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 +1,3 @@
1
+ cl /DASMV /I..\.. /O2 /c gvmat32c.c
2
+ ml /coff /Zi /c /Flgvmat32.lst gvmat32.asm
3
+ ml /coff /Zi /c /Flinffas32.lst inffas32.asm
@@ -0,0 +1,21 @@
1
+
2
+ Summary
3
+ -------
4
+ This directory contains ASM implementations of the functions
5
+ longest_match() and inflate_fast().
6
+
7
+
8
+ Use instructions
9
+ ----------------
10
+ Copy these files into the zlib source directory, then run the
11
+ appropriate makefile, as suggested below.
12
+
13
+
14
+ Build instructions
15
+ ------------------
16
+ * With Microsoft C and MASM:
17
+ nmake -f win32/Makefile.msc LOC="-DASMV -DASMINF" OBJA="gvmat32c.obj gvmat32.obj inffas32.obj"
18
+
19
+ * With Borland C and TASM:
20
+ make -f win32/Makefile.bor LOCAL_ZLIB="-DASMV -DASMINF" OBJA="gvmat32c.obj gvmat32.obj inffas32.obj" OBJPA="+gvmat32c.obj+gvmat32.obj+inffas32.obj"
21
+
@@ -0,0 +1,67 @@
1
+ Change in 1.01e (12 feb 05)
2
+ - Fix in zipOpen2 for globalcomment (Rolf Kalbermatter)
3
+ - Fix possible memory leak in unzip.c (Zoran Stevanovic)
4
+
5
+ Change in 1.01b (20 may 04)
6
+ - Integrate patch from Debian package (submited by Mark Brown)
7
+ - Add tools mztools from Xavier Roche
8
+
9
+ Change in 1.01 (8 may 04)
10
+ - fix buffer overrun risk in unzip.c (Xavier Roche)
11
+ - fix a minor buffer insecurity in minizip.c (Mike Whittaker)
12
+
13
+ Change in 1.00: (10 sept 03)
14
+ - rename to 1.00
15
+ - cosmetic code change
16
+
17
+ Change in 0.22: (19 May 03)
18
+ - crypting support (unless you define NOCRYPT)
19
+ - append file in existing zipfile
20
+
21
+ Change in 0.21: (10 Mar 03)
22
+ - bug fixes
23
+
24
+ Change in 0.17: (27 Jan 02)
25
+ - bug fixes
26
+
27
+ Change in 0.16: (19 Jan 02)
28
+ - Support of ioapi for virtualize zip file access
29
+
30
+ Change in 0.15: (19 Mar 98)
31
+ - fix memory leak in minizip.c
32
+
33
+ Change in 0.14: (10 Mar 98)
34
+ - fix bugs in minizip.c sample for zipping big file
35
+ - fix problem in month in date handling
36
+ - fix bug in unzlocal_GetCurrentFileInfoInternal in unzip.c for
37
+ comment handling
38
+
39
+ Change in 0.13: (6 Mar 98)
40
+ - fix bugs in zip.c
41
+ - add real minizip sample
42
+
43
+ Change in 0.12: (4 Mar 98)
44
+ - add zip.c and zip.h for creates .zip file
45
+ - fix change_file_date in miniunz.c for Unix (Jean-loup Gailly)
46
+ - fix miniunz.c for file without specific record for directory
47
+
48
+ Change in 0.11: (3 Mar 98)
49
+ - fix bug in unzGetCurrentFileInfo for get extra field and comment
50
+ - enhance miniunz sample, remove the bad unztst.c sample
51
+
52
+ Change in 0.10: (2 Mar 98)
53
+ - fix bug in unzReadCurrentFile
54
+ - rename unzip* to unz* function and structure
55
+ - remove Windows-like hungary notation variable name
56
+ - modify some structure in unzip.h
57
+ - add somes comment in source
58
+ - remove unzipGetcCurrentFile function
59
+ - replace ZUNZEXPORT by ZEXPORT
60
+ - add unzGetLocalExtrafield for get the local extrafield info
61
+ - add a new sample, miniunz.c
62
+
63
+ Change in 0.4: (25 Feb 98)
64
+ - suppress the type unzipFileInZip.
65
+ Only on file in the zipfile can be open at the same time
66
+ - fix somes typo in code
67
+ - added tm_unz structure in unzip_file_info (date/time in readable format)
@@ -0,0 +1,25 @@
1
+ CC=cc
2
+ CFLAGS=-O -I../..
3
+
4
+ UNZ_OBJS = miniunz.o unzip.o ioapi.o ../../libz.a
5
+ ZIP_OBJS = minizip.o zip.o ioapi.o ../../libz.a
6
+
7
+ .c.o:
8
+ $(CC) -c $(CFLAGS) $*.c
9
+
10
+ all: miniunz minizip
11
+
12
+ miniunz: $(UNZ_OBJS)
13
+ $(CC) $(CFLAGS) -o $@ $(UNZ_OBJS)
14
+
15
+ minizip: $(ZIP_OBJS)
16
+ $(CC) $(CFLAGS) -o $@ $(ZIP_OBJS)
17
+
18
+ test: miniunz minizip
19
+ ./minizip test readme.txt
20
+ ./miniunz -l test.zip
21
+ mv readme.txt readme.old
22
+ ./miniunz test.zip
23
+
24
+ clean:
25
+ /bin/rm -f *.o *~ minizip miniunz
@@ -0,0 +1,132 @@
1
+ /* crypt.h -- base code for crypt/uncrypt ZIPfile
2
+
3
+
4
+ Version 1.01e, February 12th, 2005
5
+
6
+ Copyright (C) 1998-2005 Gilles Vollant
7
+
8
+ This code is a modified version of crypting code in Infozip distribution
9
+
10
+ The encryption/decryption parts of this source code (as opposed to the
11
+ non-echoing password parts) were originally written in Europe. The
12
+ whole source package can be freely distributed, including from the USA.
13
+ (Prior to January 2000, re-export from the US was a violation of US law.)
14
+
15
+ This encryption code is a direct transcription of the algorithm from
16
+ Roger Schlafly, described by Phil Katz in the file appnote.txt. This
17
+ file (appnote.txt) is distributed with the PKZIP program (even in the
18
+ version without encryption capabilities).
19
+
20
+ If you don't need crypting in your application, just define symbols
21
+ NOCRYPT and NOUNCRYPT.
22
+
23
+ This code support the "Traditional PKWARE Encryption".
24
+
25
+ The new AES encryption added on Zip format by Winzip (see the page
26
+ http://www.winzip.com/aes_info.htm ) and PKWare PKZip 5.x Strong
27
+ Encryption is not supported.
28
+ */
29
+
30
+ #define CRC32(c, b) ((*(pcrc_32_tab+(((int)(c) ^ (b)) & 0xff))) ^ ((c) >> 8))
31
+
32
+ /***********************************************************************
33
+ * Return the next byte in the pseudo-random sequence
34
+ */
35
+ static int decrypt_byte(unsigned long* pkeys, const unsigned long* pcrc_32_tab)
36
+ {
37
+ unsigned temp; /* POTENTIAL BUG: temp*(temp^1) may overflow in an
38
+ * unpredictable manner on 16-bit systems; not a problem
39
+ * with any known compiler so far, though */
40
+
41
+ temp = ((unsigned)(*(pkeys+2)) & 0xffff) | 2;
42
+ return (int)(((temp * (temp ^ 1)) >> 8) & 0xff);
43
+ }
44
+
45
+ /***********************************************************************
46
+ * Update the encryption keys with the next byte of plain text
47
+ */
48
+ static int update_keys(unsigned long* pkeys,const unsigned long* pcrc_32_tab,int c)
49
+ {
50
+ (*(pkeys+0)) = CRC32((*(pkeys+0)), c);
51
+ (*(pkeys+1)) += (*(pkeys+0)) & 0xff;
52
+ (*(pkeys+1)) = (*(pkeys+1)) * 134775813L + 1;
53
+ {
54
+ register int keyshift = (int)((*(pkeys+1)) >> 24);
55
+ (*(pkeys+2)) = CRC32((*(pkeys+2)), keyshift);
56
+ }
57
+ return c;
58
+ }
59
+
60
+
61
+ /***********************************************************************
62
+ * Initialize the encryption keys and the random header according to
63
+ * the given password.
64
+ */
65
+ static void init_keys(const char* passwd,unsigned long* pkeys,const unsigned long* pcrc_32_tab)
66
+ {
67
+ *(pkeys+0) = 305419896L;
68
+ *(pkeys+1) = 591751049L;
69
+ *(pkeys+2) = 878082192L;
70
+ while (*passwd != '\0') {
71
+ update_keys(pkeys,pcrc_32_tab,(int)*passwd);
72
+ passwd++;
73
+ }
74
+ }
75
+
76
+ #define zdecode(pkeys,pcrc_32_tab,c) \
77
+ (update_keys(pkeys,pcrc_32_tab,c ^= decrypt_byte(pkeys,pcrc_32_tab)))
78
+
79
+ #define zencode(pkeys,pcrc_32_tab,c,t) \
80
+ (t=decrypt_byte(pkeys,pcrc_32_tab), update_keys(pkeys,pcrc_32_tab,c), t^(c))
81
+
82
+ #ifdef INCLUDECRYPTINGCODE_IFCRYPTALLOWED
83
+
84
+ #define RAND_HEAD_LEN 12
85
+ /* "last resort" source for second part of crypt seed pattern */
86
+ # ifndef ZCR_SEED2
87
+ # define ZCR_SEED2 3141592654UL /* use PI as default pattern */
88
+ # endif
89
+
90
+ static int crypthead(passwd, buf, bufSize, pkeys, pcrc_32_tab, crcForCrypting)
91
+ const char *passwd; /* password string */
92
+ unsigned char *buf; /* where to write header */
93
+ int bufSize;
94
+ unsigned long* pkeys;
95
+ const unsigned long* pcrc_32_tab;
96
+ unsigned long crcForCrypting;
97
+ {
98
+ int n; /* index in random header */
99
+ int t; /* temporary */
100
+ int c; /* random byte */
101
+ unsigned char header[RAND_HEAD_LEN-2]; /* random header */
102
+ static unsigned calls = 0; /* ensure different random header each time */
103
+
104
+ if (bufSize<RAND_HEAD_LEN)
105
+ return 0;
106
+
107
+ /* First generate RAND_HEAD_LEN-2 random bytes. We encrypt the
108
+ * output of rand() to get less predictability, since rand() is
109
+ * often poorly implemented.
110
+ */
111
+ if (++calls == 1)
112
+ {
113
+ srand((unsigned)(time(NULL) ^ ZCR_SEED2));
114
+ }
115
+ init_keys(passwd, pkeys, pcrc_32_tab);
116
+ for (n = 0; n < RAND_HEAD_LEN-2; n++)
117
+ {
118
+ c = (rand() >> 7) & 0xff;
119
+ header[n] = (unsigned char)zencode(pkeys, pcrc_32_tab, c, t);
120
+ }
121
+ /* Encrypt random header (last two bytes is high word of crc) */
122
+ init_keys(passwd, pkeys, pcrc_32_tab);
123
+ for (n = 0; n < RAND_HEAD_LEN-2; n++)
124
+ {
125
+ buf[n] = (unsigned char)zencode(pkeys, pcrc_32_tab, header[n], t);
126
+ }
127
+ buf[n++] = zencode(pkeys, pcrc_32_tab, (int)(crcForCrypting >> 16) & 0xff, t);
128
+ buf[n++] = zencode(pkeys, pcrc_32_tab, (int)(crcForCrypting >> 24) & 0xff, t);
129
+ return n;
130
+ }
131
+
132
+ #endif
@@ -0,0 +1,177 @@
1
+ /* ioapi.c -- IO base function header for compress/uncompress .zip
2
+ files using zlib + zip or unzip API
3
+
4
+ Version 1.01e, February 12th, 2005
5
+
6
+ Copyright (C) 1998-2005 Gilles Vollant
7
+ */
8
+
9
+ #include <stdio.h>
10
+ #include <stdlib.h>
11
+ #include <string.h>
12
+
13
+ #include "zlib.h"
14
+ #include "ioapi.h"
15
+
16
+
17
+
18
+ /* I've found an old Unix (a SunOS 4.1.3_U1) without all SEEK_* defined.... */
19
+
20
+ #ifndef SEEK_CUR
21
+ #define SEEK_CUR 1
22
+ #endif
23
+
24
+ #ifndef SEEK_END
25
+ #define SEEK_END 2
26
+ #endif
27
+
28
+ #ifndef SEEK_SET
29
+ #define SEEK_SET 0
30
+ #endif
31
+
32
+ voidpf ZCALLBACK fopen_file_func OF((
33
+ voidpf opaque,
34
+ const char* filename,
35
+ int mode));
36
+
37
+ uLong ZCALLBACK fread_file_func OF((
38
+ voidpf opaque,
39
+ voidpf stream,
40
+ void* buf,
41
+ uLong size));
42
+
43
+ uLong ZCALLBACK fwrite_file_func OF((
44
+ voidpf opaque,
45
+ voidpf stream,
46
+ const void* buf,
47
+ uLong size));
48
+
49
+ long ZCALLBACK ftell_file_func OF((
50
+ voidpf opaque,
51
+ voidpf stream));
52
+
53
+ long ZCALLBACK fseek_file_func OF((
54
+ voidpf opaque,
55
+ voidpf stream,
56
+ uLong offset,
57
+ int origin));
58
+
59
+ int ZCALLBACK fclose_file_func OF((
60
+ voidpf opaque,
61
+ voidpf stream));
62
+
63
+ int ZCALLBACK ferror_file_func OF((
64
+ voidpf opaque,
65
+ voidpf stream));
66
+
67
+
68
+ voidpf ZCALLBACK fopen_file_func (opaque, filename, mode)
69
+ voidpf opaque;
70
+ const char* filename;
71
+ int mode;
72
+ {
73
+ FILE* file = NULL;
74
+ const char* mode_fopen = NULL;
75
+ if ((mode & ZLIB_FILEFUNC_MODE_READWRITEFILTER)==ZLIB_FILEFUNC_MODE_READ)
76
+ mode_fopen = "rb";
77
+ else
78
+ if (mode & ZLIB_FILEFUNC_MODE_EXISTING)
79
+ mode_fopen = "r+b";
80
+ else
81
+ if (mode & ZLIB_FILEFUNC_MODE_CREATE)
82
+ mode_fopen = "wb";
83
+
84
+ if ((filename!=NULL) && (mode_fopen != NULL))
85
+ file = fopen(filename, mode_fopen);
86
+ return file;
87
+ }
88
+
89
+
90
+ uLong ZCALLBACK fread_file_func (opaque, stream, buf, size)
91
+ voidpf opaque;
92
+ voidpf stream;
93
+ void* buf;
94
+ uLong size;
95
+ {
96
+ uLong ret;
97
+ ret = (uLong)fread(buf, 1, (size_t)size, (FILE *)stream);
98
+ return ret;
99
+ }
100
+
101
+
102
+ uLong ZCALLBACK fwrite_file_func (opaque, stream, buf, size)
103
+ voidpf opaque;
104
+ voidpf stream;
105
+ const void* buf;
106
+ uLong size;
107
+ {
108
+ uLong ret;
109
+ ret = (uLong)fwrite(buf, 1, (size_t)size, (FILE *)stream);
110
+ return ret;
111
+ }
112
+
113
+ long ZCALLBACK ftell_file_func (opaque, stream)
114
+ voidpf opaque;
115
+ voidpf stream;
116
+ {
117
+ long ret;
118
+ ret = ftell((FILE *)stream);
119
+ return ret;
120
+ }
121
+
122
+ long ZCALLBACK fseek_file_func (opaque, stream, offset, origin)
123
+ voidpf opaque;
124
+ voidpf stream;
125
+ uLong offset;
126
+ int origin;
127
+ {
128
+ int fseek_origin=0;
129
+ long ret;
130
+ switch (origin)
131
+ {
132
+ case ZLIB_FILEFUNC_SEEK_CUR :
133
+ fseek_origin = SEEK_CUR;
134
+ break;
135
+ case ZLIB_FILEFUNC_SEEK_END :
136
+ fseek_origin = SEEK_END;
137
+ break;
138
+ case ZLIB_FILEFUNC_SEEK_SET :
139
+ fseek_origin = SEEK_SET;
140
+ break;
141
+ default: return -1;
142
+ }
143
+ ret = 0;
144
+ fseek((FILE *)stream, offset, fseek_origin);
145
+ return ret;
146
+ }
147
+
148
+ int ZCALLBACK fclose_file_func (opaque, stream)
149
+ voidpf opaque;
150
+ voidpf stream;
151
+ {
152
+ int ret;
153
+ ret = fclose((FILE *)stream);
154
+ return ret;
155
+ }
156
+
157
+ int ZCALLBACK ferror_file_func (opaque, stream)
158
+ voidpf opaque;
159
+ voidpf stream;
160
+ {
161
+ int ret;
162
+ ret = ferror((FILE *)stream);
163
+ return ret;
164
+ }
165
+
166
+ void fill_fopen_filefunc (pzlib_filefunc_def)
167
+ zlib_filefunc_def* pzlib_filefunc_def;
168
+ {
169
+ pzlib_filefunc_def->zopen_file = fopen_file_func;
170
+ pzlib_filefunc_def->zread_file = fread_file_func;
171
+ pzlib_filefunc_def->zwrite_file = fwrite_file_func;
172
+ pzlib_filefunc_def->ztell_file = ftell_file_func;
173
+ pzlib_filefunc_def->zseek_file = fseek_file_func;
174
+ pzlib_filefunc_def->zclose_file = fclose_file_func;
175
+ pzlib_filefunc_def->zerror_file = ferror_file_func;
176
+ pzlib_filefunc_def->opaque = NULL;
177
+ }
@@ -0,0 +1,75 @@
1
+ /* ioapi.h -- IO base function header for compress/uncompress .zip
2
+ files using zlib + zip or unzip API
3
+
4
+ Version 1.01e, February 12th, 2005
5
+
6
+ Copyright (C) 1998-2005 Gilles Vollant
7
+ */
8
+
9
+ #ifndef _ZLIBIOAPI_H
10
+ #define _ZLIBIOAPI_H
11
+
12
+
13
+ #define ZLIB_FILEFUNC_SEEK_CUR (1)
14
+ #define ZLIB_FILEFUNC_SEEK_END (2)
15
+ #define ZLIB_FILEFUNC_SEEK_SET (0)
16
+
17
+ #define ZLIB_FILEFUNC_MODE_READ (1)
18
+ #define ZLIB_FILEFUNC_MODE_WRITE (2)
19
+ #define ZLIB_FILEFUNC_MODE_READWRITEFILTER (3)
20
+
21
+ #define ZLIB_FILEFUNC_MODE_EXISTING (4)
22
+ #define ZLIB_FILEFUNC_MODE_CREATE (8)
23
+
24
+
25
+ #ifndef ZCALLBACK
26
+
27
+ #if (defined(WIN32) || defined (WINDOWS) || defined (_WINDOWS)) && defined(CALLBACK) && defined (USEWINDOWS_CALLBACK)
28
+ #define ZCALLBACK CALLBACK
29
+ #else
30
+ #define ZCALLBACK
31
+ #endif
32
+ #endif
33
+
34
+ #ifdef __cplusplus
35
+ extern "C" {
36
+ #endif
37
+
38
+ typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode));
39
+ typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size));
40
+ typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size));
41
+ typedef long (ZCALLBACK *tell_file_func) OF((voidpf opaque, voidpf stream));
42
+ typedef long (ZCALLBACK *seek_file_func) OF((voidpf opaque, voidpf stream, uLong offset, int origin));
43
+ typedef int (ZCALLBACK *close_file_func) OF((voidpf opaque, voidpf stream));
44
+ typedef int (ZCALLBACK *testerror_file_func) OF((voidpf opaque, voidpf stream));
45
+
46
+ typedef struct zlib_filefunc_def_s
47
+ {
48
+ open_file_func zopen_file;
49
+ read_file_func zread_file;
50
+ write_file_func zwrite_file;
51
+ tell_file_func ztell_file;
52
+ seek_file_func zseek_file;
53
+ close_file_func zclose_file;
54
+ testerror_file_func zerror_file;
55
+ voidpf opaque;
56
+ } zlib_filefunc_def;
57
+
58
+
59
+
60
+ void fill_fopen_filefunc OF((zlib_filefunc_def* pzlib_filefunc_def));
61
+
62
+ #define ZREAD(filefunc,filestream,buf,size) ((*((filefunc).zread_file))((filefunc).opaque,filestream,buf,size))
63
+ #define ZWRITE(filefunc,filestream,buf,size) ((*((filefunc).zwrite_file))((filefunc).opaque,filestream,buf,size))
64
+ #define ZTELL(filefunc,filestream) ((*((filefunc).ztell_file))((filefunc).opaque,filestream))
65
+ #define ZSEEK(filefunc,filestream,pos,mode) ((*((filefunc).zseek_file))((filefunc).opaque,filestream,pos,mode))
66
+ #define ZCLOSE(filefunc,filestream) ((*((filefunc).zclose_file))((filefunc).opaque,filestream))
67
+ #define ZERROR(filefunc,filestream) ((*((filefunc).zerror_file))((filefunc).opaque,filestream))
68
+
69
+
70
+ #ifdef __cplusplus
71
+ }
72
+ #endif
73
+
74
+ #endif
75
+