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 +1,837 @@
1
+ /*
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+ * puff.c
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+ * Copyright (C) 2002-2004 Mark Adler
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+ * For conditions of distribution and use, see copyright notice in puff.h
5
+ * version 1.8, 9 Jan 2004
6
+ *
7
+ * puff.c is a simple inflate written to be an unambiguous way to specify the
8
+ * deflate format. It is not written for speed but rather simplicity. As a
9
+ * side benefit, this code might actually be useful when small code is more
10
+ * important than speed, such as bootstrap applications. For typical deflate
11
+ * data, zlib's inflate() is about four times as fast as puff(). zlib's
12
+ * inflate compiles to around 20K on my machine, whereas puff.c compiles to
13
+ * around 4K on my machine (a PowerPC using GNU cc). If the faster decode()
14
+ * function here is used, then puff() is only twice as slow as zlib's
15
+ * inflate().
16
+ *
17
+ * All dynamically allocated memory comes from the stack. The stack required
18
+ * is less than 2K bytes. This code is compatible with 16-bit int's and
19
+ * assumes that long's are at least 32 bits. puff.c uses the short data type,
20
+ * assumed to be 16 bits, for arrays in order to to conserve memory. The code
21
+ * works whether integers are stored big endian or little endian.
22
+ *
23
+ * In the comments below are "Format notes" that describe the inflate process
24
+ * and document some of the less obvious aspects of the format. This source
25
+ * code is meant to supplement RFC 1951, which formally describes the deflate
26
+ * format:
27
+ *
28
+ * http://www.zlib.org/rfc-deflate.html
29
+ */
30
+
31
+ /*
32
+ * Change history:
33
+ *
34
+ * 1.0 10 Feb 2002 - First version
35
+ * 1.1 17 Feb 2002 - Clarifications of some comments and notes
36
+ * - Update puff() dest and source pointers on negative
37
+ * errors to facilitate debugging deflators
38
+ * - Remove longest from struct huffman -- not needed
39
+ * - Simplify offs[] index in construct()
40
+ * - Add input size and checking, using longjmp() to
41
+ * maintain easy readability
42
+ * - Use short data type for large arrays
43
+ * - Use pointers instead of long to specify source and
44
+ * destination sizes to avoid arbitrary 4 GB limits
45
+ * 1.2 17 Mar 2002 - Add faster version of decode(), doubles speed (!),
46
+ * but leave simple version for readabilty
47
+ * - Make sure invalid distances detected if pointers
48
+ * are 16 bits
49
+ * - Fix fixed codes table error
50
+ * - Provide a scanning mode for determining size of
51
+ * uncompressed data
52
+ * 1.3 20 Mar 2002 - Go back to lengths for puff() parameters [Jean-loup]
53
+ * - Add a puff.h file for the interface
54
+ * - Add braces in puff() for else do [Jean-loup]
55
+ * - Use indexes instead of pointers for readability
56
+ * 1.4 31 Mar 2002 - Simplify construct() code set check
57
+ * - Fix some comments
58
+ * - Add FIXLCODES #define
59
+ * 1.5 6 Apr 2002 - Minor comment fixes
60
+ * 1.6 7 Aug 2002 - Minor format changes
61
+ * 1.7 3 Mar 2003 - Added test code for distribution
62
+ * - Added zlib-like license
63
+ * 1.8 9 Jan 2004 - Added some comments on no distance codes case
64
+ */
65
+
66
+ #include <setjmp.h> /* for setjmp(), longjmp(), and jmp_buf */
67
+ #include "puff.h" /* prototype for puff() */
68
+
69
+ #define local static /* for local function definitions */
70
+ #define NIL ((unsigned char *)0) /* for no output option */
71
+
72
+ /*
73
+ * Maximums for allocations and loops. It is not useful to change these --
74
+ * they are fixed by the deflate format.
75
+ */
76
+ #define MAXBITS 15 /* maximum bits in a code */
77
+ #define MAXLCODES 286 /* maximum number of literal/length codes */
78
+ #define MAXDCODES 30 /* maximum number of distance codes */
79
+ #define MAXCODES (MAXLCODES+MAXDCODES) /* maximum codes lengths to read */
80
+ #define FIXLCODES 288 /* number of fixed literal/length codes */
81
+
82
+ /* input and output state */
83
+ struct state {
84
+ /* output state */
85
+ unsigned char *out; /* output buffer */
86
+ unsigned long outlen; /* available space at out */
87
+ unsigned long outcnt; /* bytes written to out so far */
88
+
89
+ /* input state */
90
+ unsigned char *in; /* input buffer */
91
+ unsigned long inlen; /* available input at in */
92
+ unsigned long incnt; /* bytes read so far */
93
+ int bitbuf; /* bit buffer */
94
+ int bitcnt; /* number of bits in bit buffer */
95
+
96
+ /* input limit error return state for bits() and decode() */
97
+ jmp_buf env;
98
+ };
99
+
100
+ /*
101
+ * Return need bits from the input stream. This always leaves less than
102
+ * eight bits in the buffer. bits() works properly for need == 0.
103
+ *
104
+ * Format notes:
105
+ *
106
+ * - Bits are stored in bytes from the least significant bit to the most
107
+ * significant bit. Therefore bits are dropped from the bottom of the bit
108
+ * buffer, using shift right, and new bytes are appended to the top of the
109
+ * bit buffer, using shift left.
110
+ */
111
+ local int bits(struct state *s, int need)
112
+ {
113
+ long val; /* bit accumulator (can use up to 20 bits) */
114
+
115
+ /* load at least need bits into val */
116
+ val = s->bitbuf;
117
+ while (s->bitcnt < need) {
118
+ if (s->incnt == s->inlen) longjmp(s->env, 1); /* out of input */
119
+ val |= (long)(s->in[s->incnt++]) << s->bitcnt; /* load eight bits */
120
+ s->bitcnt += 8;
121
+ }
122
+
123
+ /* drop need bits and update buffer, always zero to seven bits left */
124
+ s->bitbuf = (int)(val >> need);
125
+ s->bitcnt -= need;
126
+
127
+ /* return need bits, zeroing the bits above that */
128
+ return (int)(val & ((1L << need) - 1));
129
+ }
130
+
131
+ /*
132
+ * Process a stored block.
133
+ *
134
+ * Format notes:
135
+ *
136
+ * - After the two-bit stored block type (00), the stored block length and
137
+ * stored bytes are byte-aligned for fast copying. Therefore any leftover
138
+ * bits in the byte that has the last bit of the type, as many as seven, are
139
+ * discarded. The value of the discarded bits are not defined and should not
140
+ * be checked against any expectation.
141
+ *
142
+ * - The second inverted copy of the stored block length does not have to be
143
+ * checked, but it's probably a good idea to do so anyway.
144
+ *
145
+ * - A stored block can have zero length. This is sometimes used to byte-align
146
+ * subsets of the compressed data for random access or partial recovery.
147
+ */
148
+ local int stored(struct state *s)
149
+ {
150
+ unsigned len; /* length of stored block */
151
+
152
+ /* discard leftover bits from current byte (assumes s->bitcnt < 8) */
153
+ s->bitbuf = 0;
154
+ s->bitcnt = 0;
155
+
156
+ /* get length and check against its one's complement */
157
+ if (s->incnt + 4 > s->inlen) return 2; /* not enough input */
158
+ len = s->in[s->incnt++];
159
+ len |= s->in[s->incnt++] << 8;
160
+ if (s->in[s->incnt++] != (~len & 0xff) ||
161
+ s->in[s->incnt++] != ((~len >> 8) & 0xff))
162
+ return -2; /* didn't match complement! */
163
+
164
+ /* copy len bytes from in to out */
165
+ if (s->incnt + len > s->inlen) return 2; /* not enough input */
166
+ if (s->out != NIL) {
167
+ if (s->outcnt + len > s->outlen)
168
+ return 1; /* not enough output space */
169
+ while (len--)
170
+ s->out[s->outcnt++] = s->in[s->incnt++];
171
+ }
172
+ else { /* just scanning */
173
+ s->outcnt += len;
174
+ s->incnt += len;
175
+ }
176
+
177
+ /* done with a valid stored block */
178
+ return 0;
179
+ }
180
+
181
+ /*
182
+ * Huffman code decoding tables. count[1..MAXBITS] is the number of symbols of
183
+ * each length, which for a canonical code are stepped through in order.
184
+ * symbol[] are the symbol values in canonical order, where the number of
185
+ * entries is the sum of the counts in count[]. The decoding process can be
186
+ * seen in the function decode() below.
187
+ */
188
+ struct huffman {
189
+ short *count; /* number of symbols of each length */
190
+ short *symbol; /* canonically ordered symbols */
191
+ };
192
+
193
+ /*
194
+ * Decode a code from the stream s using huffman table h. Return the symbol or
195
+ * a negative value if there is an error. If all of the lengths are zero, i.e.
196
+ * an empty code, or if the code is incomplete and an invalid code is received,
197
+ * then -9 is returned after reading MAXBITS bits.
198
+ *
199
+ * Format notes:
200
+ *
201
+ * - The codes as stored in the compressed data are bit-reversed relative to
202
+ * a simple integer ordering of codes of the same lengths. Hence below the
203
+ * bits are pulled from the compressed data one at a time and used to
204
+ * build the code value reversed from what is in the stream in order to
205
+ * permit simple integer comparisons for decoding. A table-based decoding
206
+ * scheme (as used in zlib) does not need to do this reversal.
207
+ *
208
+ * - The first code for the shortest length is all zeros. Subsequent codes of
209
+ * the same length are simply integer increments of the previous code. When
210
+ * moving up a length, a zero bit is appended to the code. For a complete
211
+ * code, the last code of the longest length will be all ones.
212
+ *
213
+ * - Incomplete codes are handled by this decoder, since they are permitted
214
+ * in the deflate format. See the format notes for fixed() and dynamic().
215
+ */
216
+ #ifdef SLOW
217
+ local int decode(struct state *s, struct huffman *h)
218
+ {
219
+ int len; /* current number of bits in code */
220
+ int code; /* len bits being decoded */
221
+ int first; /* first code of length len */
222
+ int count; /* number of codes of length len */
223
+ int index; /* index of first code of length len in symbol table */
224
+
225
+ code = first = index = 0;
226
+ for (len = 1; len <= MAXBITS; len++) {
227
+ code |= bits(s, 1); /* get next bit */
228
+ count = h->count[len];
229
+ if (code < first + count) /* if length len, return symbol */
230
+ return h->symbol[index + (code - first)];
231
+ index += count; /* else update for next length */
232
+ first += count;
233
+ first <<= 1;
234
+ code <<= 1;
235
+ }
236
+ return -9; /* ran out of codes */
237
+ }
238
+
239
+ /*
240
+ * A faster version of decode() for real applications of this code. It's not
241
+ * as readable, but it makes puff() twice as fast. And it only makes the code
242
+ * a few percent larger.
243
+ */
244
+ #else /* !SLOW */
245
+ local int decode(struct state *s, struct huffman *h)
246
+ {
247
+ int len; /* current number of bits in code */
248
+ int code; /* len bits being decoded */
249
+ int first; /* first code of length len */
250
+ int count; /* number of codes of length len */
251
+ int index; /* index of first code of length len in symbol table */
252
+ int bitbuf; /* bits from stream */
253
+ int left; /* bits left in next or left to process */
254
+ short *next; /* next number of codes */
255
+
256
+ bitbuf = s->bitbuf;
257
+ left = s->bitcnt;
258
+ code = first = index = 0;
259
+ len = 1;
260
+ next = h->count + 1;
261
+ while (1) {
262
+ while (left--) {
263
+ code |= bitbuf & 1;
264
+ bitbuf >>= 1;
265
+ count = *next++;
266
+ if (code < first + count) { /* if length len, return symbol */
267
+ s->bitbuf = bitbuf;
268
+ s->bitcnt = (s->bitcnt - len) & 7;
269
+ return h->symbol[index + (code - first)];
270
+ }
271
+ index += count; /* else update for next length */
272
+ first += count;
273
+ first <<= 1;
274
+ code <<= 1;
275
+ len++;
276
+ }
277
+ left = (MAXBITS+1) - len;
278
+ if (left == 0) break;
279
+ if (s->incnt == s->inlen) longjmp(s->env, 1); /* out of input */
280
+ bitbuf = s->in[s->incnt++];
281
+ if (left > 8) left = 8;
282
+ }
283
+ return -9; /* ran out of codes */
284
+ }
285
+ #endif /* SLOW */
286
+
287
+ /*
288
+ * Given the list of code lengths length[0..n-1] representing a canonical
289
+ * Huffman code for n symbols, construct the tables required to decode those
290
+ * codes. Those tables are the number of codes of each length, and the symbols
291
+ * sorted by length, retaining their original order within each length. The
292
+ * return value is zero for a complete code set, negative for an over-
293
+ * subscribed code set, and positive for an incomplete code set. The tables
294
+ * can be used if the return value is zero or positive, but they cannot be used
295
+ * if the return value is negative. If the return value is zero, it is not
296
+ * possible for decode() using that table to return an error--any stream of
297
+ * enough bits will resolve to a symbol. If the return value is positive, then
298
+ * it is possible for decode() using that table to return an error for received
299
+ * codes past the end of the incomplete lengths.
300
+ *
301
+ * Not used by decode(), but used for error checking, h->count[0] is the number
302
+ * of the n symbols not in the code. So n - h->count[0] is the number of
303
+ * codes. This is useful for checking for incomplete codes that have more than
304
+ * one symbol, which is an error in a dynamic block.
305
+ *
306
+ * Assumption: for all i in 0..n-1, 0 <= length[i] <= MAXBITS
307
+ * This is assured by the construction of the length arrays in dynamic() and
308
+ * fixed() and is not verified by construct().
309
+ *
310
+ * Format notes:
311
+ *
312
+ * - Permitted and expected examples of incomplete codes are one of the fixed
313
+ * codes and any code with a single symbol which in deflate is coded as one
314
+ * bit instead of zero bits. See the format notes for fixed() and dynamic().
315
+ *
316
+ * - Within a given code length, the symbols are kept in ascending order for
317
+ * the code bits definition.
318
+ */
319
+ local int construct(struct huffman *h, short *length, int n)
320
+ {
321
+ int symbol; /* current symbol when stepping through length[] */
322
+ int len; /* current length when stepping through h->count[] */
323
+ int left; /* number of possible codes left of current length */
324
+ short offs[MAXBITS+1]; /* offsets in symbol table for each length */
325
+
326
+ /* count number of codes of each length */
327
+ for (len = 0; len <= MAXBITS; len++)
328
+ h->count[len] = 0;
329
+ for (symbol = 0; symbol < n; symbol++)
330
+ (h->count[length[symbol]])++; /* assumes lengths are within bounds */
331
+ if (h->count[0] == n) /* no codes! */
332
+ return 0; /* complete, but decode() will fail */
333
+
334
+ /* check for an over-subscribed or incomplete set of lengths */
335
+ left = 1; /* one possible code of zero length */
336
+ for (len = 1; len <= MAXBITS; len++) {
337
+ left <<= 1; /* one more bit, double codes left */
338
+ left -= h->count[len]; /* deduct count from possible codes */
339
+ if (left < 0) return left; /* over-subscribed--return negative */
340
+ } /* left > 0 means incomplete */
341
+
342
+ /* generate offsets into symbol table for each length for sorting */
343
+ offs[1] = 0;
344
+ for (len = 1; len < MAXBITS; len++)
345
+ offs[len + 1] = offs[len] + h->count[len];
346
+
347
+ /*
348
+ * put symbols in table sorted by length, by symbol order within each
349
+ * length
350
+ */
351
+ for (symbol = 0; symbol < n; symbol++)
352
+ if (length[symbol] != 0)
353
+ h->symbol[offs[length[symbol]]++] = symbol;
354
+
355
+ /* return zero for complete set, positive for incomplete set */
356
+ return left;
357
+ }
358
+
359
+ /*
360
+ * Decode literal/length and distance codes until an end-of-block code.
361
+ *
362
+ * Format notes:
363
+ *
364
+ * - Compressed data that is after the block type if fixed or after the code
365
+ * description if dynamic is a combination of literals and length/distance
366
+ * pairs terminated by and end-of-block code. Literals are simply Huffman
367
+ * coded bytes. A length/distance pair is a coded length followed by a
368
+ * coded distance to represent a string that occurs earlier in the
369
+ * uncompressed data that occurs again at the current location.
370
+ *
371
+ * - Literals, lengths, and the end-of-block code are combined into a single
372
+ * code of up to 286 symbols. They are 256 literals (0..255), 29 length
373
+ * symbols (257..285), and the end-of-block symbol (256).
374
+ *
375
+ * - There are 256 possible lengths (3..258), and so 29 symbols are not enough
376
+ * to represent all of those. Lengths 3..10 and 258 are in fact represented
377
+ * by just a length symbol. Lengths 11..257 are represented as a symbol and
378
+ * some number of extra bits that are added as an integer to the base length
379
+ * of the length symbol. The number of extra bits is determined by the base
380
+ * length symbol. These are in the static arrays below, lens[] for the base
381
+ * lengths and lext[] for the corresponding number of extra bits.
382
+ *
383
+ * - The reason that 258 gets its own symbol is that the longest length is used
384
+ * often in highly redundant files. Note that 258 can also be coded as the
385
+ * base value 227 plus the maximum extra value of 31. While a good deflate
386
+ * should never do this, it is not an error, and should be decoded properly.
387
+ *
388
+ * - If a length is decoded, including its extra bits if any, then it is
389
+ * followed a distance code. There are up to 30 distance symbols. Again
390
+ * there are many more possible distances (1..32768), so extra bits are added
391
+ * to a base value represented by the symbol. The distances 1..4 get their
392
+ * own symbol, but the rest require extra bits. The base distances and
393
+ * corresponding number of extra bits are below in the static arrays dist[]
394
+ * and dext[].
395
+ *
396
+ * - Literal bytes are simply written to the output. A length/distance pair is
397
+ * an instruction to copy previously uncompressed bytes to the output. The
398
+ * copy is from distance bytes back in the output stream, copying for length
399
+ * bytes.
400
+ *
401
+ * - Distances pointing before the beginning of the output data are not
402
+ * permitted.
403
+ *
404
+ * - Overlapped copies, where the length is greater than the distance, are
405
+ * allowed and common. For example, a distance of one and a length of 258
406
+ * simply copies the last byte 258 times. A distance of four and a length of
407
+ * twelve copies the last four bytes three times. A simple forward copy
408
+ * ignoring whether the length is greater than the distance or not implements
409
+ * this correctly. You should not use memcpy() since its behavior is not
410
+ * defined for overlapped arrays. You should not use memmove() or bcopy()
411
+ * since though their behavior -is- defined for overlapping arrays, it is
412
+ * defined to do the wrong thing in this case.
413
+ */
414
+ local int codes(struct state *s,
415
+ struct huffman *lencode,
416
+ struct huffman *distcode)
417
+ {
418
+ int symbol; /* decoded symbol */
419
+ int len; /* length for copy */
420
+ unsigned dist; /* distance for copy */
421
+ static const short lens[29] = { /* Size base for length codes 257..285 */
422
+ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
423
+ 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258};
424
+ static const short lext[29] = { /* Extra bits for length codes 257..285 */
425
+ 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2,
426
+ 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 0};
427
+ static const short dists[30] = { /* Offset base for distance codes 0..29 */
428
+ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
429
+ 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
430
+ 8193, 12289, 16385, 24577};
431
+ static const short dext[30] = { /* Extra bits for distance codes 0..29 */
432
+ 0, 0, 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
433
+ 7, 7, 8, 8, 9, 9, 10, 10, 11, 11,
434
+ 12, 12, 13, 13};
435
+
436
+ /* decode literals and length/distance pairs */
437
+ do {
438
+ symbol = decode(s, lencode);
439
+ if (symbol < 0) return symbol; /* invalid symbol */
440
+ if (symbol < 256) { /* literal: symbol is the byte */
441
+ /* write out the literal */
442
+ if (s->out != NIL) {
443
+ if (s->outcnt == s->outlen) return 1;
444
+ s->out[s->outcnt] = symbol;
445
+ }
446
+ s->outcnt++;
447
+ }
448
+ else if (symbol > 256) { /* length */
449
+ /* get and compute length */
450
+ symbol -= 257;
451
+ if (symbol >= 29) return -9; /* invalid fixed code */
452
+ len = lens[symbol] + bits(s, lext[symbol]);
453
+
454
+ /* get and check distance */
455
+ symbol = decode(s, distcode);
456
+ if (symbol < 0) return symbol; /* invalid symbol */
457
+ dist = dists[symbol] + bits(s, dext[symbol]);
458
+ if (dist > s->outcnt)
459
+ return -10; /* distance too far back */
460
+
461
+ /* copy length bytes from distance bytes back */
462
+ if (s->out != NIL) {
463
+ if (s->outcnt + len > s->outlen) return 1;
464
+ while (len--) {
465
+ s->out[s->outcnt] = s->out[s->outcnt - dist];
466
+ s->outcnt++;
467
+ }
468
+ }
469
+ else
470
+ s->outcnt += len;
471
+ }
472
+ } while (symbol != 256); /* end of block symbol */
473
+
474
+ /* done with a valid fixed or dynamic block */
475
+ return 0;
476
+ }
477
+
478
+ /*
479
+ * Process a fixed codes block.
480
+ *
481
+ * Format notes:
482
+ *
483
+ * - This block type can be useful for compressing small amounts of data for
484
+ * which the size of the code descriptions in a dynamic block exceeds the
485
+ * benefit of custom codes for that block. For fixed codes, no bits are
486
+ * spent on code descriptions. Instead the code lengths for literal/length
487
+ * codes and distance codes are fixed. The specific lengths for each symbol
488
+ * can be seen in the "for" loops below.
489
+ *
490
+ * - The literal/length code is complete, but has two symbols that are invalid
491
+ * and should result in an error if received. This cannot be implemented
492
+ * simply as an incomplete code since those two symbols are in the "middle"
493
+ * of the code. They are eight bits long and the longest literal/length\
494
+ * code is nine bits. Therefore the code must be constructed with those
495
+ * symbols, and the invalid symbols must be detected after decoding.
496
+ *
497
+ * - The fixed distance codes also have two invalid symbols that should result
498
+ * in an error if received. Since all of the distance codes are the same
499
+ * length, this can be implemented as an incomplete code. Then the invalid
500
+ * codes are detected while decoding.
501
+ */
502
+ local int fixed(struct state *s)
503
+ {
504
+ static int virgin = 1;
505
+ static short lencnt[MAXBITS+1], lensym[FIXLCODES];
506
+ static short distcnt[MAXBITS+1], distsym[MAXDCODES];
507
+ static struct huffman lencode = {lencnt, lensym};
508
+ static struct huffman distcode = {distcnt, distsym};
509
+
510
+ /* build fixed huffman tables if first call (may not be thread safe) */
511
+ if (virgin) {
512
+ int symbol;
513
+ short lengths[FIXLCODES];
514
+
515
+ /* literal/length table */
516
+ for (symbol = 0; symbol < 144; symbol++)
517
+ lengths[symbol] = 8;
518
+ for (; symbol < 256; symbol++)
519
+ lengths[symbol] = 9;
520
+ for (; symbol < 280; symbol++)
521
+ lengths[symbol] = 7;
522
+ for (; symbol < FIXLCODES; symbol++)
523
+ lengths[symbol] = 8;
524
+ construct(&lencode, lengths, FIXLCODES);
525
+
526
+ /* distance table */
527
+ for (symbol = 0; symbol < MAXDCODES; symbol++)
528
+ lengths[symbol] = 5;
529
+ construct(&distcode, lengths, MAXDCODES);
530
+
531
+ /* do this just once */
532
+ virgin = 0;
533
+ }
534
+
535
+ /* decode data until end-of-block code */
536
+ return codes(s, &lencode, &distcode);
537
+ }
538
+
539
+ /*
540
+ * Process a dynamic codes block.
541
+ *
542
+ * Format notes:
543
+ *
544
+ * - A dynamic block starts with a description of the literal/length and
545
+ * distance codes for that block. New dynamic blocks allow the compressor to
546
+ * rapidly adapt to changing data with new codes optimized for that data.
547
+ *
548
+ * - The codes used by the deflate format are "canonical", which means that
549
+ * the actual bits of the codes are generated in an unambiguous way simply
550
+ * from the number of bits in each code. Therefore the code descriptions
551
+ * are simply a list of code lengths for each symbol.
552
+ *
553
+ * - The code lengths are stored in order for the symbols, so lengths are
554
+ * provided for each of the literal/length symbols, and for each of the
555
+ * distance symbols.
556
+ *
557
+ * - If a symbol is not used in the block, this is represented by a zero as
558
+ * as the code length. This does not mean a zero-length code, but rather
559
+ * that no code should be created for this symbol. There is no way in the
560
+ * deflate format to represent a zero-length code.
561
+ *
562
+ * - The maximum number of bits in a code is 15, so the possible lengths for
563
+ * any code are 1..15.
564
+ *
565
+ * - The fact that a length of zero is not permitted for a code has an
566
+ * interesting consequence. Normally if only one symbol is used for a given
567
+ * code, then in fact that code could be represented with zero bits. However
568
+ * in deflate, that code has to be at least one bit. So for example, if
569
+ * only a single distance base symbol appears in a block, then it will be
570
+ * represented by a single code of length one, in particular one 0 bit. This
571
+ * is an incomplete code, since if a 1 bit is received, it has no meaning,
572
+ * and should result in an error. So incomplete distance codes of one symbol
573
+ * should be permitted, and the receipt of invalid codes should be handled.
574
+ *
575
+ * - It is also possible to have a single literal/length code, but that code
576
+ * must be the end-of-block code, since every dynamic block has one. This
577
+ * is not the most efficient way to create an empty block (an empty fixed
578
+ * block is fewer bits), but it is allowed by the format. So incomplete
579
+ * literal/length codes of one symbol should also be permitted.
580
+ *
581
+ * - If there are only literal codes and no lengths, then there are no distance
582
+ * codes. This is represented by one distance code with zero bits.
583
+ *
584
+ * - The list of up to 286 length/literal lengths and up to 30 distance lengths
585
+ * are themselves compressed using Huffman codes and run-length encoding. In
586
+ * the list of code lengths, a 0 symbol means no code, a 1..15 symbol means
587
+ * that length, and the symbols 16, 17, and 18 are run-length instructions.
588
+ * Each of 16, 17, and 18 are follwed by extra bits to define the length of
589
+ * the run. 16 copies the last length 3 to 6 times. 17 represents 3 to 10
590
+ * zero lengths, and 18 represents 11 to 138 zero lengths. Unused symbols
591
+ * are common, hence the special coding for zero lengths.
592
+ *
593
+ * - The symbols for 0..18 are Huffman coded, and so that code must be
594
+ * described first. This is simply a sequence of up to 19 three-bit values
595
+ * representing no code (0) or the code length for that symbol (1..7).
596
+ *
597
+ * - A dynamic block starts with three fixed-size counts from which is computed
598
+ * the number of literal/length code lengths, the number of distance code
599
+ * lengths, and the number of code length code lengths (ok, you come up with
600
+ * a better name!) in the code descriptions. For the literal/length and
601
+ * distance codes, lengths after those provided are considered zero, i.e. no
602
+ * code. The code length code lengths are received in a permuted order (see
603
+ * the order[] array below) to make a short code length code length list more
604
+ * likely. As it turns out, very short and very long codes are less likely
605
+ * to be seen in a dynamic code description, hence what may appear initially
606
+ * to be a peculiar ordering.
607
+ *
608
+ * - Given the number of literal/length code lengths (nlen) and distance code
609
+ * lengths (ndist), then they are treated as one long list of nlen + ndist
610
+ * code lengths. Therefore run-length coding can and often does cross the
611
+ * boundary between the two sets of lengths.
612
+ *
613
+ * - So to summarize, the code description at the start of a dynamic block is
614
+ * three counts for the number of code lengths for the literal/length codes,
615
+ * the distance codes, and the code length codes. This is followed by the
616
+ * code length code lengths, three bits each. This is used to construct the
617
+ * code length code which is used to read the remainder of the lengths. Then
618
+ * the literal/length code lengths and distance lengths are read as a single
619
+ * set of lengths using the code length codes. Codes are constructed from
620
+ * the resulting two sets of lengths, and then finally you can start
621
+ * decoding actual compressed data in the block.
622
+ *
623
+ * - For reference, a "typical" size for the code description in a dynamic
624
+ * block is around 80 bytes.
625
+ */
626
+ local int dynamic(struct state *s)
627
+ {
628
+ int nlen, ndist, ncode; /* number of lengths in descriptor */
629
+ int index; /* index of lengths[] */
630
+ int err; /* construct() return value */
631
+ short lengths[MAXCODES]; /* descriptor code lengths */
632
+ short lencnt[MAXBITS+1], lensym[MAXLCODES]; /* lencode memory */
633
+ short distcnt[MAXBITS+1], distsym[MAXDCODES]; /* distcode memory */
634
+ struct huffman lencode = {lencnt, lensym}; /* length code */
635
+ struct huffman distcode = {distcnt, distsym}; /* distance code */
636
+ static const short order[19] = /* permutation of code length codes */
637
+ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
638
+
639
+ /* get number of lengths in each table, check lengths */
640
+ nlen = bits(s, 5) + 257;
641
+ ndist = bits(s, 5) + 1;
642
+ ncode = bits(s, 4) + 4;
643
+ if (nlen > MAXLCODES || ndist > MAXDCODES)
644
+ return -3; /* bad counts */
645
+
646
+ /* read code length code lengths (really), missing lengths are zero */
647
+ for (index = 0; index < ncode; index++)
648
+ lengths[order[index]] = bits(s, 3);
649
+ for (; index < 19; index++)
650
+ lengths[order[index]] = 0;
651
+
652
+ /* build huffman table for code lengths codes (use lencode temporarily) */
653
+ err = construct(&lencode, lengths, 19);
654
+ if (err != 0) return -4; /* require complete code set here */
655
+
656
+ /* read length/literal and distance code length tables */
657
+ index = 0;
658
+ while (index < nlen + ndist) {
659
+ int symbol; /* decoded value */
660
+ int len; /* last length to repeat */
661
+
662
+ symbol = decode(s, &lencode);
663
+ if (symbol < 16) /* length in 0..15 */
664
+ lengths[index++] = symbol;
665
+ else { /* repeat instruction */
666
+ len = 0; /* assume repeating zeros */
667
+ if (symbol == 16) { /* repeat last length 3..6 times */
668
+ if (index == 0) return -5; /* no last length! */
669
+ len = lengths[index - 1]; /* last length */
670
+ symbol = 3 + bits(s, 2);
671
+ }
672
+ else if (symbol == 17) /* repeat zero 3..10 times */
673
+ symbol = 3 + bits(s, 3);
674
+ else /* == 18, repeat zero 11..138 times */
675
+ symbol = 11 + bits(s, 7);
676
+ if (index + symbol > nlen + ndist)
677
+ return -6; /* too many lengths! */
678
+ while (symbol--) /* repeat last or zero symbol times */
679
+ lengths[index++] = len;
680
+ }
681
+ }
682
+
683
+ /* build huffman table for literal/length codes */
684
+ err = construct(&lencode, lengths, nlen);
685
+ if (err < 0 || (err > 0 && nlen - lencode.count[0] != 1))
686
+ return -7; /* only allow incomplete codes if just one code */
687
+
688
+ /* build huffman table for distance codes */
689
+ err = construct(&distcode, lengths + nlen, ndist);
690
+ if (err < 0 || (err > 0 && ndist - distcode.count[0] != 1))
691
+ return -8; /* only allow incomplete codes if just one code */
692
+
693
+ /* decode data until end-of-block code */
694
+ return codes(s, &lencode, &distcode);
695
+ }
696
+
697
+ /*
698
+ * Inflate source to dest. On return, destlen and sourcelen are updated to the
699
+ * size of the uncompressed data and the size of the deflate data respectively.
700
+ * On success, the return value of puff() is zero. If there is an error in the
701
+ * source data, i.e. it is not in the deflate format, then a negative value is
702
+ * returned. If there is not enough input available or there is not enough
703
+ * output space, then a positive error is returned. In that case, destlen and
704
+ * sourcelen are not updated to facilitate retrying from the beginning with the
705
+ * provision of more input data or more output space. In the case of invalid
706
+ * inflate data (a negative error), the dest and source pointers are updated to
707
+ * facilitate the debugging of deflators.
708
+ *
709
+ * puff() also has a mode to determine the size of the uncompressed output with
710
+ * no output written. For this dest must be (unsigned char *)0. In this case,
711
+ * the input value of *destlen is ignored, and on return *destlen is set to the
712
+ * size of the uncompressed output.
713
+ *
714
+ * The return codes are:
715
+ *
716
+ * 2: available inflate data did not terminate
717
+ * 1: output space exhausted before completing inflate
718
+ * 0: successful inflate
719
+ * -1: invalid block type (type == 3)
720
+ * -2: stored block length did not match one's complement
721
+ * -3: dynamic block code description: too many length or distance codes
722
+ * -4: dynamic block code description: code lengths codes incomplete
723
+ * -5: dynamic block code description: repeat lengths with no first length
724
+ * -6: dynamic block code description: repeat more than specified lengths
725
+ * -7: dynamic block code description: invalid literal/length code lengths
726
+ * -8: dynamic block code description: invalid distance code lengths
727
+ * -9: invalid literal/length or distance code in fixed or dynamic block
728
+ * -10: distance is too far back in fixed or dynamic block
729
+ *
730
+ * Format notes:
731
+ *
732
+ * - Three bits are read for each block to determine the kind of block and
733
+ * whether or not it is the last block. Then the block is decoded and the
734
+ * process repeated if it was not the last block.
735
+ *
736
+ * - The leftover bits in the last byte of the deflate data after the last
737
+ * block (if it was a fixed or dynamic block) are undefined and have no
738
+ * expected values to check.
739
+ */
740
+ int puff(unsigned char *dest, /* pointer to destination pointer */
741
+ unsigned long *destlen, /* amount of output space */
742
+ unsigned char *source, /* pointer to source data pointer */
743
+ unsigned long *sourcelen) /* amount of input available */
744
+ {
745
+ struct state s; /* input/output state */
746
+ int last, type; /* block information */
747
+ int err; /* return value */
748
+
749
+ /* initialize output state */
750
+ s.out = dest;
751
+ s.outlen = *destlen; /* ignored if dest is NIL */
752
+ s.outcnt = 0;
753
+
754
+ /* initialize input state */
755
+ s.in = source;
756
+ s.inlen = *sourcelen;
757
+ s.incnt = 0;
758
+ s.bitbuf = 0;
759
+ s.bitcnt = 0;
760
+
761
+ /* return if bits() or decode() tries to read past available input */
762
+ if (setjmp(s.env) != 0) /* if came back here via longjmp() */
763
+ err = 2; /* then skip do-loop, return error */
764
+ else {
765
+ /* process blocks until last block or error */
766
+ do {
767
+ last = bits(&s, 1); /* one if last block */
768
+ type = bits(&s, 2); /* block type 0..3 */
769
+ err = type == 0 ? stored(&s) :
770
+ (type == 1 ? fixed(&s) :
771
+ (type == 2 ? dynamic(&s) :
772
+ -1)); /* type == 3, invalid */
773
+ if (err != 0) break; /* return with error */
774
+ } while (!last);
775
+ }
776
+
777
+ /* update the lengths and return */
778
+ if (err <= 0) {
779
+ *destlen = s.outcnt;
780
+ *sourcelen = s.incnt;
781
+ }
782
+ return err;
783
+ }
784
+
785
+ #ifdef TEST
786
+ /* Example of how to use puff() */
787
+ #include <stdio.h>
788
+ #include <stdlib.h>
789
+ #include <sys/types.h>
790
+ #include <sys/stat.h>
791
+
792
+ local unsigned char *yank(char *name, unsigned long *len)
793
+ {
794
+ unsigned long size;
795
+ unsigned char *buf;
796
+ FILE *in;
797
+ struct stat s;
798
+
799
+ *len = 0;
800
+ if (stat(name, &s)) return NULL;
801
+ if ((s.st_mode & S_IFMT) != S_IFREG) return NULL;
802
+ size = (unsigned long)(s.st_size);
803
+ if (size == 0 || (off_t)size != s.st_size) return NULL;
804
+ in = fopen(name, "r");
805
+ if (in == NULL) return NULL;
806
+ buf = malloc(size);
807
+ if (buf != NULL && fread(buf, 1, size, in) != size) {
808
+ free(buf);
809
+ buf = NULL;
810
+ }
811
+ fclose(in);
812
+ *len = size;
813
+ return buf;
814
+ }
815
+
816
+ int main(int argc, char **argv)
817
+ {
818
+ int ret;
819
+ unsigned char *source;
820
+ unsigned long len, sourcelen, destlen;
821
+
822
+ if (argc < 2) return 2;
823
+ source = yank(argv[1], &len);
824
+ if (source == NULL) return 2;
825
+ sourcelen = len;
826
+ ret = puff(NIL, &destlen, source, &sourcelen);
827
+ if (ret)
828
+ printf("puff() failed with return code %d\n", ret);
829
+ else {
830
+ printf("puff() succeeded uncompressing %lu bytes\n", destlen);
831
+ if (sourcelen < len) printf("%lu compressed bytes unused\n",
832
+ len - sourcelen);
833
+ }
834
+ free(source);
835
+ return ret;
836
+ }
837
+ #endif