bio-velvet_underground 0.0.1

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Files changed (286) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.travis.yml +13 -0
  5. data/Gemfile +19 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +53 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/ext/bioruby.patch +60 -0
  11. data/ext/mkrf_conf.rb +50 -0
  12. data/ext/src/Makefile +125 -0
  13. data/ext/src/src/allocArray.c +305 -0
  14. data/ext/src/src/allocArray.h +86 -0
  15. data/ext/src/src/autoOpen.c +107 -0
  16. data/ext/src/src/autoOpen.h +18 -0
  17. data/ext/src/src/binarySequences.c +813 -0
  18. data/ext/src/src/binarySequences.h +125 -0
  19. data/ext/src/src/concatenatedGraph.c +233 -0
  20. data/ext/src/src/concatenatedGraph.h +30 -0
  21. data/ext/src/src/concatenatedPreGraph.c +262 -0
  22. data/ext/src/src/concatenatedPreGraph.h +29 -0
  23. data/ext/src/src/correctedGraph.c +2642 -0
  24. data/ext/src/src/correctedGraph.h +32 -0
  25. data/ext/src/src/dfib.c +509 -0
  26. data/ext/src/src/dfib.h +69 -0
  27. data/ext/src/src/dfibHeap.c +89 -0
  28. data/ext/src/src/dfibHeap.h +39 -0
  29. data/ext/src/src/dfibpriv.h +105 -0
  30. data/ext/src/src/fib.c +628 -0
  31. data/ext/src/src/fib.h +78 -0
  32. data/ext/src/src/fibHeap.c +79 -0
  33. data/ext/src/src/fibHeap.h +41 -0
  34. data/ext/src/src/fibpriv.h +110 -0
  35. data/ext/src/src/globals.h +153 -0
  36. data/ext/src/src/graph.c +3983 -0
  37. data/ext/src/src/graph.h +233 -0
  38. data/ext/src/src/graphReConstruction.c +1472 -0
  39. data/ext/src/src/graphReConstruction.h +30 -0
  40. data/ext/src/src/graphStats.c +2167 -0
  41. data/ext/src/src/graphStats.h +72 -0
  42. data/ext/src/src/kmer.c +652 -0
  43. data/ext/src/src/kmer.h +73 -0
  44. data/ext/src/src/kmerOccurenceTable.c +236 -0
  45. data/ext/src/src/kmerOccurenceTable.h +44 -0
  46. data/ext/src/src/kseq.h +223 -0
  47. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  48. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  49. data/ext/src/src/passageMarker.c +677 -0
  50. data/ext/src/src/passageMarker.h +137 -0
  51. data/ext/src/src/preGraph.c +1717 -0
  52. data/ext/src/src/preGraph.h +106 -0
  53. data/ext/src/src/preGraphConstruction.c +990 -0
  54. data/ext/src/src/preGraphConstruction.h +26 -0
  55. data/ext/src/src/readCoherentGraph.c +557 -0
  56. data/ext/src/src/readCoherentGraph.h +30 -0
  57. data/ext/src/src/readSet.c +1734 -0
  58. data/ext/src/src/readSet.h +67 -0
  59. data/ext/src/src/recycleBin.c +199 -0
  60. data/ext/src/src/recycleBin.h +58 -0
  61. data/ext/src/src/roadMap.c +342 -0
  62. data/ext/src/src/roadMap.h +65 -0
  63. data/ext/src/src/run.c +318 -0
  64. data/ext/src/src/run.h +52 -0
  65. data/ext/src/src/run2.c +712 -0
  66. data/ext/src/src/scaffold.c +1876 -0
  67. data/ext/src/src/scaffold.h +64 -0
  68. data/ext/src/src/shortReadPairs.c +1243 -0
  69. data/ext/src/src/shortReadPairs.h +32 -0
  70. data/ext/src/src/splay.c +259 -0
  71. data/ext/src/src/splay.h +43 -0
  72. data/ext/src/src/splayTable.c +1315 -0
  73. data/ext/src/src/splayTable.h +31 -0
  74. data/ext/src/src/tightString.c +362 -0
  75. data/ext/src/src/tightString.h +82 -0
  76. data/ext/src/src/utility.c +199 -0
  77. data/ext/src/src/utility.h +98 -0
  78. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  79. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  80. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  81. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  82. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  83. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  84. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  85. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  86. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  87. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  88. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  89. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
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  92. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  93. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  94. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
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  107. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  108. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  109. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  110. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  111. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  112. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  113. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  114. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  115. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  116. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  117. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  118. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  119. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  120. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
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  129. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
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  131. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
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  136. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
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  141. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
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  145. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
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  250. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  251. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  252. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  253. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  254. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  255. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  256. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  257. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  258. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  259. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  260. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  261. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  262. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  263. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  264. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  265. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  266. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  267. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  268. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  269. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  270. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  271. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  272. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  273. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  274. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  275. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  276. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  277. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  278. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  279. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  280. data/lib/bio-velvet_underground.rb +12 -0
  281. data/lib/bio-velvet_underground/external/VERSION +1 -0
  282. data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
  283. data/spec/binary_sequence_store_spec.rb +27 -0
  284. data/spec/data/1/CnyUnifiedSeq +0 -0
  285. data/spec/spec_helper.rb +31 -0
  286. metadata +456 -0
@@ -0,0 +1,31 @@
1
+ /* puff.h
2
+ Copyright (C) 2002, 2003 Mark Adler, all rights reserved
3
+ version 1.7, 3 Mar 2002
4
+
5
+ This software is provided 'as-is', without any express or implied
6
+ warranty. In no event will the author be held liable for any damages
7
+ arising from the use of this software.
8
+
9
+ Permission is granted to anyone to use this software for any purpose,
10
+ including commercial applications, and to alter it and redistribute it
11
+ freely, subject to the following restrictions:
12
+
13
+ 1. The origin of this software must not be misrepresented; you must not
14
+ claim that you wrote the original software. If you use this software
15
+ in a product, an acknowledgment in the product documentation would be
16
+ appreciated but is not required.
17
+ 2. Altered source versions must be plainly marked as such, and must not be
18
+ misrepresented as being the original software.
19
+ 3. This notice may not be removed or altered from any source distribution.
20
+
21
+ Mark Adler madler@alumni.caltech.edu
22
+ */
23
+
24
+
25
+ /*
26
+ * See puff.c for purpose and usage.
27
+ */
28
+ int puff(unsigned char *dest, /* pointer to destination pointer */
29
+ unsigned long *destlen, /* amount of output space */
30
+ unsigned char *source, /* pointer to source data pointer */
31
+ unsigned long *sourcelen); /* amount of input available */
@@ -0,0 +1,275 @@
1
+ #include <stdio.h>
2
+ #include <stdlib.h>
3
+ #include <windows.h>
4
+
5
+ #include "zlib.h"
6
+
7
+
8
+ void MyDoMinus64(LARGE_INTEGER *R,LARGE_INTEGER A,LARGE_INTEGER B)
9
+ {
10
+ R->HighPart = A.HighPart - B.HighPart;
11
+ if (A.LowPart >= B.LowPart)
12
+ R->LowPart = A.LowPart - B.LowPart;
13
+ else
14
+ {
15
+ R->LowPart = A.LowPart - B.LowPart;
16
+ R->HighPart --;
17
+ }
18
+ }
19
+
20
+ #ifdef _M_X64
21
+ // see http://msdn2.microsoft.com/library/twchhe95(en-us,vs.80).aspx for __rdtsc
22
+ unsigned __int64 __rdtsc(void);
23
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
24
+ {
25
+ // printf("rdtsc = %I64x\n",__rdtsc());
26
+ pbeginTime64->QuadPart=__rdtsc();
27
+ }
28
+
29
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
30
+ {
31
+ LARGE_INTEGER LIres;
32
+ unsigned _int64 res=__rdtsc()-((unsigned _int64)(beginTime64.QuadPart));
33
+ LIres.QuadPart=res;
34
+ // printf("rdtsc = %I64x\n",__rdtsc());
35
+ return LIres;
36
+ }
37
+ #else
38
+ #ifdef _M_IX86
39
+ void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
40
+ {
41
+ DWORD dwEdx,dwEax;
42
+ _asm
43
+ {
44
+ rdtsc
45
+ mov dwEax,eax
46
+ mov dwEdx,edx
47
+ }
48
+ pbeginTime64->LowPart=dwEax;
49
+ pbeginTime64->HighPart=dwEdx;
50
+ }
51
+
52
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
53
+ {
54
+ myGetRDTSC32(pbeginTime64);
55
+ }
56
+
57
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
58
+ {
59
+ LARGE_INTEGER LIres,endTime64;
60
+ myGetRDTSC32(&endTime64);
61
+
62
+ LIres.LowPart=LIres.HighPart=0;
63
+ MyDoMinus64(&LIres,endTime64,beginTime64);
64
+ return LIres;
65
+ }
66
+ #else
67
+ void myGetRDTSC32(LARGE_INTEGER * pbeginTime64)
68
+ {
69
+ }
70
+
71
+ void BeginCountRdtsc(LARGE_INTEGER * pbeginTime64)
72
+ {
73
+ }
74
+
75
+ LARGE_INTEGER GetResRdtsc(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
76
+ {
77
+ LARGE_INTEGER lr;
78
+ lr.QuadPart=0;
79
+ return lr;
80
+ }
81
+ #endif
82
+ #endif
83
+
84
+ void BeginCountPerfCounter(LARGE_INTEGER * pbeginTime64,BOOL fComputeTimeQueryPerf)
85
+ {
86
+ if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(pbeginTime64)))
87
+ {
88
+ pbeginTime64->LowPart = GetTickCount();
89
+ pbeginTime64->HighPart = 0;
90
+ }
91
+ }
92
+
93
+ DWORD GetMsecSincePerfCounter(LARGE_INTEGER beginTime64,BOOL fComputeTimeQueryPerf)
94
+ {
95
+ LARGE_INTEGER endTime64,ticksPerSecond,ticks;
96
+ DWORDLONG ticksShifted,tickSecShifted;
97
+ DWORD dwLog=16+0;
98
+ DWORD dwRet;
99
+ if ((!fComputeTimeQueryPerf) || (!QueryPerformanceCounter(&endTime64)))
100
+ dwRet = (GetTickCount() - beginTime64.LowPart)*1;
101
+ else
102
+ {
103
+ MyDoMinus64(&ticks,endTime64,beginTime64);
104
+ QueryPerformanceFrequency(&ticksPerSecond);
105
+
106
+
107
+ {
108
+ ticksShifted = Int64ShrlMod32(*(DWORDLONG*)&ticks,dwLog);
109
+ tickSecShifted = Int64ShrlMod32(*(DWORDLONG*)&ticksPerSecond,dwLog);
110
+
111
+ }
112
+
113
+ dwRet = (DWORD)((((DWORD)ticksShifted)*1000)/(DWORD)(tickSecShifted));
114
+ dwRet *=1;
115
+ }
116
+ return dwRet;
117
+ }
118
+
119
+ int ReadFileMemory(const char* filename,long* plFileSize,void** pFilePtr)
120
+ {
121
+ FILE* stream;
122
+ void* ptr;
123
+ int retVal=1;
124
+ stream=fopen(filename, "rb");
125
+ if (stream==NULL)
126
+ return 0;
127
+
128
+ fseek(stream,0,SEEK_END);
129
+
130
+ *plFileSize=ftell(stream);
131
+ fseek(stream,0,SEEK_SET);
132
+ ptr=malloc((*plFileSize)+1);
133
+ if (ptr==NULL)
134
+ retVal=0;
135
+ else
136
+ {
137
+ if (fread(ptr, 1, *plFileSize,stream) != (*plFileSize))
138
+ retVal=0;
139
+ }
140
+ fclose(stream);
141
+ *pFilePtr=ptr;
142
+ return retVal;
143
+ }
144
+
145
+ int main(int argc, char *argv[])
146
+ {
147
+ int BlockSizeCompress=0x8000;
148
+ int BlockSizeUncompress=0x8000;
149
+ int cprLevel=Z_DEFAULT_COMPRESSION ;
150
+ long lFileSize;
151
+ unsigned char* FilePtr;
152
+ long lBufferSizeCpr;
153
+ long lBufferSizeUncpr;
154
+ long lCompressedSize=0;
155
+ unsigned char* CprPtr;
156
+ unsigned char* UncprPtr;
157
+ long lSizeCpr,lSizeUncpr;
158
+ DWORD dwGetTick,dwMsecQP;
159
+ LARGE_INTEGER li_qp,li_rdtsc,dwResRdtsc;
160
+
161
+ if (argc<=1)
162
+ {
163
+ printf("run TestZlib <File> [BlockSizeCompress] [BlockSizeUncompress] [compres. level]\n");
164
+ return 0;
165
+ }
166
+
167
+ if (ReadFileMemory(argv[1],&lFileSize,&FilePtr)==0)
168
+ {
169
+ printf("error reading %s\n",argv[1]);
170
+ return 1;
171
+ }
172
+ else printf("file %s read, %u bytes\n",argv[1],lFileSize);
173
+
174
+ if (argc>=3)
175
+ BlockSizeCompress=atol(argv[2]);
176
+
177
+ if (argc>=4)
178
+ BlockSizeUncompress=atol(argv[3]);
179
+
180
+ if (argc>=5)
181
+ cprLevel=(int)atol(argv[4]);
182
+
183
+ lBufferSizeCpr = lFileSize + (lFileSize/0x10) + 0x200;
184
+ lBufferSizeUncpr = lBufferSizeCpr;
185
+
186
+ CprPtr=(unsigned char*)malloc(lBufferSizeCpr + BlockSizeCompress);
187
+
188
+ BeginCountPerfCounter(&li_qp,TRUE);
189
+ dwGetTick=GetTickCount();
190
+ BeginCountRdtsc(&li_rdtsc);
191
+ {
192
+ z_stream zcpr;
193
+ int ret=Z_OK;
194
+ long lOrigToDo = lFileSize;
195
+ long lOrigDone = 0;
196
+ int step=0;
197
+ memset(&zcpr,0,sizeof(z_stream));
198
+ deflateInit(&zcpr,cprLevel);
199
+
200
+ zcpr.next_in = FilePtr;
201
+ zcpr.next_out = CprPtr;
202
+
203
+
204
+ do
205
+ {
206
+ long all_read_before = zcpr.total_in;
207
+ zcpr.avail_in = min(lOrigToDo,BlockSizeCompress);
208
+ zcpr.avail_out = BlockSizeCompress;
209
+ ret=deflate(&zcpr,(zcpr.avail_in==lOrigToDo) ? Z_FINISH : Z_SYNC_FLUSH);
210
+ lOrigDone += (zcpr.total_in-all_read_before);
211
+ lOrigToDo -= (zcpr.total_in-all_read_before);
212
+ step++;
213
+ } while (ret==Z_OK);
214
+
215
+ lSizeCpr=zcpr.total_out;
216
+ deflateEnd(&zcpr);
217
+ dwGetTick=GetTickCount()-dwGetTick;
218
+ dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
219
+ dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
220
+ printf("total compress size = %u, in %u step\n",lSizeCpr,step);
221
+ printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
222
+ printf("defcpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
223
+ printf("defcpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
224
+ }
225
+
226
+ CprPtr=(unsigned char*)realloc(CprPtr,lSizeCpr);
227
+ UncprPtr=(unsigned char*)malloc(lBufferSizeUncpr + BlockSizeUncompress);
228
+
229
+ BeginCountPerfCounter(&li_qp,TRUE);
230
+ dwGetTick=GetTickCount();
231
+ BeginCountRdtsc(&li_rdtsc);
232
+ {
233
+ z_stream zcpr;
234
+ int ret=Z_OK;
235
+ long lOrigToDo = lSizeCpr;
236
+ long lOrigDone = 0;
237
+ int step=0;
238
+ memset(&zcpr,0,sizeof(z_stream));
239
+ inflateInit(&zcpr);
240
+
241
+ zcpr.next_in = CprPtr;
242
+ zcpr.next_out = UncprPtr;
243
+
244
+
245
+ do
246
+ {
247
+ long all_read_before = zcpr.total_in;
248
+ zcpr.avail_in = min(lOrigToDo,BlockSizeUncompress);
249
+ zcpr.avail_out = BlockSizeUncompress;
250
+ ret=inflate(&zcpr,Z_SYNC_FLUSH);
251
+ lOrigDone += (zcpr.total_in-all_read_before);
252
+ lOrigToDo -= (zcpr.total_in-all_read_before);
253
+ step++;
254
+ } while (ret==Z_OK);
255
+
256
+ lSizeUncpr=zcpr.total_out;
257
+ inflateEnd(&zcpr);
258
+ dwGetTick=GetTickCount()-dwGetTick;
259
+ dwMsecQP=GetMsecSincePerfCounter(li_qp,TRUE);
260
+ dwResRdtsc=GetResRdtsc(li_rdtsc,TRUE);
261
+ printf("total uncompress size = %u, in %u step\n",lSizeUncpr,step);
262
+ printf("time = %u msec = %f sec\n",dwGetTick,dwGetTick/(double)1000.);
263
+ printf("uncpr time QP = %u msec = %f sec\n",dwMsecQP,dwMsecQP/(double)1000.);
264
+ printf("uncpr result rdtsc = %I64x\n\n",dwResRdtsc.QuadPart);
265
+ }
266
+
267
+ if (lSizeUncpr==lFileSize)
268
+ {
269
+ if (memcmp(FilePtr,UncprPtr,lFileSize)==0)
270
+ printf("compare ok\n");
271
+
272
+ }
273
+
274
+ return 0;
275
+ }
@@ -0,0 +1,10 @@
1
+ To build testzLib with Visual Studio 2005:
2
+
3
+ copy to a directory file from :
4
+ - root of zLib tree
5
+ - contrib/testzlib
6
+ - contrib/masmx86
7
+ - contrib/masmx64
8
+ - contrib/vstudio/vc7
9
+
10
+ and open testzlib8.sln
@@ -0,0 +1,14 @@
1
+ CC=cc
2
+ CFLAGS=-g
3
+
4
+ untgz: untgz.o ../../libz.a
5
+ $(CC) $(CFLAGS) -o untgz untgz.o -L../.. -lz
6
+
7
+ untgz.o: untgz.c ../../zlib.h
8
+ $(CC) $(CFLAGS) -c -I../.. untgz.c
9
+
10
+ ../../libz.a:
11
+ cd ../..; ./configure; make
12
+
13
+ clean:
14
+ rm -f untgz untgz.o *~
@@ -0,0 +1,17 @@
1
+ CC=cl
2
+ CFLAGS=-MD
3
+
4
+ untgz.exe: untgz.obj ..\..\zlib.lib
5
+ $(CC) $(CFLAGS) untgz.obj ..\..\zlib.lib
6
+
7
+ untgz.obj: untgz.c ..\..\zlib.h
8
+ $(CC) $(CFLAGS) -c -I..\.. untgz.c
9
+
10
+ ..\..\zlib.lib:
11
+ cd ..\..
12
+ $(MAKE) -f win32\makefile.msc
13
+ cd contrib\untgz
14
+
15
+ clean:
16
+ -del untgz.obj
17
+ -del untgz.exe
@@ -0,0 +1,674 @@
1
+ /*
2
+ * untgz.c -- Display contents and extract files from a gzip'd TAR file
3
+ *
4
+ * written by Pedro A. Aranda Gutierrez <paag@tid.es>
5
+ * adaptation to Unix by Jean-loup Gailly <jloup@gzip.org>
6
+ * various fixes by Cosmin Truta <cosmint@cs.ubbcluj.ro>
7
+ */
8
+
9
+ #include <stdio.h>
10
+ #include <stdlib.h>
11
+ #include <string.h>
12
+ #include <time.h>
13
+ #include <errno.h>
14
+
15
+ #include "zlib.h"
16
+
17
+ #ifdef unix
18
+ # include <unistd.h>
19
+ #else
20
+ # include <direct.h>
21
+ # include <io.h>
22
+ #endif
23
+
24
+ #ifdef WIN32
25
+ #include <windows.h>
26
+ # ifndef F_OK
27
+ # define F_OK 0
28
+ # endif
29
+ # define mkdir(dirname,mode) _mkdir(dirname)
30
+ # ifdef _MSC_VER
31
+ # define access(path,mode) _access(path,mode)
32
+ # define chmod(path,mode) _chmod(path,mode)
33
+ # define strdup(str) _strdup(str)
34
+ # endif
35
+ #else
36
+ # include <utime.h>
37
+ #endif
38
+
39
+
40
+ /* values used in typeflag field */
41
+
42
+ #define REGTYPE '0' /* regular file */
43
+ #define AREGTYPE '\0' /* regular file */
44
+ #define LNKTYPE '1' /* link */
45
+ #define SYMTYPE '2' /* reserved */
46
+ #define CHRTYPE '3' /* character special */
47
+ #define BLKTYPE '4' /* block special */
48
+ #define DIRTYPE '5' /* directory */
49
+ #define FIFOTYPE '6' /* FIFO special */
50
+ #define CONTTYPE '7' /* reserved */
51
+
52
+ /* GNU tar extensions */
53
+
54
+ #define GNUTYPE_DUMPDIR 'D' /* file names from dumped directory */
55
+ #define GNUTYPE_LONGLINK 'K' /* long link name */
56
+ #define GNUTYPE_LONGNAME 'L' /* long file name */
57
+ #define GNUTYPE_MULTIVOL 'M' /* continuation of file from another volume */
58
+ #define GNUTYPE_NAMES 'N' /* file name that does not fit into main hdr */
59
+ #define GNUTYPE_SPARSE 'S' /* sparse file */
60
+ #define GNUTYPE_VOLHDR 'V' /* tape/volume header */
61
+
62
+
63
+ /* tar header */
64
+
65
+ #define BLOCKSIZE 512
66
+ #define SHORTNAMESIZE 100
67
+
68
+ struct tar_header
69
+ { /* byte offset */
70
+ char name[100]; /* 0 */
71
+ char mode[8]; /* 100 */
72
+ char uid[8]; /* 108 */
73
+ char gid[8]; /* 116 */
74
+ char size[12]; /* 124 */
75
+ char mtime[12]; /* 136 */
76
+ char chksum[8]; /* 148 */
77
+ char typeflag; /* 156 */
78
+ char linkname[100]; /* 157 */
79
+ char magic[6]; /* 257 */
80
+ char version[2]; /* 263 */
81
+ char uname[32]; /* 265 */
82
+ char gname[32]; /* 297 */
83
+ char devmajor[8]; /* 329 */
84
+ char devminor[8]; /* 337 */
85
+ char prefix[155]; /* 345 */
86
+ /* 500 */
87
+ };
88
+
89
+ union tar_buffer
90
+ {
91
+ char buffer[BLOCKSIZE];
92
+ struct tar_header header;
93
+ };
94
+
95
+ struct attr_item
96
+ {
97
+ struct attr_item *next;
98
+ char *fname;
99
+ int mode;
100
+ time_t time;
101
+ };
102
+
103
+ enum { TGZ_EXTRACT, TGZ_LIST, TGZ_INVALID };
104
+
105
+ char *TGZfname OF((const char *));
106
+ void TGZnotfound OF((const char *));
107
+
108
+ int getoct OF((char *, int));
109
+ char *strtime OF((time_t *));
110
+ int setfiletime OF((char *, time_t));
111
+ void push_attr OF((struct attr_item **, char *, int, time_t));
112
+ void restore_attr OF((struct attr_item **));
113
+
114
+ int ExprMatch OF((char *, char *));
115
+
116
+ int makedir OF((char *));
117
+ int matchname OF((int, int, char **, char *));
118
+
119
+ void error OF((const char *));
120
+ int tar OF((gzFile, int, int, int, char **));
121
+
122
+ void help OF((int));
123
+ int main OF((int, char **));
124
+
125
+ char *prog;
126
+
127
+ const char *TGZsuffix[] = { "\0", ".tar", ".tar.gz", ".taz", ".tgz", NULL };
128
+
129
+ /* return the file name of the TGZ archive */
130
+ /* or NULL if it does not exist */
131
+
132
+ char *TGZfname (const char *arcname)
133
+ {
134
+ static char buffer[1024];
135
+ int origlen,i;
136
+
137
+ strcpy(buffer,arcname);
138
+ origlen = strlen(buffer);
139
+
140
+ for (i=0; TGZsuffix[i]; i++)
141
+ {
142
+ strcpy(buffer+origlen,TGZsuffix[i]);
143
+ if (access(buffer,F_OK) == 0)
144
+ return buffer;
145
+ }
146
+ return NULL;
147
+ }
148
+
149
+
150
+ /* error message for the filename */
151
+
152
+ void TGZnotfound (const char *arcname)
153
+ {
154
+ int i;
155
+
156
+ fprintf(stderr,"%s: Couldn't find ",prog);
157
+ for (i=0;TGZsuffix[i];i++)
158
+ fprintf(stderr,(TGZsuffix[i+1]) ? "%s%s, " : "or %s%s\n",
159
+ arcname,
160
+ TGZsuffix[i]);
161
+ exit(1);
162
+ }
163
+
164
+
165
+ /* convert octal digits to int */
166
+ /* on error return -1 */
167
+
168
+ int getoct (char *p,int width)
169
+ {
170
+ int result = 0;
171
+ char c;
172
+
173
+ while (width--)
174
+ {
175
+ c = *p++;
176
+ if (c == 0)
177
+ break;
178
+ if (c == ' ')
179
+ continue;
180
+ if (c < '0' || c > '7')
181
+ return -1;
182
+ result = result * 8 + (c - '0');
183
+ }
184
+ return result;
185
+ }
186
+
187
+
188
+ /* convert time_t to string */
189
+ /* use the "YYYY/MM/DD hh:mm:ss" format */
190
+
191
+ char *strtime (time_t *t)
192
+ {
193
+ struct tm *local;
194
+ static char result[32];
195
+
196
+ local = localtime(t);
197
+ sprintf(result,"%4d/%02d/%02d %02d:%02d:%02d",
198
+ local->tm_year+1900, local->tm_mon+1, local->tm_mday,
199
+ local->tm_hour, local->tm_min, local->tm_sec);
200
+ return result;
201
+ }
202
+
203
+
204
+ /* set file time */
205
+
206
+ int setfiletime (char *fname,time_t ftime)
207
+ {
208
+ #ifdef WIN32
209
+ static int isWinNT = -1;
210
+ SYSTEMTIME st;
211
+ FILETIME locft, modft;
212
+ struct tm *loctm;
213
+ HANDLE hFile;
214
+ int result;
215
+
216
+ loctm = localtime(&ftime);
217
+ if (loctm == NULL)
218
+ return -1;
219
+
220
+ st.wYear = (WORD)loctm->tm_year + 1900;
221
+ st.wMonth = (WORD)loctm->tm_mon + 1;
222
+ st.wDayOfWeek = (WORD)loctm->tm_wday;
223
+ st.wDay = (WORD)loctm->tm_mday;
224
+ st.wHour = (WORD)loctm->tm_hour;
225
+ st.wMinute = (WORD)loctm->tm_min;
226
+ st.wSecond = (WORD)loctm->tm_sec;
227
+ st.wMilliseconds = 0;
228
+ if (!SystemTimeToFileTime(&st, &locft) ||
229
+ !LocalFileTimeToFileTime(&locft, &modft))
230
+ return -1;
231
+
232
+ if (isWinNT < 0)
233
+ isWinNT = (GetVersion() < 0x80000000) ? 1 : 0;
234
+ hFile = CreateFile(fname, GENERIC_WRITE, 0, NULL, OPEN_EXISTING,
235
+ (isWinNT ? FILE_FLAG_BACKUP_SEMANTICS : 0),
236
+ NULL);
237
+ if (hFile == INVALID_HANDLE_VALUE)
238
+ return -1;
239
+ result = SetFileTime(hFile, NULL, NULL, &modft) ? 0 : -1;
240
+ CloseHandle(hFile);
241
+ return result;
242
+ #else
243
+ struct utimbuf settime;
244
+
245
+ settime.actime = settime.modtime = ftime;
246
+ return utime(fname,&settime);
247
+ #endif
248
+ }
249
+
250
+
251
+ /* push file attributes */
252
+
253
+ void push_attr(struct attr_item **list,char *fname,int mode,time_t time)
254
+ {
255
+ struct attr_item *item;
256
+
257
+ item = (struct attr_item *)malloc(sizeof(struct attr_item));
258
+ if (item == NULL)
259
+ error("Out of memory");
260
+ item->fname = strdup(fname);
261
+ item->mode = mode;
262
+ item->time = time;
263
+ item->next = *list;
264
+ *list = item;
265
+ }
266
+
267
+
268
+ /* restore file attributes */
269
+
270
+ void restore_attr(struct attr_item **list)
271
+ {
272
+ struct attr_item *item, *prev;
273
+
274
+ for (item = *list; item != NULL; )
275
+ {
276
+ setfiletime(item->fname,item->time);
277
+ chmod(item->fname,item->mode);
278
+ prev = item;
279
+ item = item->next;
280
+ free(prev);
281
+ }
282
+ *list = NULL;
283
+ }
284
+
285
+
286
+ /* match regular expression */
287
+
288
+ #define ISSPECIAL(c) (((c) == '*') || ((c) == '/'))
289
+
290
+ int ExprMatch (char *string,char *expr)
291
+ {
292
+ while (1)
293
+ {
294
+ if (ISSPECIAL(*expr))
295
+ {
296
+ if (*expr == '/')
297
+ {
298
+ if (*string != '\\' && *string != '/')
299
+ return 0;
300
+ string ++; expr++;
301
+ }
302
+ else if (*expr == '*')
303
+ {
304
+ if (*expr ++ == 0)
305
+ return 1;
306
+ while (*++string != *expr)
307
+ if (*string == 0)
308
+ return 0;
309
+ }
310
+ }
311
+ else
312
+ {
313
+ if (*string != *expr)
314
+ return 0;
315
+ if (*expr++ == 0)
316
+ return 1;
317
+ string++;
318
+ }
319
+ }
320
+ }
321
+
322
+
323
+ /* recursive mkdir */
324
+ /* abort on ENOENT; ignore other errors like "directory already exists" */
325
+ /* return 1 if OK */
326
+ /* 0 on error */
327
+
328
+ int makedir (char *newdir)
329
+ {
330
+ char *buffer = strdup(newdir);
331
+ char *p;
332
+ int len = strlen(buffer);
333
+
334
+ if (len <= 0) {
335
+ free(buffer);
336
+ return 0;
337
+ }
338
+ if (buffer[len-1] == '/') {
339
+ buffer[len-1] = '\0';
340
+ }
341
+ if (mkdir(buffer, 0755) == 0)
342
+ {
343
+ free(buffer);
344
+ return 1;
345
+ }
346
+
347
+ p = buffer+1;
348
+ while (1)
349
+ {
350
+ char hold;
351
+
352
+ while(*p && *p != '\\' && *p != '/')
353
+ p++;
354
+ hold = *p;
355
+ *p = 0;
356
+ if ((mkdir(buffer, 0755) == -1) && (errno == ENOENT))
357
+ {
358
+ fprintf(stderr,"%s: Couldn't create directory %s\n",prog,buffer);
359
+ free(buffer);
360
+ return 0;
361
+ }
362
+ if (hold == 0)
363
+ break;
364
+ *p++ = hold;
365
+ }
366
+ free(buffer);
367
+ return 1;
368
+ }
369
+
370
+
371
+ int matchname (int arg,int argc,char **argv,char *fname)
372
+ {
373
+ if (arg == argc) /* no arguments given (untgz tgzarchive) */
374
+ return 1;
375
+
376
+ while (arg < argc)
377
+ if (ExprMatch(fname,argv[arg++]))
378
+ return 1;
379
+
380
+ return 0; /* ignore this for the moment being */
381
+ }
382
+
383
+
384
+ /* tar file list or extract */
385
+
386
+ int tar (gzFile in,int action,int arg,int argc,char **argv)
387
+ {
388
+ union tar_buffer buffer;
389
+ int len;
390
+ int err;
391
+ int getheader = 1;
392
+ int remaining = 0;
393
+ FILE *outfile = NULL;
394
+ char fname[BLOCKSIZE];
395
+ int tarmode;
396
+ time_t tartime;
397
+ struct attr_item *attributes = NULL;
398
+
399
+ if (action == TGZ_LIST)
400
+ printf(" date time size file\n"
401
+ " ---------- -------- --------- -------------------------------------\n");
402
+ while (1)
403
+ {
404
+ len = gzread(in, &buffer, BLOCKSIZE);
405
+ if (len < 0)
406
+ error(gzerror(in, &err));
407
+ /*
408
+ * Always expect complete blocks to process
409
+ * the tar information.
410
+ */
411
+ if (len != BLOCKSIZE)
412
+ {
413
+ action = TGZ_INVALID; /* force error exit */
414
+ remaining = 0; /* force I/O cleanup */
415
+ }
416
+
417
+ /*
418
+ * If we have to get a tar header
419
+ */
420
+ if (getheader >= 1)
421
+ {
422
+ /*
423
+ * if we met the end of the tar
424
+ * or the end-of-tar block,
425
+ * we are done
426
+ */
427
+ if (len == 0 || buffer.header.name[0] == 0)
428
+ break;
429
+
430
+ tarmode = getoct(buffer.header.mode,8);
431
+ tartime = (time_t)getoct(buffer.header.mtime,12);
432
+ if (tarmode == -1 || tartime == (time_t)-1)
433
+ {
434
+ buffer.header.name[0] = 0;
435
+ action = TGZ_INVALID;
436
+ }
437
+
438
+ if (getheader == 1)
439
+ {
440
+ strncpy(fname,buffer.header.name,SHORTNAMESIZE);
441
+ if (fname[SHORTNAMESIZE-1] != 0)
442
+ fname[SHORTNAMESIZE] = 0;
443
+ }
444
+ else
445
+ {
446
+ /*
447
+ * The file name is longer than SHORTNAMESIZE
448
+ */
449
+ if (strncmp(fname,buffer.header.name,SHORTNAMESIZE-1) != 0)
450
+ error("bad long name");
451
+ getheader = 1;
452
+ }
453
+
454
+ /*
455
+ * Act according to the type flag
456
+ */
457
+ switch (buffer.header.typeflag)
458
+ {
459
+ case DIRTYPE:
460
+ if (action == TGZ_LIST)
461
+ printf(" %s <dir> %s\n",strtime(&tartime),fname);
462
+ if (action == TGZ_EXTRACT)
463
+ {
464
+ makedir(fname);
465
+ push_attr(&attributes,fname,tarmode,tartime);
466
+ }
467
+ break;
468
+ case REGTYPE:
469
+ case AREGTYPE:
470
+ remaining = getoct(buffer.header.size,12);
471
+ if (remaining == -1)
472
+ {
473
+ action = TGZ_INVALID;
474
+ break;
475
+ }
476
+ if (action == TGZ_LIST)
477
+ printf(" %s %9d %s\n",strtime(&tartime),remaining,fname);
478
+ else if (action == TGZ_EXTRACT)
479
+ {
480
+ if (matchname(arg,argc,argv,fname))
481
+ {
482
+ outfile = fopen(fname,"wb");
483
+ if (outfile == NULL) {
484
+ /* try creating directory */
485
+ char *p = strrchr(fname, '/');
486
+ if (p != NULL) {
487
+ *p = '\0';
488
+ makedir(fname);
489
+ *p = '/';
490
+ outfile = fopen(fname,"wb");
491
+ }
492
+ }
493
+ if (outfile != NULL)
494
+ printf("Extracting %s\n",fname);
495
+ else
496
+ fprintf(stderr, "%s: Couldn't create %s",prog,fname);
497
+ }
498
+ else
499
+ outfile = NULL;
500
+ }
501
+ getheader = 0;
502
+ break;
503
+ case GNUTYPE_LONGLINK:
504
+ case GNUTYPE_LONGNAME:
505
+ remaining = getoct(buffer.header.size,12);
506
+ if (remaining < 0 || remaining >= BLOCKSIZE)
507
+ {
508
+ action = TGZ_INVALID;
509
+ break;
510
+ }
511
+ len = gzread(in, fname, BLOCKSIZE);
512
+ if (len < 0)
513
+ error(gzerror(in, &err));
514
+ if (fname[BLOCKSIZE-1] != 0 || (int)strlen(fname) > remaining)
515
+ {
516
+ action = TGZ_INVALID;
517
+ break;
518
+ }
519
+ getheader = 2;
520
+ break;
521
+ default:
522
+ if (action == TGZ_LIST)
523
+ printf(" %s <---> %s\n",strtime(&tartime),fname);
524
+ break;
525
+ }
526
+ }
527
+ else
528
+ {
529
+ unsigned int bytes = (remaining > BLOCKSIZE) ? BLOCKSIZE : remaining;
530
+
531
+ if (outfile != NULL)
532
+ {
533
+ if (fwrite(&buffer,sizeof(char),bytes,outfile) != bytes)
534
+ {
535
+ fprintf(stderr,
536
+ "%s: Error writing %s -- skipping\n",prog,fname);
537
+ fclose(outfile);
538
+ outfile = NULL;
539
+ remove(fname);
540
+ }
541
+ }
542
+ remaining -= bytes;
543
+ }
544
+
545
+ if (remaining == 0)
546
+ {
547
+ getheader = 1;
548
+ if (outfile != NULL)
549
+ {
550
+ fclose(outfile);
551
+ outfile = NULL;
552
+ if (action != TGZ_INVALID)
553
+ push_attr(&attributes,fname,tarmode,tartime);
554
+ }
555
+ }
556
+
557
+ /*
558
+ * Abandon if errors are found
559
+ */
560
+ if (action == TGZ_INVALID)
561
+ {
562
+ error("broken archive");
563
+ break;
564
+ }
565
+ }
566
+
567
+ /*
568
+ * Restore file modes and time stamps
569
+ */
570
+ restore_attr(&attributes);
571
+
572
+ if (gzclose(in) != Z_OK)
573
+ error("failed gzclose");
574
+
575
+ return 0;
576
+ }
577
+
578
+
579
+ /* ============================================================ */
580
+
581
+ void help(int exitval)
582
+ {
583
+ printf("untgz version 0.2.1\n"
584
+ " using zlib version %s\n\n",
585
+ zlibVersion());
586
+ printf("Usage: untgz file.tgz extract all files\n"
587
+ " untgz file.tgz fname ... extract selected files\n"
588
+ " untgz -l file.tgz list archive contents\n"
589
+ " untgz -h display this help\n");
590
+ exit(exitval);
591
+ }
592
+
593
+ void error(const char *msg)
594
+ {
595
+ fprintf(stderr, "%s: %s\n", prog, msg);
596
+ exit(1);
597
+ }
598
+
599
+
600
+ /* ============================================================ */
601
+
602
+ #if defined(WIN32) && defined(__GNUC__)
603
+ int _CRT_glob = 0; /* disable argument globbing in MinGW */
604
+ #endif
605
+
606
+ int main(int argc,char **argv)
607
+ {
608
+ int action = TGZ_EXTRACT;
609
+ int arg = 1;
610
+ char *TGZfile;
611
+ gzFile *f;
612
+
613
+ prog = strrchr(argv[0],'\\');
614
+ if (prog == NULL)
615
+ {
616
+ prog = strrchr(argv[0],'/');
617
+ if (prog == NULL)
618
+ {
619
+ prog = strrchr(argv[0],':');
620
+ if (prog == NULL)
621
+ prog = argv[0];
622
+ else
623
+ prog++;
624
+ }
625
+ else
626
+ prog++;
627
+ }
628
+ else
629
+ prog++;
630
+
631
+ if (argc == 1)
632
+ help(0);
633
+
634
+ if (strcmp(argv[arg],"-l") == 0)
635
+ {
636
+ action = TGZ_LIST;
637
+ if (argc == ++arg)
638
+ help(0);
639
+ }
640
+ else if (strcmp(argv[arg],"-h") == 0)
641
+ {
642
+ help(0);
643
+ }
644
+
645
+ if ((TGZfile = TGZfname(argv[arg])) == NULL)
646
+ TGZnotfound(argv[arg]);
647
+
648
+ ++arg;
649
+ if ((action == TGZ_LIST) && (arg != argc))
650
+ help(1);
651
+
652
+ /*
653
+ * Process the TGZ file
654
+ */
655
+ switch(action)
656
+ {
657
+ case TGZ_LIST:
658
+ case TGZ_EXTRACT:
659
+ f = gzopen(TGZfile,"rb");
660
+ if (f == NULL)
661
+ {
662
+ fprintf(stderr,"%s: Couldn't gzopen %s\n",prog,TGZfile);
663
+ return 1;
664
+ }
665
+ exit(tar(f, action, arg, argc, argv));
666
+ break;
667
+
668
+ default:
669
+ error("Unknown option");
670
+ exit(1);
671
+ }
672
+
673
+ return 0;
674
+ }