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 +1,1026 @@
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+ /* gzio.c -- IO on .gz files
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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
+ * Compile this file with -DNO_GZCOMPRESS to avoid the compression code.
6
+ */
7
+
8
+ /* @(#) $Id$ */
9
+
10
+ #include <stdio.h>
11
+
12
+ #include "zutil.h"
13
+
14
+ #ifdef NO_DEFLATE /* for compatibility with old definition */
15
+ # define NO_GZCOMPRESS
16
+ #endif
17
+
18
+ #ifndef NO_DUMMY_DECL
19
+ struct internal_state {int dummy;}; /* for buggy compilers */
20
+ #endif
21
+
22
+ #ifndef Z_BUFSIZE
23
+ # ifdef MAXSEG_64K
24
+ # define Z_BUFSIZE 4096 /* minimize memory usage for 16-bit DOS */
25
+ # else
26
+ # define Z_BUFSIZE 16384
27
+ # endif
28
+ #endif
29
+ #ifndef Z_PRINTF_BUFSIZE
30
+ # define Z_PRINTF_BUFSIZE 4096
31
+ #endif
32
+
33
+ #ifdef __MVS__
34
+ # pragma map (fdopen , "\174\174FDOPEN")
35
+ FILE *fdopen(int, const char *);
36
+ #endif
37
+
38
+ #ifndef STDC
39
+ extern voidp malloc OF((uInt size));
40
+ extern void free OF((voidpf ptr));
41
+ #endif
42
+
43
+ #define ALLOC(size) malloc(size)
44
+ #define TRYFREE(p) {if (p) free(p);}
45
+
46
+ static int const gz_magic[2] = {0x1f, 0x8b}; /* gzip magic header */
47
+
48
+ /* gzip flag byte */
49
+ #define ASCII_FLAG 0x01 /* bit 0 set: file probably ascii text */
50
+ #define HEAD_CRC 0x02 /* bit 1 set: header CRC present */
51
+ #define EXTRA_FIELD 0x04 /* bit 2 set: extra field present */
52
+ #define ORIG_NAME 0x08 /* bit 3 set: original file name present */
53
+ #define COMMENT 0x10 /* bit 4 set: file comment present */
54
+ #define RESERVED 0xE0 /* bits 5..7: reserved */
55
+
56
+ typedef struct gz_stream {
57
+ z_stream stream;
58
+ int z_err; /* error code for last stream operation */
59
+ int z_eof; /* set if end of input file */
60
+ FILE *file; /* .gz file */
61
+ Byte *inbuf; /* input buffer */
62
+ Byte *outbuf; /* output buffer */
63
+ uLong crc; /* crc32 of uncompressed data */
64
+ char *msg; /* error message */
65
+ char *path; /* path name for debugging only */
66
+ int transparent; /* 1 if input file is not a .gz file */
67
+ char mode; /* 'w' or 'r' */
68
+ z_off_t start; /* start of compressed data in file (header skipped) */
69
+ z_off_t in; /* bytes into deflate or inflate */
70
+ z_off_t out; /* bytes out of deflate or inflate */
71
+ int back; /* one character push-back */
72
+ int last; /* true if push-back is last character */
73
+ } gz_stream;
74
+
75
+
76
+ local gzFile gz_open OF((const char *path, const char *mode, int fd));
77
+ local int do_flush OF((gzFile file, int flush));
78
+ local int get_byte OF((gz_stream *s));
79
+ local void check_header OF((gz_stream *s));
80
+ local int destroy OF((gz_stream *s));
81
+ local void putLong OF((FILE *file, uLong x));
82
+ local uLong getLong OF((gz_stream *s));
83
+
84
+ /* ===========================================================================
85
+ Opens a gzip (.gz) file for reading or writing. The mode parameter
86
+ is as in fopen ("rb" or "wb"). The file is given either by file descriptor
87
+ or path name (if fd == -1).
88
+ gz_open returns NULL if the file could not be opened or if there was
89
+ insufficient memory to allocate the (de)compression state; errno
90
+ can be checked to distinguish the two cases (if errno is zero, the
91
+ zlib error is Z_MEM_ERROR).
92
+ */
93
+ local gzFile gz_open (path, mode, fd)
94
+ const char *path;
95
+ const char *mode;
96
+ int fd;
97
+ {
98
+ int err;
99
+ int level = Z_DEFAULT_COMPRESSION; /* compression level */
100
+ int strategy = Z_DEFAULT_STRATEGY; /* compression strategy */
101
+ char *p = (char*)mode;
102
+ gz_stream *s;
103
+ char fmode[80]; /* copy of mode, without the compression level */
104
+ char *m = fmode;
105
+
106
+ if (!path || !mode) return Z_NULL;
107
+
108
+ s = (gz_stream *)ALLOC(sizeof(gz_stream));
109
+ if (!s) return Z_NULL;
110
+
111
+ s->stream.zalloc = (alloc_func)0;
112
+ s->stream.zfree = (free_func)0;
113
+ s->stream.opaque = (voidpf)0;
114
+ s->stream.next_in = s->inbuf = Z_NULL;
115
+ s->stream.next_out = s->outbuf = Z_NULL;
116
+ s->stream.avail_in = s->stream.avail_out = 0;
117
+ s->file = NULL;
118
+ s->z_err = Z_OK;
119
+ s->z_eof = 0;
120
+ s->in = 0;
121
+ s->out = 0;
122
+ s->back = EOF;
123
+ s->crc = crc32(0L, Z_NULL, 0);
124
+ s->msg = NULL;
125
+ s->transparent = 0;
126
+
127
+ s->path = (char*)ALLOC(strlen(path)+1);
128
+ if (s->path == NULL) {
129
+ return destroy(s), (gzFile)Z_NULL;
130
+ }
131
+ strcpy(s->path, path); /* do this early for debugging */
132
+
133
+ s->mode = '\0';
134
+ do {
135
+ if (*p == 'r') s->mode = 'r';
136
+ if (*p == 'w' || *p == 'a') s->mode = 'w';
137
+ if (*p >= '0' && *p <= '9') {
138
+ level = *p - '0';
139
+ } else if (*p == 'f') {
140
+ strategy = Z_FILTERED;
141
+ } else if (*p == 'h') {
142
+ strategy = Z_HUFFMAN_ONLY;
143
+ } else if (*p == 'R') {
144
+ strategy = Z_RLE;
145
+ } else {
146
+ *m++ = *p; /* copy the mode */
147
+ }
148
+ } while (*p++ && m != fmode + sizeof(fmode));
149
+ if (s->mode == '\0') return destroy(s), (gzFile)Z_NULL;
150
+
151
+ if (s->mode == 'w') {
152
+ #ifdef NO_GZCOMPRESS
153
+ err = Z_STREAM_ERROR;
154
+ #else
155
+ err = deflateInit2(&(s->stream), level,
156
+ Z_DEFLATED, -MAX_WBITS, DEF_MEM_LEVEL, strategy);
157
+ /* windowBits is passed < 0 to suppress zlib header */
158
+
159
+ s->stream.next_out = s->outbuf = (Byte*)ALLOC(Z_BUFSIZE);
160
+ #endif
161
+ if (err != Z_OK || s->outbuf == Z_NULL) {
162
+ return destroy(s), (gzFile)Z_NULL;
163
+ }
164
+ } else {
165
+ s->stream.next_in = s->inbuf = (Byte*)ALLOC(Z_BUFSIZE);
166
+
167
+ err = inflateInit2(&(s->stream), -MAX_WBITS);
168
+ /* windowBits is passed < 0 to tell that there is no zlib header.
169
+ * Note that in this case inflate *requires* an extra "dummy" byte
170
+ * after the compressed stream in order to complete decompression and
171
+ * return Z_STREAM_END. Here the gzip CRC32 ensures that 4 bytes are
172
+ * present after the compressed stream.
173
+ */
174
+ if (err != Z_OK || s->inbuf == Z_NULL) {
175
+ return destroy(s), (gzFile)Z_NULL;
176
+ }
177
+ }
178
+ s->stream.avail_out = Z_BUFSIZE;
179
+
180
+ errno = 0;
181
+ s->file = fd < 0 ? F_OPEN(path, fmode) : (FILE*)fdopen(fd, fmode);
182
+
183
+ if (s->file == NULL) {
184
+ return destroy(s), (gzFile)Z_NULL;
185
+ }
186
+ if (s->mode == 'w') {
187
+ /* Write a very simple .gz header:
188
+ */
189
+ fprintf(s->file, "%c%c%c%c%c%c%c%c%c%c", gz_magic[0], gz_magic[1],
190
+ Z_DEFLATED, 0 /*flags*/, 0,0,0,0 /*time*/, 0 /*xflags*/, OS_CODE);
191
+ s->start = 10L;
192
+ /* We use 10L instead of ftell(s->file) to because ftell causes an
193
+ * fflush on some systems. This version of the library doesn't use
194
+ * start anyway in write mode, so this initialization is not
195
+ * necessary.
196
+ */
197
+ } else {
198
+ check_header(s); /* skip the .gz header */
199
+ s->start = ftell(s->file) - s->stream.avail_in;
200
+ }
201
+
202
+ return (gzFile)s;
203
+ }
204
+
205
+ /* ===========================================================================
206
+ Opens a gzip (.gz) file for reading or writing.
207
+ */
208
+ gzFile ZEXPORT gzopen (path, mode)
209
+ const char *path;
210
+ const char *mode;
211
+ {
212
+ return gz_open (path, mode, -1);
213
+ }
214
+
215
+ /* ===========================================================================
216
+ Associate a gzFile with the file descriptor fd. fd is not dup'ed here
217
+ to mimic the behavio(u)r of fdopen.
218
+ */
219
+ gzFile ZEXPORT gzdopen (fd, mode)
220
+ int fd;
221
+ const char *mode;
222
+ {
223
+ char name[46]; /* allow for up to 128-bit integers */
224
+
225
+ if (fd < 0) return (gzFile)Z_NULL;
226
+ sprintf(name, "<fd:%d>", fd); /* for debugging */
227
+
228
+ return gz_open (name, mode, fd);
229
+ }
230
+
231
+ /* ===========================================================================
232
+ * Update the compression level and strategy
233
+ */
234
+ int ZEXPORT gzsetparams (file, level, strategy)
235
+ gzFile file;
236
+ int level;
237
+ int strategy;
238
+ {
239
+ gz_stream *s = (gz_stream*)file;
240
+
241
+ if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR;
242
+
243
+ /* Make room to allow flushing */
244
+ if (s->stream.avail_out == 0) {
245
+
246
+ s->stream.next_out = s->outbuf;
247
+ if (fwrite(s->outbuf, 1, Z_BUFSIZE, s->file) != Z_BUFSIZE) {
248
+ s->z_err = Z_ERRNO;
249
+ }
250
+ s->stream.avail_out = Z_BUFSIZE;
251
+ }
252
+
253
+ return deflateParams (&(s->stream), level, strategy);
254
+ }
255
+
256
+ /* ===========================================================================
257
+ Read a byte from a gz_stream; update next_in and avail_in. Return EOF
258
+ for end of file.
259
+ IN assertion: the stream s has been sucessfully opened for reading.
260
+ */
261
+ local int get_byte(s)
262
+ gz_stream *s;
263
+ {
264
+ if (s->z_eof) return EOF;
265
+ if (s->stream.avail_in == 0) {
266
+ errno = 0;
267
+ s->stream.avail_in = (uInt)fread(s->inbuf, 1, Z_BUFSIZE, s->file);
268
+ if (s->stream.avail_in == 0) {
269
+ s->z_eof = 1;
270
+ if (ferror(s->file)) s->z_err = Z_ERRNO;
271
+ return EOF;
272
+ }
273
+ s->stream.next_in = s->inbuf;
274
+ }
275
+ s->stream.avail_in--;
276
+ return *(s->stream.next_in)++;
277
+ }
278
+
279
+ /* ===========================================================================
280
+ Check the gzip header of a gz_stream opened for reading. Set the stream
281
+ mode to transparent if the gzip magic header is not present; set s->err
282
+ to Z_DATA_ERROR if the magic header is present but the rest of the header
283
+ is incorrect.
284
+ IN assertion: the stream s has already been created sucessfully;
285
+ s->stream.avail_in is zero for the first time, but may be non-zero
286
+ for concatenated .gz files.
287
+ */
288
+ local void check_header(s)
289
+ gz_stream *s;
290
+ {
291
+ int method; /* method byte */
292
+ int flags; /* flags byte */
293
+ uInt len;
294
+ int c;
295
+
296
+ /* Assure two bytes in the buffer so we can peek ahead -- handle case
297
+ where first byte of header is at the end of the buffer after the last
298
+ gzip segment */
299
+ len = s->stream.avail_in;
300
+ if (len < 2) {
301
+ if (len) s->inbuf[0] = s->stream.next_in[0];
302
+ errno = 0;
303
+ len = (uInt)fread(s->inbuf + len, 1, Z_BUFSIZE >> len, s->file);
304
+ if (len == 0 && ferror(s->file)) s->z_err = Z_ERRNO;
305
+ s->stream.avail_in += len;
306
+ s->stream.next_in = s->inbuf;
307
+ if (s->stream.avail_in < 2) {
308
+ s->transparent = s->stream.avail_in;
309
+ return;
310
+ }
311
+ }
312
+
313
+ /* Peek ahead to check the gzip magic header */
314
+ if (s->stream.next_in[0] != gz_magic[0] ||
315
+ s->stream.next_in[1] != gz_magic[1]) {
316
+ s->transparent = 1;
317
+ return;
318
+ }
319
+ s->stream.avail_in -= 2;
320
+ s->stream.next_in += 2;
321
+
322
+ /* Check the rest of the gzip header */
323
+ method = get_byte(s);
324
+ flags = get_byte(s);
325
+ if (method != Z_DEFLATED || (flags & RESERVED) != 0) {
326
+ s->z_err = Z_DATA_ERROR;
327
+ return;
328
+ }
329
+
330
+ /* Discard time, xflags and OS code: */
331
+ for (len = 0; len < 6; len++) (void)get_byte(s);
332
+
333
+ if ((flags & EXTRA_FIELD) != 0) { /* skip the extra field */
334
+ len = (uInt)get_byte(s);
335
+ len += ((uInt)get_byte(s))<<8;
336
+ /* len is garbage if EOF but the loop below will quit anyway */
337
+ while (len-- != 0 && get_byte(s) != EOF) ;
338
+ }
339
+ if ((flags & ORIG_NAME) != 0) { /* skip the original file name */
340
+ while ((c = get_byte(s)) != 0 && c != EOF) ;
341
+ }
342
+ if ((flags & COMMENT) != 0) { /* skip the .gz file comment */
343
+ while ((c = get_byte(s)) != 0 && c != EOF) ;
344
+ }
345
+ if ((flags & HEAD_CRC) != 0) { /* skip the header crc */
346
+ for (len = 0; len < 2; len++) (void)get_byte(s);
347
+ }
348
+ s->z_err = s->z_eof ? Z_DATA_ERROR : Z_OK;
349
+ }
350
+
351
+ /* ===========================================================================
352
+ * Cleanup then free the given gz_stream. Return a zlib error code.
353
+ Try freeing in the reverse order of allocations.
354
+ */
355
+ local int destroy (s)
356
+ gz_stream *s;
357
+ {
358
+ int err = Z_OK;
359
+
360
+ if (!s) return Z_STREAM_ERROR;
361
+
362
+ TRYFREE(s->msg);
363
+
364
+ if (s->stream.state != NULL) {
365
+ if (s->mode == 'w') {
366
+ #ifdef NO_GZCOMPRESS
367
+ err = Z_STREAM_ERROR;
368
+ #else
369
+ err = deflateEnd(&(s->stream));
370
+ #endif
371
+ } else if (s->mode == 'r') {
372
+ err = inflateEnd(&(s->stream));
373
+ }
374
+ }
375
+ if (s->file != NULL && fclose(s->file)) {
376
+ #ifdef ESPIPE
377
+ if (errno != ESPIPE) /* fclose is broken for pipes in HP/UX */
378
+ #endif
379
+ err = Z_ERRNO;
380
+ }
381
+ if (s->z_err < 0) err = s->z_err;
382
+
383
+ TRYFREE(s->inbuf);
384
+ TRYFREE(s->outbuf);
385
+ TRYFREE(s->path);
386
+ TRYFREE(s);
387
+ return err;
388
+ }
389
+
390
+ /* ===========================================================================
391
+ Reads the given number of uncompressed bytes from the compressed file.
392
+ gzread returns the number of bytes actually read (0 for end of file).
393
+ */
394
+ int ZEXPORT gzread (file, buf, len)
395
+ gzFile file;
396
+ voidp buf;
397
+ unsigned len;
398
+ {
399
+ gz_stream *s = (gz_stream*)file;
400
+ Bytef *start = (Bytef*)buf; /* starting point for crc computation */
401
+ Byte *next_out; /* == stream.next_out but not forced far (for MSDOS) */
402
+
403
+ if (s == NULL || s->mode != 'r') return Z_STREAM_ERROR;
404
+
405
+ if (s->z_err == Z_DATA_ERROR || s->z_err == Z_ERRNO) return -1;
406
+ if (s->z_err == Z_STREAM_END) return 0; /* EOF */
407
+
408
+ next_out = (Byte*)buf;
409
+ s->stream.next_out = (Bytef*)buf;
410
+ s->stream.avail_out = len;
411
+
412
+ if (s->stream.avail_out && s->back != EOF) {
413
+ *next_out++ = s->back;
414
+ s->stream.next_out++;
415
+ s->stream.avail_out--;
416
+ s->back = EOF;
417
+ s->out++;
418
+ start++;
419
+ if (s->last) {
420
+ s->z_err = Z_STREAM_END;
421
+ return 1;
422
+ }
423
+ }
424
+
425
+ while (s->stream.avail_out != 0) {
426
+
427
+ if (s->transparent) {
428
+ /* Copy first the lookahead bytes: */
429
+ uInt n = s->stream.avail_in;
430
+ if (n > s->stream.avail_out) n = s->stream.avail_out;
431
+ if (n > 0) {
432
+ zmemcpy(s->stream.next_out, s->stream.next_in, n);
433
+ next_out += n;
434
+ s->stream.next_out = next_out;
435
+ s->stream.next_in += n;
436
+ s->stream.avail_out -= n;
437
+ s->stream.avail_in -= n;
438
+ }
439
+ if (s->stream.avail_out > 0) {
440
+ s->stream.avail_out -=
441
+ (uInt)fread(next_out, 1, s->stream.avail_out, s->file);
442
+ }
443
+ len -= s->stream.avail_out;
444
+ s->in += len;
445
+ s->out += len;
446
+ if (len == 0) s->z_eof = 1;
447
+ return (int)len;
448
+ }
449
+ if (s->stream.avail_in == 0 && !s->z_eof) {
450
+
451
+ errno = 0;
452
+ s->stream.avail_in = (uInt)fread(s->inbuf, 1, Z_BUFSIZE, s->file);
453
+ if (s->stream.avail_in == 0) {
454
+ s->z_eof = 1;
455
+ if (ferror(s->file)) {
456
+ s->z_err = Z_ERRNO;
457
+ break;
458
+ }
459
+ }
460
+ s->stream.next_in = s->inbuf;
461
+ }
462
+ s->in += s->stream.avail_in;
463
+ s->out += s->stream.avail_out;
464
+ s->z_err = inflate(&(s->stream), Z_NO_FLUSH);
465
+ s->in -= s->stream.avail_in;
466
+ s->out -= s->stream.avail_out;
467
+
468
+ if (s->z_err == Z_STREAM_END) {
469
+ /* Check CRC and original size */
470
+ s->crc = crc32(s->crc, start, (uInt)(s->stream.next_out - start));
471
+ start = s->stream.next_out;
472
+
473
+ if (getLong(s) != s->crc) {
474
+ s->z_err = Z_DATA_ERROR;
475
+ } else {
476
+ (void)getLong(s);
477
+ /* The uncompressed length returned by above getlong() may be
478
+ * different from s->out in case of concatenated .gz files.
479
+ * Check for such files:
480
+ */
481
+ check_header(s);
482
+ if (s->z_err == Z_OK) {
483
+ inflateReset(&(s->stream));
484
+ s->crc = crc32(0L, Z_NULL, 0);
485
+ }
486
+ }
487
+ }
488
+ if (s->z_err != Z_OK || s->z_eof) break;
489
+ }
490
+ s->crc = crc32(s->crc, start, (uInt)(s->stream.next_out - start));
491
+
492
+ if (len == s->stream.avail_out &&
493
+ (s->z_err == Z_DATA_ERROR || s->z_err == Z_ERRNO))
494
+ return -1;
495
+ return (int)(len - s->stream.avail_out);
496
+ }
497
+
498
+
499
+ /* ===========================================================================
500
+ Reads one byte from the compressed file. gzgetc returns this byte
501
+ or -1 in case of end of file or error.
502
+ */
503
+ int ZEXPORT gzgetc(file)
504
+ gzFile file;
505
+ {
506
+ unsigned char c;
507
+
508
+ return gzread(file, &c, 1) == 1 ? c : -1;
509
+ }
510
+
511
+
512
+ /* ===========================================================================
513
+ Push one byte back onto the stream.
514
+ */
515
+ int ZEXPORT gzungetc(c, file)
516
+ int c;
517
+ gzFile file;
518
+ {
519
+ gz_stream *s = (gz_stream*)file;
520
+
521
+ if (s == NULL || s->mode != 'r' || c == EOF || s->back != EOF) return EOF;
522
+ s->back = c;
523
+ s->out--;
524
+ s->last = (s->z_err == Z_STREAM_END);
525
+ if (s->last) s->z_err = Z_OK;
526
+ s->z_eof = 0;
527
+ return c;
528
+ }
529
+
530
+
531
+ /* ===========================================================================
532
+ Reads bytes from the compressed file until len-1 characters are
533
+ read, or a newline character is read and transferred to buf, or an
534
+ end-of-file condition is encountered. The string is then terminated
535
+ with a null character.
536
+ gzgets returns buf, or Z_NULL in case of error.
537
+
538
+ The current implementation is not optimized at all.
539
+ */
540
+ char * ZEXPORT gzgets(file, buf, len)
541
+ gzFile file;
542
+ char *buf;
543
+ int len;
544
+ {
545
+ char *b = buf;
546
+ if (buf == Z_NULL || len <= 0) return Z_NULL;
547
+
548
+ while (--len > 0 && gzread(file, buf, 1) == 1 && *buf++ != '\n') ;
549
+ *buf = '\0';
550
+ return b == buf && len > 0 ? Z_NULL : b;
551
+ }
552
+
553
+
554
+ #ifndef NO_GZCOMPRESS
555
+ /* ===========================================================================
556
+ Writes the given number of uncompressed bytes into the compressed file.
557
+ gzwrite returns the number of bytes actually written (0 in case of error).
558
+ */
559
+ int ZEXPORT gzwrite (file, buf, len)
560
+ gzFile file;
561
+ voidpc buf;
562
+ unsigned len;
563
+ {
564
+ gz_stream *s = (gz_stream*)file;
565
+
566
+ if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR;
567
+
568
+ s->stream.next_in = (Bytef*)buf;
569
+ s->stream.avail_in = len;
570
+
571
+ while (s->stream.avail_in != 0) {
572
+
573
+ if (s->stream.avail_out == 0) {
574
+
575
+ s->stream.next_out = s->outbuf;
576
+ if (fwrite(s->outbuf, 1, Z_BUFSIZE, s->file) != Z_BUFSIZE) {
577
+ s->z_err = Z_ERRNO;
578
+ break;
579
+ }
580
+ s->stream.avail_out = Z_BUFSIZE;
581
+ }
582
+ s->in += s->stream.avail_in;
583
+ s->out += s->stream.avail_out;
584
+ s->z_err = deflate(&(s->stream), Z_NO_FLUSH);
585
+ s->in -= s->stream.avail_in;
586
+ s->out -= s->stream.avail_out;
587
+ if (s->z_err != Z_OK) break;
588
+ }
589
+ s->crc = crc32(s->crc, (const Bytef *)buf, len);
590
+
591
+ return (int)(len - s->stream.avail_in);
592
+ }
593
+
594
+
595
+ /* ===========================================================================
596
+ Converts, formats, and writes the args to the compressed file under
597
+ control of the format string, as in fprintf. gzprintf returns the number of
598
+ uncompressed bytes actually written (0 in case of error).
599
+ */
600
+ #ifdef STDC
601
+ #include <stdarg.h>
602
+
603
+ int ZEXPORTVA gzprintf (gzFile file, const char *format, /* args */ ...)
604
+ {
605
+ char buf[Z_PRINTF_BUFSIZE];
606
+ va_list va;
607
+ int len;
608
+
609
+ buf[sizeof(buf) - 1] = 0;
610
+ va_start(va, format);
611
+ #ifdef NO_vsnprintf
612
+ # ifdef HAS_vsprintf_void
613
+ (void)vsprintf(buf, format, va);
614
+ va_end(va);
615
+ for (len = 0; len < sizeof(buf); len++)
616
+ if (buf[len] == 0) break;
617
+ # else
618
+ len = vsprintf(buf, format, va);
619
+ va_end(va);
620
+ # endif
621
+ #else
622
+ # ifdef HAS_vsnprintf_void
623
+ (void)vsnprintf(buf, sizeof(buf), format, va);
624
+ va_end(va);
625
+ len = strlen(buf);
626
+ # else
627
+ len = vsnprintf(buf, sizeof(buf), format, va);
628
+ va_end(va);
629
+ # endif
630
+ #endif
631
+ if (len <= 0 || len >= (int)sizeof(buf) || buf[sizeof(buf) - 1] != 0)
632
+ return 0;
633
+ return gzwrite(file, buf, (unsigned)len);
634
+ }
635
+ #else /* not ANSI C */
636
+
637
+ int ZEXPORTVA gzprintf (file, format, a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
638
+ a11, a12, a13, a14, a15, a16, a17, a18, a19, a20)
639
+ gzFile file;
640
+ const char *format;
641
+ int a1, a2, a3, a4, a5, a6, a7, a8, a9, a10,
642
+ a11, a12, a13, a14, a15, a16, a17, a18, a19, a20;
643
+ {
644
+ char buf[Z_PRINTF_BUFSIZE];
645
+ int len;
646
+
647
+ buf[sizeof(buf) - 1] = 0;
648
+ #ifdef NO_snprintf
649
+ # ifdef HAS_sprintf_void
650
+ sprintf(buf, format, a1, a2, a3, a4, a5, a6, a7, a8,
651
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
652
+ for (len = 0; len < sizeof(buf); len++)
653
+ if (buf[len] == 0) break;
654
+ # else
655
+ len = sprintf(buf, format, a1, a2, a3, a4, a5, a6, a7, a8,
656
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
657
+ # endif
658
+ #else
659
+ # ifdef HAS_snprintf_void
660
+ snprintf(buf, sizeof(buf), format, a1, a2, a3, a4, a5, a6, a7, a8,
661
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
662
+ len = strlen(buf);
663
+ # else
664
+ len = snprintf(buf, sizeof(buf), format, a1, a2, a3, a4, a5, a6, a7, a8,
665
+ a9, a10, a11, a12, a13, a14, a15, a16, a17, a18, a19, a20);
666
+ # endif
667
+ #endif
668
+ if (len <= 0 || len >= sizeof(buf) || buf[sizeof(buf) - 1] != 0)
669
+ return 0;
670
+ return gzwrite(file, buf, len);
671
+ }
672
+ #endif
673
+
674
+ /* ===========================================================================
675
+ Writes c, converted to an unsigned char, into the compressed file.
676
+ gzputc returns the value that was written, or -1 in case of error.
677
+ */
678
+ int ZEXPORT gzputc(file, c)
679
+ gzFile file;
680
+ int c;
681
+ {
682
+ unsigned char cc = (unsigned char) c; /* required for big endian systems */
683
+
684
+ return gzwrite(file, &cc, 1) == 1 ? (int)cc : -1;
685
+ }
686
+
687
+
688
+ /* ===========================================================================
689
+ Writes the given null-terminated string to the compressed file, excluding
690
+ the terminating null character.
691
+ gzputs returns the number of characters written, or -1 in case of error.
692
+ */
693
+ int ZEXPORT gzputs(file, s)
694
+ gzFile file;
695
+ const char *s;
696
+ {
697
+ return gzwrite(file, (char*)s, (unsigned)strlen(s));
698
+ }
699
+
700
+
701
+ /* ===========================================================================
702
+ Flushes all pending output into the compressed file. The parameter
703
+ flush is as in the deflate() function.
704
+ */
705
+ local int do_flush (file, flush)
706
+ gzFile file;
707
+ int flush;
708
+ {
709
+ uInt len;
710
+ int done = 0;
711
+ gz_stream *s = (gz_stream*)file;
712
+
713
+ if (s == NULL || s->mode != 'w') return Z_STREAM_ERROR;
714
+
715
+ s->stream.avail_in = 0; /* should be zero already anyway */
716
+
717
+ for (;;) {
718
+ len = Z_BUFSIZE - s->stream.avail_out;
719
+
720
+ if (len != 0) {
721
+ if ((uInt)fwrite(s->outbuf, 1, len, s->file) != len) {
722
+ s->z_err = Z_ERRNO;
723
+ return Z_ERRNO;
724
+ }
725
+ s->stream.next_out = s->outbuf;
726
+ s->stream.avail_out = Z_BUFSIZE;
727
+ }
728
+ if (done) break;
729
+ s->out += s->stream.avail_out;
730
+ s->z_err = deflate(&(s->stream), flush);
731
+ s->out -= s->stream.avail_out;
732
+
733
+ /* Ignore the second of two consecutive flushes: */
734
+ if (len == 0 && s->z_err == Z_BUF_ERROR) s->z_err = Z_OK;
735
+
736
+ /* deflate has finished flushing only when it hasn't used up
737
+ * all the available space in the output buffer:
738
+ */
739
+ done = (s->stream.avail_out != 0 || s->z_err == Z_STREAM_END);
740
+
741
+ if (s->z_err != Z_OK && s->z_err != Z_STREAM_END) break;
742
+ }
743
+ return s->z_err == Z_STREAM_END ? Z_OK : s->z_err;
744
+ }
745
+
746
+ int ZEXPORT gzflush (file, flush)
747
+ gzFile file;
748
+ int flush;
749
+ {
750
+ gz_stream *s = (gz_stream*)file;
751
+ int err = do_flush (file, flush);
752
+
753
+ if (err) return err;
754
+ fflush(s->file);
755
+ return s->z_err == Z_STREAM_END ? Z_OK : s->z_err;
756
+ }
757
+ #endif /* NO_GZCOMPRESS */
758
+
759
+ /* ===========================================================================
760
+ Sets the starting position for the next gzread or gzwrite on the given
761
+ compressed file. The offset represents a number of bytes in the
762
+ gzseek returns the resulting offset location as measured in bytes from
763
+ the beginning of the uncompressed stream, or -1 in case of error.
764
+ SEEK_END is not implemented, returns error.
765
+ In this version of the library, gzseek can be extremely slow.
766
+ */
767
+ z_off_t ZEXPORT gzseek (file, offset, whence)
768
+ gzFile file;
769
+ z_off_t offset;
770
+ int whence;
771
+ {
772
+ gz_stream *s = (gz_stream*)file;
773
+
774
+ if (s == NULL || whence == SEEK_END ||
775
+ s->z_err == Z_ERRNO || s->z_err == Z_DATA_ERROR) {
776
+ return -1L;
777
+ }
778
+
779
+ if (s->mode == 'w') {
780
+ #ifdef NO_GZCOMPRESS
781
+ return -1L;
782
+ #else
783
+ if (whence == SEEK_SET) {
784
+ offset -= s->in;
785
+ }
786
+ if (offset < 0) return -1L;
787
+
788
+ /* At this point, offset is the number of zero bytes to write. */
789
+ if (s->inbuf == Z_NULL) {
790
+ s->inbuf = (Byte*)ALLOC(Z_BUFSIZE); /* for seeking */
791
+ if (s->inbuf == Z_NULL) return -1L;
792
+ zmemzero(s->inbuf, Z_BUFSIZE);
793
+ }
794
+ while (offset > 0) {
795
+ uInt size = Z_BUFSIZE;
796
+ if (offset < Z_BUFSIZE) size = (uInt)offset;
797
+
798
+ size = gzwrite(file, s->inbuf, size);
799
+ if (size == 0) return -1L;
800
+
801
+ offset -= size;
802
+ }
803
+ return s->in;
804
+ #endif
805
+ }
806
+ /* Rest of function is for reading only */
807
+
808
+ /* compute absolute position */
809
+ if (whence == SEEK_CUR) {
810
+ offset += s->out;
811
+ }
812
+ if (offset < 0) return -1L;
813
+
814
+ if (s->transparent) {
815
+ /* map to fseek */
816
+ s->back = EOF;
817
+ s->stream.avail_in = 0;
818
+ s->stream.next_in = s->inbuf;
819
+ if (fseek(s->file, offset, SEEK_SET) < 0) return -1L;
820
+
821
+ s->in = s->out = offset;
822
+ return offset;
823
+ }
824
+
825
+ /* For a negative seek, rewind and use positive seek */
826
+ if (offset >= s->out) {
827
+ offset -= s->out;
828
+ } else if (gzrewind(file) < 0) {
829
+ return -1L;
830
+ }
831
+ /* offset is now the number of bytes to skip. */
832
+
833
+ if (offset != 0 && s->outbuf == Z_NULL) {
834
+ s->outbuf = (Byte*)ALLOC(Z_BUFSIZE);
835
+ if (s->outbuf == Z_NULL) return -1L;
836
+ }
837
+ if (offset && s->back != EOF) {
838
+ s->back = EOF;
839
+ s->out++;
840
+ offset--;
841
+ if (s->last) s->z_err = Z_STREAM_END;
842
+ }
843
+ while (offset > 0) {
844
+ int size = Z_BUFSIZE;
845
+ if (offset < Z_BUFSIZE) size = (int)offset;
846
+
847
+ size = gzread(file, s->outbuf, (uInt)size);
848
+ if (size <= 0) return -1L;
849
+ offset -= size;
850
+ }
851
+ return s->out;
852
+ }
853
+
854
+ /* ===========================================================================
855
+ Rewinds input file.
856
+ */
857
+ int ZEXPORT gzrewind (file)
858
+ gzFile file;
859
+ {
860
+ gz_stream *s = (gz_stream*)file;
861
+
862
+ if (s == NULL || s->mode != 'r') return -1;
863
+
864
+ s->z_err = Z_OK;
865
+ s->z_eof = 0;
866
+ s->back = EOF;
867
+ s->stream.avail_in = 0;
868
+ s->stream.next_in = s->inbuf;
869
+ s->crc = crc32(0L, Z_NULL, 0);
870
+ if (!s->transparent) (void)inflateReset(&s->stream);
871
+ s->in = 0;
872
+ s->out = 0;
873
+ return fseek(s->file, s->start, SEEK_SET);
874
+ }
875
+
876
+ /* ===========================================================================
877
+ Returns the starting position for the next gzread or gzwrite on the
878
+ given compressed file. This position represents a number of bytes in the
879
+ uncompressed data stream.
880
+ */
881
+ z_off_t ZEXPORT gztell (file)
882
+ gzFile file;
883
+ {
884
+ return gzseek(file, 0L, SEEK_CUR);
885
+ }
886
+
887
+ /* ===========================================================================
888
+ Returns 1 when EOF has previously been detected reading the given
889
+ input stream, otherwise zero.
890
+ */
891
+ int ZEXPORT gzeof (file)
892
+ gzFile file;
893
+ {
894
+ gz_stream *s = (gz_stream*)file;
895
+
896
+ /* With concatenated compressed files that can have embedded
897
+ * crc trailers, z_eof is no longer the only/best indicator of EOF
898
+ * on a gz_stream. Handle end-of-stream error explicitly here.
899
+ */
900
+ if (s == NULL || s->mode != 'r') return 0;
901
+ if (s->z_eof) return 1;
902
+ return s->z_err == Z_STREAM_END;
903
+ }
904
+
905
+ /* ===========================================================================
906
+ Returns 1 if reading and doing so transparently, otherwise zero.
907
+ */
908
+ int ZEXPORT gzdirect (file)
909
+ gzFile file;
910
+ {
911
+ gz_stream *s = (gz_stream*)file;
912
+
913
+ if (s == NULL || s->mode != 'r') return 0;
914
+ return s->transparent;
915
+ }
916
+
917
+ /* ===========================================================================
918
+ Outputs a long in LSB order to the given file
919
+ */
920
+ local void putLong (file, x)
921
+ FILE *file;
922
+ uLong x;
923
+ {
924
+ int n;
925
+ for (n = 0; n < 4; n++) {
926
+ fputc((int)(x & 0xff), file);
927
+ x >>= 8;
928
+ }
929
+ }
930
+
931
+ /* ===========================================================================
932
+ Reads a long in LSB order from the given gz_stream. Sets z_err in case
933
+ of error.
934
+ */
935
+ local uLong getLong (s)
936
+ gz_stream *s;
937
+ {
938
+ uLong x = (uLong)get_byte(s);
939
+ int c;
940
+
941
+ x += ((uLong)get_byte(s))<<8;
942
+ x += ((uLong)get_byte(s))<<16;
943
+ c = get_byte(s);
944
+ if (c == EOF) s->z_err = Z_DATA_ERROR;
945
+ x += ((uLong)c)<<24;
946
+ return x;
947
+ }
948
+
949
+ /* ===========================================================================
950
+ Flushes all pending output if necessary, closes the compressed file
951
+ and deallocates all the (de)compression state.
952
+ */
953
+ int ZEXPORT gzclose (file)
954
+ gzFile file;
955
+ {
956
+ gz_stream *s = (gz_stream*)file;
957
+
958
+ if (s == NULL) return Z_STREAM_ERROR;
959
+
960
+ if (s->mode == 'w') {
961
+ #ifdef NO_GZCOMPRESS
962
+ return Z_STREAM_ERROR;
963
+ #else
964
+ if (do_flush (file, Z_FINISH) != Z_OK)
965
+ return destroy((gz_stream*)file);
966
+
967
+ putLong (s->file, s->crc);
968
+ putLong (s->file, (uLong)(s->in & 0xffffffff));
969
+ #endif
970
+ }
971
+ return destroy((gz_stream*)file);
972
+ }
973
+
974
+ #ifdef STDC
975
+ # define zstrerror(errnum) strerror(errnum)
976
+ #else
977
+ # define zstrerror(errnum) ""
978
+ #endif
979
+
980
+ /* ===========================================================================
981
+ Returns the error message for the last error which occurred on the
982
+ given compressed file. errnum is set to zlib error number. If an
983
+ error occurred in the file system and not in the compression library,
984
+ errnum is set to Z_ERRNO and the application may consult errno
985
+ to get the exact error code.
986
+ */
987
+ const char * ZEXPORT gzerror (file, errnum)
988
+ gzFile file;
989
+ int *errnum;
990
+ {
991
+ char *m;
992
+ gz_stream *s = (gz_stream*)file;
993
+
994
+ if (s == NULL) {
995
+ *errnum = Z_STREAM_ERROR;
996
+ return (const char*)ERR_MSG(Z_STREAM_ERROR);
997
+ }
998
+ *errnum = s->z_err;
999
+ if (*errnum == Z_OK) return (const char*)"";
1000
+
1001
+ m = (char*)(*errnum == Z_ERRNO ? zstrerror(errno) : s->stream.msg);
1002
+
1003
+ if (m == NULL || *m == '\0') m = (char*)ERR_MSG(s->z_err);
1004
+
1005
+ TRYFREE(s->msg);
1006
+ s->msg = (char*)ALLOC(strlen(s->path) + strlen(m) + 3);
1007
+ if (s->msg == Z_NULL) return (const char*)ERR_MSG(Z_MEM_ERROR);
1008
+ strcpy(s->msg, s->path);
1009
+ strcat(s->msg, ": ");
1010
+ strcat(s->msg, m);
1011
+ return (const char*)s->msg;
1012
+ }
1013
+
1014
+ /* ===========================================================================
1015
+ Clear the error and end-of-file flags, and do the same for the real file.
1016
+ */
1017
+ void ZEXPORT gzclearerr (file)
1018
+ gzFile file;
1019
+ {
1020
+ gz_stream *s = (gz_stream*)file;
1021
+
1022
+ if (s == NULL) return;
1023
+ if (s->z_err != Z_STREAM_END) s->z_err = Z_OK;
1024
+ s->z_eof = 0;
1025
+ clearerr(s->file);
1026
+ }