header + 12, filetime);
148
+ WRITE_16(header + 14, filedate);
149
+ WRITE_32(header + 16, crc);
150
+ WRITE_32(header + 20, cpsize);
151
+ WRITE_32(header + 24, uncpsize);
152
+ WRITE_16(header + 28, fnsize);
153
+ WRITE_16(header + 30, extsize);
154
+ WRITE_16(header + 32, comsize);
155
+ WRITE_16(header + 34, 0); /* disk # */
156
+ WRITE_16(header + 36, 0); /* int attrb */
157
+ WRITE_32(header + 38, 0); /* ext attrb */
158
+ WRITE_32(header + 42, currentOffset);
159
+ /* Header */
160
+ if (fwrite(header, 1, 46, fpOutCD) == 46) {
161
+ offsetCD += 46;
162
+
163
+ /* Filename */
164
+ if (fnsize > 0) {
165
+ if (fwrite(filename, 1, fnsize, fpOutCD) == fnsize) {
166
+ offsetCD += fnsize;
167
+ } else {
168
+ err = Z_ERRNO;
169
+ break;
170
+ }
171
+ } else {
172
+ err = Z_STREAM_ERROR;
173
+ break;
174
+ }
175
+
176
+ /* Extra field */
177
+ if (extsize > 0) {
178
+ if (fwrite(extra, 1, extsize, fpOutCD) == extsize) {
179
+ offsetCD += extsize;
180
+ } else {
181
+ err = Z_ERRNO;
182
+ break;
183
+ }
184
+ }
185
+
186
+ /* Comment field */
187
+ if (comsize > 0) {
188
+ if ((int)fwrite(comment, 1, comsize, fpOutCD) == comsize) {
189
+ offsetCD += comsize;
190
+ } else {
191
+ err = Z_ERRNO;
192
+ break;
193
+ }
194
+ }
195
+
196
+
197
+ } else {
198
+ err = Z_ERRNO;
199
+ break;
200
+ }
201
+ }
202
+
203
+ /* Success */
204
+ entries++;
205
+
206
+ } else {
207
+ break;
208
+ }
209
+ }
210
+
211
+ /* Final central directory */
212
+ {
213
+ int entriesZip = entries;
214
+ char header[22];
215
+ char* comment = ""; // "ZIP File recovered by zlib/minizip/mztools";
216
+ int comsize = (int) strlen(comment);
217
+ if (entriesZip > 0xffff) {
218
+ entriesZip = 0xffff;
219
+ }
220
+ WRITE_32(header, 0x06054b50);
221
+ WRITE_16(header + 4, 0); /* disk # */
222
+ WRITE_16(header + 6, 0); /* disk # */
223
+ WRITE_16(header + 8, entriesZip); /* hack */
224
+ WRITE_16(header + 10, entriesZip); /* hack */
225
+ WRITE_32(header + 12, offsetCD); /* size of CD */
226
+ WRITE_32(header + 16, offset); /* offset to CD */
227
+ WRITE_16(header + 20, comsize); /* comment */
228
+
229
+ /* Header */
230
+ if (fwrite(header, 1, 22, fpOutCD) == 22) {
231
+
232
+ /* Comment field */
233
+ if (comsize > 0) {
234
+ if ((int)fwrite(comment, 1, comsize, fpOutCD) != comsize) {
235
+ err = Z_ERRNO;
236
+ }
237
+ }
238
+
239
+ } else {
240
+ err = Z_ERRNO;
241
+ }
242
+ }
243
+
244
+ /* Final merge (file + central directory) */
245
+ fclose(fpOutCD);
246
+ if (err == Z_OK) {
247
+ fpOutCD = fopen(fileOutTmp, "rb");
248
+ if (fpOutCD != NULL) {
249
+ int nRead;
250
+ char buffer[8192];
251
+ while ( (nRead = (int)fread(buffer, 1, sizeof(buffer), fpOutCD)) > 0) {
252
+ if ((int)fwrite(buffer, 1, nRead, fpOut) != nRead) {
253
+ err = Z_ERRNO;
254
+ break;
255
+ }
256
+ }
257
+ fclose(fpOutCD);
258
+ }
259
+ }
260
+
261
+ /* Close */
262
+ fclose(fpZip);
263
+ fclose(fpOut);
264
+
265
+ /* Wipe temporary file */
266
+ (void)remove(fileOutTmp);
267
+
268
+ /* Number of recovered entries */
269
+ if (err == Z_OK) {
270
+ if (nRecovered != NULL) {
271
+ *nRecovered = entries;
272
+ }
273
+ if (bytesRecovered != NULL) {
274
+ *bytesRecovered = totalBytes;
275
+ }
276
+ }
277
+ } else {
278
+ err = Z_STREAM_ERROR;
279
+ }
280
+ return err;
281
+ }