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 +1,191 @@
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+ /* zpipe.c: example of proper use of zlib's inflate() and deflate()
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+ Not copyrighted -- provided to the public domain
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+ Version 1.2 9 November 2004 Mark Adler */
4
+
5
+ /* Version history:
6
+ 1.0 30 Oct 2004 First version
7
+ 1.1 8 Nov 2004 Add void casting for unused return values
8
+ Use switch statement for inflate() return values
9
+ 1.2 9 Nov 2004 Add assertions to document zlib guarantees
10
+ 1.3 6 Apr 2005 Remove incorrect assertion in inf()
11
+ */
12
+
13
+ #include <stdio.h>
14
+ #include <string.h>
15
+ #include <assert.h>
16
+ #include "zlib.h"
17
+
18
+ #define CHUNK 16384
19
+
20
+ /* Compress from file source to file dest until EOF on source.
21
+ def() returns Z_OK on success, Z_MEM_ERROR if memory could not be
22
+ allocated for processing, Z_STREAM_ERROR if an invalid compression
23
+ level is supplied, Z_VERSION_ERROR if the version of zlib.h and the
24
+ version of the library linked do not match, or Z_ERRNO if there is
25
+ an error reading or writing the files. */
26
+ int def(FILE *source, FILE *dest, int level)
27
+ {
28
+ int ret, flush;
29
+ unsigned have;
30
+ z_stream strm;
31
+ char in[CHUNK];
32
+ char out[CHUNK];
33
+
34
+ /* allocate deflate state */
35
+ strm.zalloc = Z_NULL;
36
+ strm.zfree = Z_NULL;
37
+ strm.opaque = Z_NULL;
38
+ ret = deflateInit(&strm, level);
39
+ if (ret != Z_OK)
40
+ return ret;
41
+
42
+ /* compress until end of file */
43
+ do {
44
+ strm.avail_in = fread(in, 1, CHUNK, source);
45
+ if (ferror(source)) {
46
+ (void)deflateEnd(&strm);
47
+ return Z_ERRNO;
48
+ }
49
+ flush = feof(source) ? Z_FINISH : Z_NO_FLUSH;
50
+ strm.next_in = in;
51
+
52
+ /* run deflate() on input until output buffer not full, finish
53
+ compression if all of source has been read in */
54
+ do {
55
+ strm.avail_out = CHUNK;
56
+ strm.next_out = out;
57
+ ret = deflate(&strm, flush); /* no bad return value */
58
+ assert(ret != Z_STREAM_ERROR); /* state not clobbered */
59
+ have = CHUNK - strm.avail_out;
60
+ if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
61
+ (void)deflateEnd(&strm);
62
+ return Z_ERRNO;
63
+ }
64
+ } while (strm.avail_out == 0);
65
+ assert(strm.avail_in == 0); /* all input will be used */
66
+
67
+ /* done when last data in file processed */
68
+ } while (flush != Z_FINISH);
69
+ assert(ret == Z_STREAM_END); /* stream will be complete */
70
+
71
+ /* clean up and return */
72
+ (void)deflateEnd(&strm);
73
+ return Z_OK;
74
+ }
75
+
76
+ /* Decompress from file source to file dest until stream ends or EOF.
77
+ inf() returns Z_OK on success, Z_MEM_ERROR if memory could not be
78
+ allocated for processing, Z_DATA_ERROR if the deflate data is
79
+ invalid or incomplete, Z_VERSION_ERROR if the version of zlib.h and
80
+ the version of the library linked do not match, or Z_ERRNO if there
81
+ is an error reading or writing the files. */
82
+ int inf(FILE *source, FILE *dest)
83
+ {
84
+ int ret;
85
+ unsigned have;
86
+ z_stream strm;
87
+ char in[CHUNK];
88
+ char out[CHUNK];
89
+
90
+ /* allocate inflate state */
91
+ strm.zalloc = Z_NULL;
92
+ strm.zfree = Z_NULL;
93
+ strm.opaque = Z_NULL;
94
+ strm.avail_in = 0;
95
+ strm.next_in = Z_NULL;
96
+ ret = inflateInit(&strm);
97
+ if (ret != Z_OK)
98
+ return ret;
99
+
100
+ /* decompress until deflate stream ends or end of file */
101
+ do {
102
+ strm.avail_in = fread(in, 1, CHUNK, source);
103
+ if (ferror(source)) {
104
+ (void)inflateEnd(&strm);
105
+ return Z_ERRNO;
106
+ }
107
+ if (strm.avail_in == 0)
108
+ break;
109
+ strm.next_in = in;
110
+
111
+ /* run inflate() on input until output buffer not full */
112
+ do {
113
+ strm.avail_out = CHUNK;
114
+ strm.next_out = out;
115
+ ret = inflate(&strm, Z_NO_FLUSH);
116
+ assert(ret != Z_STREAM_ERROR); /* state not clobbered */
117
+ switch (ret) {
118
+ case Z_NEED_DICT:
119
+ ret = Z_DATA_ERROR; /* and fall through */
120
+ case Z_DATA_ERROR:
121
+ case Z_MEM_ERROR:
122
+ (void)inflateEnd(&strm);
123
+ return ret;
124
+ }
125
+ have = CHUNK - strm.avail_out;
126
+ if (fwrite(out, 1, have, dest) != have || ferror(dest)) {
127
+ (void)inflateEnd(&strm);
128
+ return Z_ERRNO;
129
+ }
130
+ } while (strm.avail_out == 0);
131
+
132
+ /* done when inflate() says it's done */
133
+ } while (ret != Z_STREAM_END);
134
+
135
+ /* clean up and return */
136
+ (void)inflateEnd(&strm);
137
+ return ret == Z_STREAM_END ? Z_OK : Z_DATA_ERROR;
138
+ }
139
+
140
+ /* report a zlib or i/o error */
141
+ void zerr(int ret)
142
+ {
143
+ fputs("zpipe: ", stderr);
144
+ switch (ret) {
145
+ case Z_ERRNO:
146
+ if (ferror(stdin))
147
+ fputs("error reading stdin\n", stderr);
148
+ if (ferror(stdout))
149
+ fputs("error writing stdout\n", stderr);
150
+ break;
151
+ case Z_STREAM_ERROR:
152
+ fputs("invalid compression level\n", stderr);
153
+ break;
154
+ case Z_DATA_ERROR:
155
+ fputs("invalid or incomplete deflate data\n", stderr);
156
+ break;
157
+ case Z_MEM_ERROR:
158
+ fputs("out of memory\n", stderr);
159
+ break;
160
+ case Z_VERSION_ERROR:
161
+ fputs("zlib version mismatch!\n", stderr);
162
+ }
163
+ }
164
+
165
+ /* compress or decompress from stdin to stdout */
166
+ int main(int argc, char **argv)
167
+ {
168
+ int ret;
169
+
170
+ /* do compression if no arguments */
171
+ if (argc == 1) {
172
+ ret = def(stdin, stdout, Z_DEFAULT_COMPRESSION);
173
+ if (ret != Z_OK)
174
+ zerr(ret);
175
+ return ret;
176
+ }
177
+
178
+ /* do decompression if -d specified */
179
+ else if (argc == 2 && strcmp(argv[1], "-d") == 0) {
180
+ ret = inf(stdin, stdout);
181
+ if (ret != Z_OK)
182
+ zerr(ret);
183
+ return ret;
184
+ }
185
+
186
+ /* otherwise, report usage */
187
+ else {
188
+ fputs("zpipe usage: zpipe [-d] < source > dest\n", stderr);
189
+ return 1;
190
+ }
191
+ }
@@ -0,0 +1,404 @@
1
+ /* zran.c -- example of zlib/gzip stream indexing and random access
2
+ * Copyright (C) 2005 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ Version 1.0 29 May 2005 Mark Adler */
5
+
6
+ /* Illustrate the use of Z_BLOCK, inflatePrime(), and inflateSetDictionary()
7
+ for random access of a compressed file. A file containing a zlib or gzip
8
+ stream is provided on the command line. The compressed stream is decoded in
9
+ its entirety, and an index built with access points about every SPAN bytes
10
+ in the uncompressed output. The compressed file is left open, and can then
11
+ be read randomly, having to decompress on the average SPAN/2 uncompressed
12
+ bytes before getting to the desired block of data.
13
+
14
+ An access point can be created at the start of any deflate block, by saving
15
+ the starting file offset and bit of that block, and the 32K bytes of
16
+ uncompressed data that precede that block. Also the uncompressed offset of
17
+ that block is saved to provide a referece for locating a desired starting
18
+ point in the uncompressed stream. build_index() works by decompressing the
19
+ input zlib or gzip stream a block at a time, and at the end of each block
20
+ deciding if enough uncompressed data has gone by to justify the creation of
21
+ a new access point. If so, that point is saved in a data structure that
22
+ grows as needed to accommodate the points.
23
+
24
+ To use the index, an offset in the uncompressed data is provided, for which
25
+ the latest accees point at or preceding that offset is located in the index.
26
+ The input file is positioned to the specified location in the index, and if
27
+ necessary the first few bits of the compressed data is read from the file.
28
+ inflate is initialized with those bits and the 32K of uncompressed data, and
29
+ the decompression then proceeds until the desired offset in the file is
30
+ reached. Then the decompression continues to read the desired uncompressed
31
+ data from the file.
32
+
33
+ Another approach would be to generate the index on demand. In that case,
34
+ requests for random access reads from the compressed data would try to use
35
+ the index, but if a read far enough past the end of the index is required,
36
+ then further index entries would be generated and added.
37
+
38
+ There is some fair bit of overhead to starting inflation for the random
39
+ access, mainly copying the 32K byte dictionary. So if small pieces of the
40
+ file are being accessed, it would make sense to implement a cache to hold
41
+ some lookahead and avoid many calls to extract() for small lengths.
42
+
43
+ Another way to build an index would be to use inflateCopy(). That would
44
+ not be constrained to have access points at block boundaries, but requires
45
+ more memory per access point, and also cannot be saved to file due to the
46
+ use of pointers in the state. The approach here allows for storage of the
47
+ index in a file.
48
+ */
49
+
50
+ #include <stdio.h>
51
+ #include <stdlib.h>
52
+ #include <string.h>
53
+ #include "zlib.h"
54
+
55
+ #define local static
56
+
57
+ #define SPAN 1048576L /* desired distance between access points */
58
+ #define WINSIZE 32768U /* sliding window size */
59
+ #define CHUNK 16384 /* file input buffer size */
60
+
61
+ /* access point entry */
62
+ struct point {
63
+ off_t out; /* corresponding offset in uncompressed data */
64
+ off_t in; /* offset in input file of first full byte */
65
+ int bits; /* number of bits (1-7) from byte at in - 1, or 0 */
66
+ unsigned char window[WINSIZE]; /* preceding 32K of uncompressed data */
67
+ };
68
+
69
+ /* access point list */
70
+ struct access {
71
+ int have; /* number of list entries filled in */
72
+ int size; /* number of list entries allocated */
73
+ struct point *list; /* allocated list */
74
+ };
75
+
76
+ /* Deallocate an index built by build_index() */
77
+ local void free_index(struct access *index)
78
+ {
79
+ if (index != NULL) {
80
+ free(index->list);
81
+ free(index);
82
+ }
83
+ }
84
+
85
+ /* Add an entry to the access point list. If out of memory, deallocate the
86
+ existing list and return NULL. */
87
+ local struct access *addpoint(struct access *index, int bits,
88
+ off_t in, off_t out, unsigned left, unsigned char *window)
89
+ {
90
+ struct point *next;
91
+
92
+ /* if list is empty, create it (start with eight points) */
93
+ if (index == NULL) {
94
+ index = malloc(sizeof(struct access));
95
+ if (index == NULL) return NULL;
96
+ index->list = malloc(sizeof(struct point) << 3);
97
+ if (index->list == NULL) {
98
+ free(index);
99
+ return NULL;
100
+ }
101
+ index->size = 8;
102
+ index->have = 0;
103
+ }
104
+
105
+ /* if list is full, make it bigger */
106
+ else if (index->have == index->size) {
107
+ index->size <<= 1;
108
+ next = realloc(index->list, sizeof(struct point) * index->size);
109
+ if (next == NULL) {
110
+ free_index(index);
111
+ return NULL;
112
+ }
113
+ index->list = next;
114
+ }
115
+
116
+ /* fill in entry and increment how many we have */
117
+ next = index->list + index->have;
118
+ next->bits = bits;
119
+ next->in = in;
120
+ next->out = out;
121
+ if (left)
122
+ memcpy(next->window, window + WINSIZE - left, left);
123
+ if (left < WINSIZE)
124
+ memcpy(next->window + left, window, WINSIZE - left);
125
+ index->have++;
126
+
127
+ /* return list, possibly reallocated */
128
+ return index;
129
+ }
130
+
131
+ /* Make one entire pass through the compressed stream and build an index, with
132
+ access points about every span bytes of uncompressed output -- span is
133
+ chosen to balance the speed of random access against the memory requirements
134
+ of the list, about 32K bytes per access point. Note that data after the end
135
+ of the first zlib or gzip stream in the file is ignored. build_index()
136
+ returns the number of access points on success (>= 1), Z_MEM_ERROR for out
137
+ of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a
138
+ file read error. On success, *built points to the resulting index. */
139
+ local int build_index(FILE *in, off_t span, struct access **built)
140
+ {
141
+ int ret;
142
+ off_t totin, totout; /* our own total counters to avoid 4GB limit */
143
+ off_t last; /* totout value of last access point */
144
+ struct access *index; /* access points being generated */
145
+ z_stream strm;
146
+ unsigned char input[CHUNK];
147
+ unsigned char window[WINSIZE];
148
+
149
+ /* initialize inflate */
150
+ strm.zalloc = Z_NULL;
151
+ strm.zfree = Z_NULL;
152
+ strm.opaque = Z_NULL;
153
+ strm.avail_in = 0;
154
+ strm.next_in = Z_NULL;
155
+ ret = inflateInit2(&strm, 47); /* automatic zlib or gzip decoding */
156
+ if (ret != Z_OK)
157
+ return ret;
158
+
159
+ /* inflate the input, maintain a sliding window, and build an index -- this
160
+ also validates the integrity of the compressed data using the check
161
+ information at the end of the gzip or zlib stream */
162
+ totin = totout = last = 0;
163
+ index = NULL; /* will be allocated by first addpoint() */
164
+ strm.avail_out = 0;
165
+ do {
166
+ /* get some compressed data from input file */
167
+ strm.avail_in = fread(input, 1, CHUNK, in);
168
+ if (ferror(in)) {
169
+ ret = Z_ERRNO;
170
+ goto build_index_error;
171
+ }
172
+ if (strm.avail_in == 0) {
173
+ ret = Z_DATA_ERROR;
174
+ goto build_index_error;
175
+ }
176
+ strm.next_in = input;
177
+
178
+ /* process all of that, or until end of stream */
179
+ do {
180
+ /* reset sliding window if necessary */
181
+ if (strm.avail_out == 0) {
182
+ strm.avail_out = WINSIZE;
183
+ strm.next_out = window;
184
+ }
185
+
186
+ /* inflate until out of input, output, or at end of block --
187
+ update the total input and output counters */
188
+ totin += strm.avail_in;
189
+ totout += strm.avail_out;
190
+ ret = inflate(&strm, Z_BLOCK); /* return at end of block */
191
+ totin -= strm.avail_in;
192
+ totout -= strm.avail_out;
193
+ if (ret == Z_NEED_DICT)
194
+ ret = Z_DATA_ERROR;
195
+ if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR)
196
+ goto build_index_error;
197
+ if (ret == Z_STREAM_END)
198
+ break;
199
+
200
+ /* if at end of block, consider adding an index entry (note that if
201
+ data_type indicates an end-of-block, then all of the
202
+ uncompressed data from that block has been delivered, and none
203
+ of the compressed data after that block has been consumed,
204
+ except for up to seven bits) -- the totout == 0 provides an
205
+ entry point after the zlib or gzip header, and assures that the
206
+ index always has at least one access point; we avoid creating an
207
+ access point after the last block by checking bit 6 of data_type
208
+ */
209
+ if ((strm.data_type & 128) && !(strm.data_type & 64) &&
210
+ (totout == 0 || totout - last > span)) {
211
+ index = addpoint(index, strm.data_type & 7, totin,
212
+ totout, strm.avail_out, window);
213
+ if (index == NULL) {
214
+ ret = Z_MEM_ERROR;
215
+ goto build_index_error;
216
+ }
217
+ last = totout;
218
+ }
219
+ } while (strm.avail_in != 0);
220
+ } while (ret != Z_STREAM_END);
221
+
222
+ /* clean up and return index (release unused entries in list) */
223
+ (void)inflateEnd(&strm);
224
+ index = realloc(index, sizeof(struct point) * index->have);
225
+ index->size = index->have;
226
+ *built = index;
227
+ return index->size;
228
+
229
+ /* return error */
230
+ build_index_error:
231
+ (void)inflateEnd(&strm);
232
+ if (index != NULL)
233
+ free_index(index);
234
+ return ret;
235
+ }
236
+
237
+ /* Use the index to read len bytes from offset into buf, return bytes read or
238
+ negative for error (Z_DATA_ERROR or Z_MEM_ERROR). If data is requested past
239
+ the end of the uncompressed data, then extract() will return a value less
240
+ than len, indicating how much as actually read into buf. This function
241
+ should not return a data error unless the file was modified since the index
242
+ was generated. extract() may also return Z_ERRNO if there is an error on
243
+ reading or seeking the input file. */
244
+ local int extract(FILE *in, struct access *index, off_t offset,
245
+ unsigned char *buf, int len)
246
+ {
247
+ int ret, skip;
248
+ z_stream strm;
249
+ struct point *here;
250
+ unsigned char input[CHUNK];
251
+ unsigned char discard[WINSIZE];
252
+
253
+ /* proceed only if something reasonable to do */
254
+ if (len < 0)
255
+ return 0;
256
+
257
+ /* find where in stream to start */
258
+ here = index->list;
259
+ ret = index->have;
260
+ while (--ret && here[1].out <= offset)
261
+ here++;
262
+
263
+ /* initialize file and inflate state to start there */
264
+ strm.zalloc = Z_NULL;
265
+ strm.zfree = Z_NULL;
266
+ strm.opaque = Z_NULL;
267
+ strm.avail_in = 0;
268
+ strm.next_in = Z_NULL;
269
+ ret = inflateInit2(&strm, -15); /* raw inflate */
270
+ if (ret != Z_OK)
271
+ return ret;
272
+ ret = fseeko(in, here->in - (here->bits ? 1 : 0), SEEK_SET);
273
+ if (ret == -1)
274
+ goto extract_ret;
275
+ if (here->bits) {
276
+ ret = getc(in);
277
+ if (ret == -1) {
278
+ ret = ferror(in) ? Z_ERRNO : Z_DATA_ERROR;
279
+ goto extract_ret;
280
+ }
281
+ (void)inflatePrime(&strm, here->bits, ret >> (8 - here->bits));
282
+ }
283
+ (void)inflateSetDictionary(&strm, here->window, WINSIZE);
284
+
285
+ /* skip uncompressed bytes until offset reached, then satisfy request */
286
+ offset -= here->out;
287
+ strm.avail_in = 0;
288
+ skip = 1; /* while skipping to offset */
289
+ do {
290
+ /* define where to put uncompressed data, and how much */
291
+ if (offset == 0 && skip) { /* at offset now */
292
+ strm.avail_out = len;
293
+ strm.next_out = buf;
294
+ skip = 0; /* only do this once */
295
+ }
296
+ if (offset > WINSIZE) { /* skip WINSIZE bytes */
297
+ strm.avail_out = WINSIZE;
298
+ strm.next_out = discard;
299
+ offset -= WINSIZE;
300
+ }
301
+ else if (offset != 0) { /* last skip */
302
+ strm.avail_out = (unsigned)offset;
303
+ strm.next_out = discard;
304
+ offset = 0;
305
+ }
306
+
307
+ /* uncompress until avail_out filled, or end of stream */
308
+ do {
309
+ if (strm.avail_in == 0) {
310
+ strm.avail_in = fread(input, 1, CHUNK, in);
311
+ if (ferror(in)) {
312
+ ret = Z_ERRNO;
313
+ goto extract_ret;
314
+ }
315
+ if (strm.avail_in == 0) {
316
+ ret = Z_DATA_ERROR;
317
+ goto extract_ret;
318
+ }
319
+ strm.next_in = input;
320
+ }
321
+ ret = inflate(&strm, Z_NO_FLUSH); /* normal inflate */
322
+ if (ret == Z_NEED_DICT)
323
+ ret = Z_DATA_ERROR;
324
+ if (ret == Z_MEM_ERROR || ret == Z_DATA_ERROR)
325
+ goto extract_ret;
326
+ if (ret == Z_STREAM_END)
327
+ break;
328
+ } while (strm.avail_out != 0);
329
+
330
+ /* if reach end of stream, then don't keep trying to get more */
331
+ if (ret == Z_STREAM_END)
332
+ break;
333
+
334
+ /* do until offset reached and requested data read, or stream ends */
335
+ } while (skip);
336
+
337
+ /* compute number of uncompressed bytes read after offset */
338
+ ret = skip ? 0 : len - strm.avail_out;
339
+
340
+ /* clean up and return bytes read or error */
341
+ extract_ret:
342
+ (void)inflateEnd(&strm);
343
+ return ret;
344
+ }
345
+
346
+ /* Demonstrate the use of build_index() and extract() by processing the file
347
+ provided on the command line, and the extracting 16K from about 2/3rds of
348
+ the way through the uncompressed output, and writing that to stdout. */
349
+ int main(int argc, char **argv)
350
+ {
351
+ int len;
352
+ off_t offset;
353
+ FILE *in;
354
+ struct access *index;
355
+ unsigned char buf[CHUNK];
356
+
357
+ /* open input file */
358
+ if (argc != 2) {
359
+ fprintf(stderr, "usage: zran file.gz\n");
360
+ return 1;
361
+ }
362
+ in = fopen(argv[1], "rb");
363
+ if (in == NULL) {
364
+ fprintf(stderr, "zran: could not open %s for reading\n", argv[1]);
365
+ return 1;
366
+ }
367
+
368
+ /* build index */
369
+ len = build_index(in, SPAN, &index);
370
+ if (len < 0) {
371
+ fclose(in);
372
+ switch (len) {
373
+ case Z_MEM_ERROR:
374
+ fprintf(stderr, "zran: out of memory\n");
375
+ break;
376
+ case Z_DATA_ERROR:
377
+ fprintf(stderr, "zran: compressed data error in %s\n", argv[1]);
378
+ break;
379
+ case Z_ERRNO:
380
+ fprintf(stderr, "zran: read error on %s\n", argv[1]);
381
+ break;
382
+ default:
383
+ fprintf(stderr, "zran: error %d while building index\n", len);
384
+ }
385
+ return 1;
386
+ }
387
+ fprintf(stderr, "zran: built index with %d access points\n", len);
388
+
389
+ /* use index by reading some bytes from an arbitrary offset */
390
+ offset = (index->list[index->have - 1].out << 1) / 3;
391
+ len = extract(in, index, offset, buf, CHUNK);
392
+ if (len < 0)
393
+ fprintf(stderr, "zran: extraction failed: %s error\n",
394
+ len == Z_MEM_ERROR ? "out of memory" : "input corrupted");
395
+ else {
396
+ fwrite(buf, 1, len, stdout);
397
+ fprintf(stderr, "zran: extracted %d bytes at %llu\n", len, offset);
398
+ }
399
+
400
+ /* clean up and exit */
401
+ free_index(index);
402
+ fclose(in);
403
+ return 0;
404
+ }