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 +1,500 @@
1
+ /* gzappend -- command to append to a gzip file
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+
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+ Copyright (C) 2003 Mark Adler, all rights reserved
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+ version 1.1, 4 Nov 2003
5
+
6
+ This software is provided 'as-is', without any express or implied
7
+ warranty. In no event will the author be held liable for any damages
8
+ arising from the use of this software.
9
+
10
+ Permission is granted to anyone to use this software for any purpose,
11
+ including commercial applications, and to alter it and redistribute it
12
+ freely, subject to the following restrictions:
13
+
14
+ 1. The origin of this software must not be misrepresented; you must not
15
+ claim that you wrote the original software. If you use this software
16
+ in a product, an acknowledgment in the product documentation would be
17
+ appreciated but is not required.
18
+ 2. Altered source versions must be plainly marked as such, and must not be
19
+ misrepresented as being the original software.
20
+ 3. This notice may not be removed or altered from any source distribution.
21
+
22
+ Mark Adler madler@alumni.caltech.edu
23
+ */
24
+
25
+ /*
26
+ * Change history:
27
+ *
28
+ * 1.0 19 Oct 2003 - First version
29
+ * 1.1 4 Nov 2003 - Expand and clarify some comments and notes
30
+ * - Add version and copyright to help
31
+ * - Send help to stdout instead of stderr
32
+ * - Add some preemptive typecasts
33
+ * - Add L to constants in lseek() calls
34
+ * - Remove some debugging information in error messages
35
+ * - Use new data_type definition for zlib 1.2.1
36
+ * - Simplfy and unify file operations
37
+ * - Finish off gzip file in gztack()
38
+ * - Use deflatePrime() instead of adding empty blocks
39
+ * - Keep gzip file clean on appended file read errors
40
+ * - Use in-place rotate instead of auxiliary buffer
41
+ * (Why you ask? Because it was fun to write!)
42
+ */
43
+
44
+ /*
45
+ gzappend takes a gzip file and appends to it, compressing files from the
46
+ command line or data from stdin. The gzip file is written to directly, to
47
+ avoid copying that file, in case it's large. Note that this results in the
48
+ unfriendly behavior that if gzappend fails, the gzip file is corrupted.
49
+
50
+ This program was written to illustrate the use of the new Z_BLOCK option of
51
+ zlib 1.2.x's inflate() function. This option returns from inflate() at each
52
+ block boundary to facilitate locating and modifying the last block bit at
53
+ the start of the final deflate block. Also whether using Z_BLOCK or not,
54
+ another required feature of zlib 1.2.x is that inflate() now provides the
55
+ number of unusued bits in the last input byte used. gzappend will not work
56
+ with versions of zlib earlier than 1.2.1.
57
+
58
+ gzappend first decompresses the gzip file internally, discarding all but
59
+ the last 32K of uncompressed data, and noting the location of the last block
60
+ bit and the number of unused bits in the last byte of the compressed data.
61
+ The gzip trailer containing the CRC-32 and length of the uncompressed data
62
+ is verified. This trailer will be later overwritten.
63
+
64
+ Then the last block bit is cleared by seeking back in the file and rewriting
65
+ the byte that contains it. Seeking forward, the last byte of the compressed
66
+ data is saved along with the number of unused bits to initialize deflate.
67
+
68
+ A deflate process is initialized, using the last 32K of the uncompressed
69
+ data from the gzip file to initialize the dictionary. If the total
70
+ uncompressed data was less than 32K, then all of it is used to initialize
71
+ the dictionary. The deflate output bit buffer is also initialized with the
72
+ last bits from the original deflate stream. From here on, the data to
73
+ append is simply compressed using deflate, and written to the gzip file.
74
+ When that is complete, the new CRC-32 and uncompressed length are written
75
+ as the trailer of the gzip file.
76
+ */
77
+
78
+ #include <stdio.h>
79
+ #include <stdlib.h>
80
+ #include <string.h>
81
+ #include <fcntl.h>
82
+ #include <unistd.h>
83
+ #include "zlib.h"
84
+
85
+ #define local static
86
+ #define LGCHUNK 14
87
+ #define CHUNK (1U << LGCHUNK)
88
+ #define DSIZE 32768U
89
+
90
+ /* print an error message and terminate with extreme prejudice */
91
+ local void bye(char *msg1, char *msg2)
92
+ {
93
+ fprintf(stderr, "gzappend error: %s%s\n", msg1, msg2);
94
+ exit(1);
95
+ }
96
+
97
+ /* return the greatest common divisor of a and b using Euclid's algorithm,
98
+ modified to be fast when one argument much greater than the other, and
99
+ coded to avoid unnecessary swapping */
100
+ local unsigned gcd(unsigned a, unsigned b)
101
+ {
102
+ unsigned c;
103
+
104
+ while (a && b)
105
+ if (a > b) {
106
+ c = b;
107
+ while (a - c >= c)
108
+ c <<= 1;
109
+ a -= c;
110
+ }
111
+ else {
112
+ c = a;
113
+ while (b - c >= c)
114
+ c <<= 1;
115
+ b -= c;
116
+ }
117
+ return a + b;
118
+ }
119
+
120
+ /* rotate list[0..len-1] left by rot positions, in place */
121
+ local void rotate(unsigned char *list, unsigned len, unsigned rot)
122
+ {
123
+ unsigned char tmp;
124
+ unsigned cycles;
125
+ unsigned char *start, *last, *to, *from;
126
+
127
+ /* normalize rot and handle degenerate cases */
128
+ if (len < 2) return;
129
+ if (rot >= len) rot %= len;
130
+ if (rot == 0) return;
131
+
132
+ /* pointer to last entry in list */
133
+ last = list + (len - 1);
134
+
135
+ /* do simple left shift by one */
136
+ if (rot == 1) {
137
+ tmp = *list;
138
+ memcpy(list, list + 1, len - 1);
139
+ *last = tmp;
140
+ return;
141
+ }
142
+
143
+ /* do simple right shift by one */
144
+ if (rot == len - 1) {
145
+ tmp = *last;
146
+ memmove(list + 1, list, len - 1);
147
+ *list = tmp;
148
+ return;
149
+ }
150
+
151
+ /* otherwise do rotate as a set of cycles in place */
152
+ cycles = gcd(len, rot); /* number of cycles */
153
+ do {
154
+ start = from = list + cycles; /* start index is arbitrary */
155
+ tmp = *from; /* save entry to be overwritten */
156
+ for (;;) {
157
+ to = from; /* next step in cycle */
158
+ from += rot; /* go right rot positions */
159
+ if (from > last) from -= len; /* (pointer better not wrap) */
160
+ if (from == start) break; /* all but one shifted */
161
+ *to = *from; /* shift left */
162
+ }
163
+ *to = tmp; /* complete the circle */
164
+ } while (--cycles);
165
+ }
166
+
167
+ /* structure for gzip file read operations */
168
+ typedef struct {
169
+ int fd; /* file descriptor */
170
+ int size; /* 1 << size is bytes in buf */
171
+ unsigned left; /* bytes available at next */
172
+ unsigned char *buf; /* buffer */
173
+ unsigned char *next; /* next byte in buffer */
174
+ char *name; /* file name for error messages */
175
+ } file;
176
+
177
+ /* reload buffer */
178
+ local int readin(file *in)
179
+ {
180
+ int len;
181
+
182
+ len = read(in->fd, in->buf, 1 << in->size);
183
+ if (len == -1) bye("error reading ", in->name);
184
+ in->left = (unsigned)len;
185
+ in->next = in->buf;
186
+ return len;
187
+ }
188
+
189
+ /* read from file in, exit if end-of-file */
190
+ local int readmore(file *in)
191
+ {
192
+ if (readin(in) == 0) bye("unexpected end of ", in->name);
193
+ return 0;
194
+ }
195
+
196
+ #define read1(in) (in->left == 0 ? readmore(in) : 0, \
197
+ in->left--, *(in->next)++)
198
+
199
+ /* skip over n bytes of in */
200
+ local void skip(file *in, unsigned n)
201
+ {
202
+ unsigned bypass;
203
+
204
+ if (n > in->left) {
205
+ n -= in->left;
206
+ bypass = n & ~((1U << in->size) - 1);
207
+ if (bypass) {
208
+ if (lseek(in->fd, (off_t)bypass, SEEK_CUR) == -1)
209
+ bye("seeking ", in->name);
210
+ n -= bypass;
211
+ }
212
+ readmore(in);
213
+ if (n > in->left)
214
+ bye("unexpected end of ", in->name);
215
+ }
216
+ in->left -= n;
217
+ in->next += n;
218
+ }
219
+
220
+ /* read a four-byte unsigned integer, little-endian, from in */
221
+ unsigned long read4(file *in)
222
+ {
223
+ unsigned long val;
224
+
225
+ val = read1(in);
226
+ val += (unsigned)read1(in) << 8;
227
+ val += (unsigned long)read1(in) << 16;
228
+ val += (unsigned long)read1(in) << 24;
229
+ return val;
230
+ }
231
+
232
+ /* skip over gzip header */
233
+ local void gzheader(file *in)
234
+ {
235
+ int flags;
236
+ unsigned n;
237
+
238
+ if (read1(in) != 31 || read1(in) != 139) bye(in->name, " not a gzip file");
239
+ if (read1(in) != 8) bye("unknown compression method in", in->name);
240
+ flags = read1(in);
241
+ if (flags & 0xe0) bye("unknown header flags set in", in->name);
242
+ skip(in, 6);
243
+ if (flags & 4) {
244
+ n = read1(in);
245
+ n += (unsigned)(read1(in)) << 8;
246
+ skip(in, n);
247
+ }
248
+ if (flags & 8) while (read1(in) != 0) ;
249
+ if (flags & 16) while (read1(in) != 0) ;
250
+ if (flags & 2) skip(in, 2);
251
+ }
252
+
253
+ /* decompress gzip file "name", return strm with a deflate stream ready to
254
+ continue compression of the data in the gzip file, and return a file
255
+ descriptor pointing to where to write the compressed data -- the deflate
256
+ stream is initialized to compress using level "level" */
257
+ local int gzscan(char *name, z_stream *strm, int level)
258
+ {
259
+ int ret, lastbit, left, full;
260
+ unsigned have;
261
+ unsigned long crc, tot;
262
+ unsigned char *window;
263
+ off_t lastoff, end;
264
+ file gz;
265
+
266
+ /* open gzip file */
267
+ gz.name = name;
268
+ gz.fd = open(name, O_RDWR, 0);
269
+ if (gz.fd == -1) bye("cannot open ", name);
270
+ gz.buf = malloc(CHUNK);
271
+ if (gz.buf == NULL) bye("out of memory", "");
272
+ gz.size = LGCHUNK;
273
+ gz.left = 0;
274
+
275
+ /* skip gzip header */
276
+ gzheader(&gz);
277
+
278
+ /* prepare to decompress */
279
+ window = malloc(DSIZE);
280
+ if (window == NULL) bye("out of memory", "");
281
+ strm->zalloc = Z_NULL;
282
+ strm->zfree = Z_NULL;
283
+ strm->opaque = Z_NULL;
284
+ ret = inflateInit2(strm, -15);
285
+ if (ret != Z_OK) bye("out of memory", " or library mismatch");
286
+
287
+ /* decompress the deflate stream, saving append information */
288
+ lastbit = 0;
289
+ lastoff = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
290
+ left = 0;
291
+ strm->avail_in = gz.left;
292
+ strm->next_in = gz.next;
293
+ crc = crc32(0L, Z_NULL, 0);
294
+ have = full = 0;
295
+ do {
296
+ /* if needed, get more input */
297
+ if (strm->avail_in == 0) {
298
+ readmore(&gz);
299
+ strm->avail_in = gz.left;
300
+ strm->next_in = gz.next;
301
+ }
302
+
303
+ /* set up output to next available section of sliding window */
304
+ strm->avail_out = DSIZE - have;
305
+ strm->next_out = window + have;
306
+
307
+ /* inflate and check for errors */
308
+ ret = inflate(strm, Z_BLOCK);
309
+ if (ret == Z_STREAM_ERROR) bye("internal stream error!", "");
310
+ if (ret == Z_MEM_ERROR) bye("out of memory", "");
311
+ if (ret == Z_DATA_ERROR)
312
+ bye("invalid compressed data--format violated in", name);
313
+
314
+ /* update crc and sliding window pointer */
315
+ crc = crc32(crc, window + have, DSIZE - have - strm->avail_out);
316
+ if (strm->avail_out)
317
+ have = DSIZE - strm->avail_out;
318
+ else {
319
+ have = 0;
320
+ full = 1;
321
+ }
322
+
323
+ /* process end of block */
324
+ if (strm->data_type & 128) {
325
+ if (strm->data_type & 64)
326
+ left = strm->data_type & 0x1f;
327
+ else {
328
+ lastbit = strm->data_type & 0x1f;
329
+ lastoff = lseek(gz.fd, 0L, SEEK_CUR) - strm->avail_in;
330
+ }
331
+ }
332
+ } while (ret != Z_STREAM_END);
333
+ inflateEnd(strm);
334
+ gz.left = strm->avail_in;
335
+ gz.next = strm->next_in;
336
+
337
+ /* save the location of the end of the compressed data */
338
+ end = lseek(gz.fd, 0L, SEEK_CUR) - gz.left;
339
+
340
+ /* check gzip trailer and save total for deflate */
341
+ if (crc != read4(&gz))
342
+ bye("invalid compressed data--crc mismatch in ", name);
343
+ tot = strm->total_out;
344
+ if ((tot & 0xffffffffUL) != read4(&gz))
345
+ bye("invalid compressed data--length mismatch in", name);
346
+
347
+ /* if not at end of file, warn */
348
+ if (gz.left || readin(&gz))
349
+ fprintf(stderr,
350
+ "gzappend warning: junk at end of gzip file overwritten\n");
351
+
352
+ /* clear last block bit */
353
+ lseek(gz.fd, lastoff - (lastbit != 0), SEEK_SET);
354
+ if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
355
+ *gz.buf = (unsigned char)(*gz.buf ^ (1 << ((8 - lastbit) & 7)));
356
+ lseek(gz.fd, -1L, SEEK_CUR);
357
+ if (write(gz.fd, gz.buf, 1) != 1) bye("writing after seek to ", name);
358
+
359
+ /* if window wrapped, build dictionary from window by rotating */
360
+ if (full) {
361
+ rotate(window, DSIZE, have);
362
+ have = DSIZE;
363
+ }
364
+
365
+ /* set up deflate stream with window, crc, total_in, and leftover bits */
366
+ ret = deflateInit2(strm, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY);
367
+ if (ret != Z_OK) bye("out of memory", "");
368
+ deflateSetDictionary(strm, window, have);
369
+ strm->adler = crc;
370
+ strm->total_in = tot;
371
+ if (left) {
372
+ lseek(gz.fd, --end, SEEK_SET);
373
+ if (read(gz.fd, gz.buf, 1) != 1) bye("reading after seek on ", name);
374
+ deflatePrime(strm, 8 - left, *gz.buf);
375
+ }
376
+ lseek(gz.fd, end, SEEK_SET);
377
+
378
+ /* clean up and return */
379
+ free(window);
380
+ free(gz.buf);
381
+ return gz.fd;
382
+ }
383
+
384
+ /* append file "name" to gzip file gd using deflate stream strm -- if last
385
+ is true, then finish off the deflate stream at the end */
386
+ local void gztack(char *name, int gd, z_stream *strm, int last)
387
+ {
388
+ int fd, len, ret;
389
+ unsigned left;
390
+ unsigned char *in, *out;
391
+
392
+ /* open file to compress and append */
393
+ fd = 0;
394
+ if (name != NULL) {
395
+ fd = open(name, O_RDONLY, 0);
396
+ if (fd == -1)
397
+ fprintf(stderr, "gzappend warning: %s not found, skipping ...\n",
398
+ name);
399
+ }
400
+
401
+ /* allocate buffers */
402
+ in = fd == -1 ? NULL : malloc(CHUNK);
403
+ out = malloc(CHUNK);
404
+ if (out == NULL) bye("out of memory", "");
405
+
406
+ /* compress input file and append to gzip file */
407
+ do {
408
+ /* get more input */
409
+ len = fd == -1 ? 0 : read(fd, in, CHUNK);
410
+ if (len == -1) {
411
+ fprintf(stderr,
412
+ "gzappend warning: error reading %s, skipping rest ...\n",
413
+ name);
414
+ len = 0;
415
+ }
416
+ strm->avail_in = (unsigned)len;
417
+ strm->next_in = in;
418
+ if (len) strm->adler = crc32(strm->adler, in, (unsigned)len);
419
+
420
+ /* compress and write all available output */
421
+ do {
422
+ strm->avail_out = CHUNK;
423
+ strm->next_out = out;
424
+ ret = deflate(strm, last && len == 0 ? Z_FINISH : Z_NO_FLUSH);
425
+ left = CHUNK - strm->avail_out;
426
+ while (left) {
427
+ len = write(gd, out + CHUNK - strm->avail_out - left, left);
428
+ if (len == -1) bye("writing gzip file", "");
429
+ left -= (unsigned)len;
430
+ }
431
+ } while (strm->avail_out == 0 && ret != Z_STREAM_END);
432
+ } while (len != 0);
433
+
434
+ /* write trailer after last entry */
435
+ if (last) {
436
+ deflateEnd(strm);
437
+ out[0] = (unsigned char)(strm->adler);
438
+ out[1] = (unsigned char)(strm->adler >> 8);
439
+ out[2] = (unsigned char)(strm->adler >> 16);
440
+ out[3] = (unsigned char)(strm->adler >> 24);
441
+ out[4] = (unsigned char)(strm->total_in);
442
+ out[5] = (unsigned char)(strm->total_in >> 8);
443
+ out[6] = (unsigned char)(strm->total_in >> 16);
444
+ out[7] = (unsigned char)(strm->total_in >> 24);
445
+ len = 8;
446
+ do {
447
+ ret = write(gd, out + 8 - len, len);
448
+ if (ret == -1) bye("writing gzip file", "");
449
+ len -= ret;
450
+ } while (len);
451
+ close(gd);
452
+ }
453
+
454
+ /* clean up and return */
455
+ free(out);
456
+ if (in != NULL) free(in);
457
+ if (fd > 0) close(fd);
458
+ }
459
+
460
+ /* process the compression level option if present, scan the gzip file, and
461
+ append the specified files, or append the data from stdin if no other file
462
+ names are provided on the command line -- the gzip file must be writable
463
+ and seekable */
464
+ int main(int argc, char **argv)
465
+ {
466
+ int gd, level;
467
+ z_stream strm;
468
+
469
+ /* ignore command name */
470
+ argv++;
471
+
472
+ /* provide usage if no arguments */
473
+ if (*argv == NULL) {
474
+ printf("gzappend 1.1 (4 Nov 2003) Copyright (C) 2003 Mark Adler\n");
475
+ printf(
476
+ "usage: gzappend [-level] file.gz [ addthis [ andthis ... ]]\n");
477
+ return 0;
478
+ }
479
+
480
+ /* set compression level */
481
+ level = Z_DEFAULT_COMPRESSION;
482
+ if (argv[0][0] == '-') {
483
+ if (argv[0][1] < '0' || argv[0][1] > '9' || argv[0][2] != 0)
484
+ bye("invalid compression level", "");
485
+ level = argv[0][1] - '0';
486
+ if (*++argv == NULL) bye("no gzip file name after options", "");
487
+ }
488
+
489
+ /* prepare to append to gzip file */
490
+ gd = gzscan(*argv++, &strm, level);
491
+
492
+ /* append files on command line, or from stdin if none */
493
+ if (*argv == NULL)
494
+ gztack(NULL, gd, &strm, 1);
495
+ else
496
+ do {
497
+ gztack(*argv, gd, &strm, argv[1] == NULL);
498
+ } while (*++argv != NULL);
499
+ return 0;
500
+ }