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 +1,322 @@
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+ /* minigzip.c -- simulate gzip using the zlib compression library
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+ * Copyright (C) 1995-2005 Jean-loup Gailly.
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ /*
7
+ * minigzip is a minimal implementation of the gzip utility. This is
8
+ * only an example of using zlib and isn't meant to replace the
9
+ * full-featured gzip. No attempt is made to deal with file systems
10
+ * limiting names to 14 or 8+3 characters, etc... Error checking is
11
+ * very limited. So use minigzip only for testing; use gzip for the
12
+ * real thing. On MSDOS, use only on file names without extension
13
+ * or in pipe mode.
14
+ */
15
+
16
+ /* @(#) $Id$ */
17
+
18
+ #include <stdio.h>
19
+ #include "zlib.h"
20
+
21
+ #ifdef STDC
22
+ # include <string.h>
23
+ # include <stdlib.h>
24
+ #endif
25
+
26
+ #ifdef USE_MMAP
27
+ # include <sys/types.h>
28
+ # include <sys/mman.h>
29
+ # include <sys/stat.h>
30
+ #endif
31
+
32
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
33
+ # include <fcntl.h>
34
+ # include <io.h>
35
+ # define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
36
+ #else
37
+ # define SET_BINARY_MODE(file)
38
+ #endif
39
+
40
+ #ifdef VMS
41
+ # define unlink delete
42
+ # define GZ_SUFFIX "-gz"
43
+ #endif
44
+ #ifdef RISCOS
45
+ # define unlink remove
46
+ # define GZ_SUFFIX "-gz"
47
+ # define fileno(file) file->__file
48
+ #endif
49
+ #if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
50
+ # include <unix.h> /* for fileno */
51
+ #endif
52
+
53
+ #ifndef WIN32 /* unlink already in stdio.h for WIN32 */
54
+ extern int unlink OF((const char *));
55
+ #endif
56
+
57
+ #ifndef GZ_SUFFIX
58
+ # define GZ_SUFFIX ".gz"
59
+ #endif
60
+ #define SUFFIX_LEN (sizeof(GZ_SUFFIX)-1)
61
+
62
+ #define BUFLEN 16384
63
+ #define MAX_NAME_LEN 1024
64
+
65
+ #ifdef MAXSEG_64K
66
+ # define local static
67
+ /* Needed for systems with limitation on stack size. */
68
+ #else
69
+ # define local
70
+ #endif
71
+
72
+ char *prog;
73
+
74
+ void error OF((const char *msg));
75
+ void gz_compress OF((FILE *in, gzFile out));
76
+ #ifdef USE_MMAP
77
+ int gz_compress_mmap OF((FILE *in, gzFile out));
78
+ #endif
79
+ void gz_uncompress OF((gzFile in, FILE *out));
80
+ void file_compress OF((char *file, char *mode));
81
+ void file_uncompress OF((char *file));
82
+ int main OF((int argc, char *argv[]));
83
+
84
+ /* ===========================================================================
85
+ * Display error message and exit
86
+ */
87
+ void error(msg)
88
+ const char *msg;
89
+ {
90
+ fprintf(stderr, "%s: %s\n", prog, msg);
91
+ exit(1);
92
+ }
93
+
94
+ /* ===========================================================================
95
+ * Compress input to output then close both files.
96
+ */
97
+
98
+ void gz_compress(in, out)
99
+ FILE *in;
100
+ gzFile out;
101
+ {
102
+ local char buf[BUFLEN];
103
+ int len;
104
+ int err;
105
+
106
+ #ifdef USE_MMAP
107
+ /* Try first compressing with mmap. If mmap fails (minigzip used in a
108
+ * pipe), use the normal fread loop.
109
+ */
110
+ if (gz_compress_mmap(in, out) == Z_OK) return;
111
+ #endif
112
+ for (;;) {
113
+ len = (int)fread(buf, 1, sizeof(buf), in);
114
+ if (ferror(in)) {
115
+ perror("fread");
116
+ exit(1);
117
+ }
118
+ if (len == 0) break;
119
+
120
+ if (gzwrite(out, buf, (unsigned)len) != len) error(gzerror(out, &err));
121
+ }
122
+ fclose(in);
123
+ if (gzclose(out) != Z_OK) error("failed gzclose");
124
+ }
125
+
126
+ #ifdef USE_MMAP /* MMAP version, Miguel Albrecht <malbrech@eso.org> */
127
+
128
+ /* Try compressing the input file at once using mmap. Return Z_OK if
129
+ * if success, Z_ERRNO otherwise.
130
+ */
131
+ int gz_compress_mmap(in, out)
132
+ FILE *in;
133
+ gzFile out;
134
+ {
135
+ int len;
136
+ int err;
137
+ int ifd = fileno(in);
138
+ caddr_t buf; /* mmap'ed buffer for the entire input file */
139
+ off_t buf_len; /* length of the input file */
140
+ struct stat sb;
141
+
142
+ /* Determine the size of the file, needed for mmap: */
143
+ if (fstat(ifd, &sb) < 0) return Z_ERRNO;
144
+ buf_len = sb.st_size;
145
+ if (buf_len <= 0) return Z_ERRNO;
146
+
147
+ /* Now do the actual mmap: */
148
+ buf = mmap((caddr_t) 0, buf_len, PROT_READ, MAP_SHARED, ifd, (off_t)0);
149
+ if (buf == (caddr_t)(-1)) return Z_ERRNO;
150
+
151
+ /* Compress the whole file at once: */
152
+ len = gzwrite(out, (char *)buf, (unsigned)buf_len);
153
+
154
+ if (len != (int)buf_len) error(gzerror(out, &err));
155
+
156
+ munmap(buf, buf_len);
157
+ fclose(in);
158
+ if (gzclose(out) != Z_OK) error("failed gzclose");
159
+ return Z_OK;
160
+ }
161
+ #endif /* USE_MMAP */
162
+
163
+ /* ===========================================================================
164
+ * Uncompress input to output then close both files.
165
+ */
166
+ void gz_uncompress(in, out)
167
+ gzFile in;
168
+ FILE *out;
169
+ {
170
+ local char buf[BUFLEN];
171
+ int len;
172
+ int err;
173
+
174
+ for (;;) {
175
+ len = gzread(in, buf, sizeof(buf));
176
+ if (len < 0) error (gzerror(in, &err));
177
+ if (len == 0) break;
178
+
179
+ if ((int)fwrite(buf, 1, (unsigned)len, out) != len) {
180
+ error("failed fwrite");
181
+ }
182
+ }
183
+ if (fclose(out)) error("failed fclose");
184
+
185
+ if (gzclose(in) != Z_OK) error("failed gzclose");
186
+ }
187
+
188
+
189
+ /* ===========================================================================
190
+ * Compress the given file: create a corresponding .gz file and remove the
191
+ * original.
192
+ */
193
+ void file_compress(file, mode)
194
+ char *file;
195
+ char *mode;
196
+ {
197
+ local char outfile[MAX_NAME_LEN];
198
+ FILE *in;
199
+ gzFile out;
200
+
201
+ strcpy(outfile, file);
202
+ strcat(outfile, GZ_SUFFIX);
203
+
204
+ in = fopen(file, "rb");
205
+ if (in == NULL) {
206
+ perror(file);
207
+ exit(1);
208
+ }
209
+ out = gzopen(outfile, mode);
210
+ if (out == NULL) {
211
+ fprintf(stderr, "%s: can't gzopen %s\n", prog, outfile);
212
+ exit(1);
213
+ }
214
+ gz_compress(in, out);
215
+
216
+ unlink(file);
217
+ }
218
+
219
+
220
+ /* ===========================================================================
221
+ * Uncompress the given file and remove the original.
222
+ */
223
+ void file_uncompress(file)
224
+ char *file;
225
+ {
226
+ local char buf[MAX_NAME_LEN];
227
+ char *infile, *outfile;
228
+ FILE *out;
229
+ gzFile in;
230
+ uInt len = (uInt)strlen(file);
231
+
232
+ strcpy(buf, file);
233
+
234
+ if (len > SUFFIX_LEN && strcmp(file+len-SUFFIX_LEN, GZ_SUFFIX) == 0) {
235
+ infile = file;
236
+ outfile = buf;
237
+ outfile[len-3] = '\0';
238
+ } else {
239
+ outfile = file;
240
+ infile = buf;
241
+ strcat(infile, GZ_SUFFIX);
242
+ }
243
+ in = gzopen(infile, "rb");
244
+ if (in == NULL) {
245
+ fprintf(stderr, "%s: can't gzopen %s\n", prog, infile);
246
+ exit(1);
247
+ }
248
+ out = fopen(outfile, "wb");
249
+ if (out == NULL) {
250
+ perror(file);
251
+ exit(1);
252
+ }
253
+
254
+ gz_uncompress(in, out);
255
+
256
+ unlink(infile);
257
+ }
258
+
259
+
260
+ /* ===========================================================================
261
+ * Usage: minigzip [-d] [-f] [-h] [-r] [-1 to -9] [files...]
262
+ * -d : decompress
263
+ * -f : compress with Z_FILTERED
264
+ * -h : compress with Z_HUFFMAN_ONLY
265
+ * -r : compress with Z_RLE
266
+ * -1 to -9 : compression level
267
+ */
268
+
269
+ int main(argc, argv)
270
+ int argc;
271
+ char *argv[];
272
+ {
273
+ int uncompr = 0;
274
+ gzFile file;
275
+ char outmode[20];
276
+
277
+ strcpy(outmode, "wb6 ");
278
+
279
+ prog = argv[0];
280
+ argc--, argv++;
281
+
282
+ while (argc > 0) {
283
+ if (strcmp(*argv, "-d") == 0)
284
+ uncompr = 1;
285
+ else if (strcmp(*argv, "-f") == 0)
286
+ outmode[3] = 'f';
287
+ else if (strcmp(*argv, "-h") == 0)
288
+ outmode[3] = 'h';
289
+ else if (strcmp(*argv, "-r") == 0)
290
+ outmode[3] = 'R';
291
+ else if ((*argv)[0] == '-' && (*argv)[1] >= '1' && (*argv)[1] <= '9' &&
292
+ (*argv)[2] == 0)
293
+ outmode[2] = (*argv)[1];
294
+ else
295
+ break;
296
+ argc--, argv++;
297
+ }
298
+ if (outmode[3] == ' ')
299
+ outmode[3] = 0;
300
+ if (argc == 0) {
301
+ SET_BINARY_MODE(stdin);
302
+ SET_BINARY_MODE(stdout);
303
+ if (uncompr) {
304
+ file = gzdopen(fileno(stdin), "rb");
305
+ if (file == NULL) error("can't gzdopen stdin");
306
+ gz_uncompress(file, stdout);
307
+ } else {
308
+ file = gzdopen(fileno(stdout), outmode);
309
+ if (file == NULL) error("can't gzdopen stdout");
310
+ gz_compress(stdin, file);
311
+ }
312
+ } else {
313
+ do {
314
+ if (uncompr) {
315
+ file_uncompress(*argv);
316
+ } else {
317
+ file_compress(*argv, outmode);
318
+ }
319
+ } while (argv++, --argc);
320
+ }
321
+ return 0;
322
+ }
@@ -0,0 +1,109 @@
1
+ # Makefile for zlib
2
+ # Borland C++
3
+ # Last updated: 15-Mar-2003
4
+
5
+ # To use, do "make -fmakefile.bor"
6
+ # To compile in small model, set below: MODEL=s
7
+
8
+ # WARNING: the small model is supported but only for small values of
9
+ # MAX_WBITS and MAX_MEM_LEVEL. For example:
10
+ # -DMAX_WBITS=11 -DDEF_WBITS=11 -DMAX_MEM_LEVEL=3
11
+ # If you wish to reduce the memory requirements (default 256K for big
12
+ # objects plus a few K), you can add to the LOC macro below:
13
+ # -DMAX_MEM_LEVEL=7 -DMAX_WBITS=14
14
+ # See zconf.h for details about the memory requirements.
15
+
16
+ # ------------ Turbo C++, Borland C++ ------------
17
+
18
+ # Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
19
+ # should be added to the environment via "set LOCAL_ZLIB=-DFOO" or added
20
+ # to the declaration of LOC here:
21
+ LOC = $(LOCAL_ZLIB)
22
+
23
+ # type for CPU required: 0: 8086, 1: 80186, 2: 80286, 3: 80386, etc.
24
+ CPU_TYP = 0
25
+
26
+ # memory model: one of s, m, c, l (small, medium, compact, large)
27
+ MODEL=l
28
+
29
+ # replace bcc with tcc for Turbo C++ 1.0, with bcc32 for the 32 bit version
30
+ CC=bcc
31
+ LD=bcc
32
+ AR=tlib
33
+
34
+ # compiler flags
35
+ # replace "-O2" by "-O -G -a -d" for Turbo C++ 1.0
36
+ CFLAGS=-O2 -Z -m$(MODEL) $(LOC)
37
+
38
+ LDFLAGS=-m$(MODEL) -f-
39
+
40
+
41
+ # variables
42
+ ZLIB_LIB = zlib_$(MODEL).lib
43
+
44
+ OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
45
+ OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
46
+ OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
47
+ OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
48
+
49
+
50
+ # targets
51
+ all: $(ZLIB_LIB) example.exe minigzip.exe
52
+
53
+ .c.obj:
54
+ $(CC) -c $(CFLAGS) $*.c
55
+
56
+ adler32.obj: adler32.c zlib.h zconf.h
57
+
58
+ compress.obj: compress.c zlib.h zconf.h
59
+
60
+ crc32.obj: crc32.c zlib.h zconf.h crc32.h
61
+
62
+ deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
63
+
64
+ gzio.obj: gzio.c zutil.h zlib.h zconf.h
65
+
66
+ infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
67
+ inffast.h inffixed.h
68
+
69
+ inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
70
+ inffast.h
71
+
72
+ inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
73
+ inffast.h inffixed.h
74
+
75
+ inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
76
+
77
+ trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
78
+
79
+ uncompr.obj: uncompr.c zlib.h zconf.h
80
+
81
+ zutil.obj: zutil.c zutil.h zlib.h zconf.h
82
+
83
+ example.obj: example.c zlib.h zconf.h
84
+
85
+ minigzip.obj: minigzip.c zlib.h zconf.h
86
+
87
+
88
+ # the command line is cut to fit in the MS-DOS 128 byte limit:
89
+ $(ZLIB_LIB): $(OBJ1) $(OBJ2)
90
+ -del $(ZLIB_LIB)
91
+ $(AR) $(ZLIB_LIB) $(OBJP1)
92
+ $(AR) $(ZLIB_LIB) $(OBJP2)
93
+
94
+ example.exe: example.obj $(ZLIB_LIB)
95
+ $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
96
+
97
+ minigzip.exe: minigzip.obj $(ZLIB_LIB)
98
+ $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
99
+
100
+ test: example.exe minigzip.exe
101
+ example
102
+ echo hello world | minigzip | minigzip -d
103
+
104
+ clean:
105
+ -del *.obj
106
+ -del *.lib
107
+ -del *.exe
108
+ -del zlib_*.bak
109
+ -del foo.gz
@@ -0,0 +1,104 @@
1
+ # Makefile for zlib. Modified for djgpp v2.0 by F. J. Donahoe, 3/15/96.
2
+ # Copyright (C) 1995-1998 Jean-loup Gailly.
3
+ # For conditions of distribution and use, see copyright notice in zlib.h
4
+
5
+ # To compile, or to compile and test, type:
6
+ #
7
+ # make -fmakefile.dj2; make test -fmakefile.dj2
8
+ #
9
+ # To install libz.a, zconf.h and zlib.h in the djgpp directories, type:
10
+ #
11
+ # make install -fmakefile.dj2
12
+ #
13
+ # after first defining LIBRARY_PATH and INCLUDE_PATH in djgpp.env as
14
+ # in the sample below if the pattern of the DJGPP distribution is to
15
+ # be followed. Remember that, while <sp>'es around <=> are ignored in
16
+ # makefiles, they are *not* in batch files or in djgpp.env.
17
+ # - - - - -
18
+ # [make]
19
+ # INCLUDE_PATH=%\>;INCLUDE_PATH%%\DJDIR%\include
20
+ # LIBRARY_PATH=%\>;LIBRARY_PATH%%\DJDIR%\lib
21
+ # BUTT=-m486
22
+ # - - - - -
23
+ # Alternately, these variables may be defined below, overriding the values
24
+ # in djgpp.env, as
25
+ # INCLUDE_PATH=c:\usr\include
26
+ # LIBRARY_PATH=c:\usr\lib
27
+
28
+ CC=gcc
29
+
30
+ #CFLAGS=-MMD -O
31
+ #CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
32
+ #CFLAGS=-MMD -g -DDEBUG
33
+ CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
34
+ -Wstrict-prototypes -Wmissing-prototypes
35
+
36
+ # If cp.exe is available, replace "copy /Y" with "cp -fp" .
37
+ CP=copy /Y
38
+ # If gnu install.exe is available, replace $(CP) with ginstall.
39
+ INSTALL=$(CP)
40
+ # The default value of RM is "rm -f." If "rm.exe" is found, comment out:
41
+ RM=del
42
+ LDLIBS=-L. -lz
43
+ LD=$(CC) -s -o
44
+ LDSHARED=$(CC)
45
+
46
+ INCL=zlib.h zconf.h
47
+ LIBS=libz.a
48
+
49
+ AR=ar rcs
50
+
51
+ prefix=/usr/local
52
+ exec_prefix = $(prefix)
53
+
54
+ OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
55
+ zutil.o inflate.o infback.o inftrees.o inffast.o
56
+
57
+ OBJA =
58
+ # to use the asm code: make OBJA=match.o
59
+
60
+ TEST_OBJS = example.o minigzip.o
61
+
62
+ all: example.exe minigzip.exe
63
+
64
+ check: test
65
+ test: all
66
+ ./example
67
+ echo hello world | .\minigzip | .\minigzip -d
68
+
69
+ %.o : %.c
70
+ $(CC) $(CFLAGS) -c $< -o $@
71
+
72
+ libz.a: $(OBJS) $(OBJA)
73
+ $(AR) $@ $(OBJS) $(OBJA)
74
+
75
+ %.exe : %.o $(LIBS)
76
+ $(LD) $@ $< $(LDLIBS)
77
+
78
+ # INCLUDE_PATH and LIBRARY_PATH were set for [make] in djgpp.env .
79
+
80
+ .PHONY : uninstall clean
81
+
82
+ install: $(INCL) $(LIBS)
83
+ -@if not exist $(INCLUDE_PATH)\nul mkdir $(INCLUDE_PATH)
84
+ -@if not exist $(LIBRARY_PATH)\nul mkdir $(LIBRARY_PATH)
85
+ $(INSTALL) zlib.h $(INCLUDE_PATH)
86
+ $(INSTALL) zconf.h $(INCLUDE_PATH)
87
+ $(INSTALL) libz.a $(LIBRARY_PATH)
88
+
89
+ uninstall:
90
+ $(RM) $(INCLUDE_PATH)\zlib.h
91
+ $(RM) $(INCLUDE_PATH)\zconf.h
92
+ $(RM) $(LIBRARY_PATH)\libz.a
93
+
94
+ clean:
95
+ $(RM) *.d
96
+ $(RM) *.o
97
+ $(RM) *.exe
98
+ $(RM) libz.a
99
+ $(RM) foo.gz
100
+
101
+ DEPS := $(wildcard *.d)
102
+ ifneq ($(DEPS),)
103
+ include $(DEPS)
104
+ endif