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 +1,339 @@
1
+
2
+ Frequently Asked Questions about zlib
3
+
4
+
5
+ If your question is not there, please check the zlib home page
6
+ http://www.zlib.org which may have more recent information.
7
+ The lastest zlib FAQ is at http://www.gzip.org/zlib/zlib_faq.html
8
+
9
+
10
+ 1. Is zlib Y2K-compliant?
11
+
12
+ Yes. zlib doesn't handle dates.
13
+
14
+ 2. Where can I get a Windows DLL version?
15
+
16
+ The zlib sources can be compiled without change to produce a DLL.
17
+ See the file win32/DLL_FAQ.txt in the zlib distribution.
18
+ Pointers to the precompiled DLL are found in the zlib web site at
19
+ http://www.zlib.org.
20
+
21
+ 3. Where can I get a Visual Basic interface to zlib?
22
+
23
+ See
24
+ * http://www.dogma.net/markn/articles/zlibtool/zlibtool.htm
25
+ * contrib/visual-basic.txt in the zlib distribution
26
+ * win32/DLL_FAQ.txt in the zlib distribution
27
+
28
+ 4. compress() returns Z_BUF_ERROR.
29
+
30
+ Make sure that before the call of compress, the length of the compressed
31
+ buffer is equal to the total size of the compressed buffer and not
32
+ zero. For Visual Basic, check that this parameter is passed by reference
33
+ ("as any"), not by value ("as long").
34
+
35
+ 5. deflate() or inflate() returns Z_BUF_ERROR.
36
+
37
+ Before making the call, make sure that avail_in and avail_out are not
38
+ zero. When setting the parameter flush equal to Z_FINISH, also make sure
39
+ that avail_out is big enough to allow processing all pending input.
40
+ Note that a Z_BUF_ERROR is not fatal--another call to deflate() or
41
+ inflate() can be made with more input or output space. A Z_BUF_ERROR
42
+ may in fact be unavoidable depending on how the functions are used, since
43
+ it is not possible to tell whether or not there is more output pending
44
+ when strm.avail_out returns with zero.
45
+
46
+ 6. Where's the zlib documentation (man pages, etc.)?
47
+
48
+ It's in zlib.h for the moment, and Francis S. Lin has converted it to a
49
+ web page zlib.html. Volunteers to transform this to Unix-style man pages,
50
+ please contact us (zlib@gzip.org). Examples of zlib usage are in the files
51
+ example.c and minigzip.c.
52
+
53
+ 7. Why don't you use GNU autoconf or libtool or ...?
54
+
55
+ Because we would like to keep zlib as a very small and simple
56
+ package. zlib is rather portable and doesn't need much configuration.
57
+
58
+ 8. I found a bug in zlib.
59
+
60
+ Most of the time, such problems are due to an incorrect usage of
61
+ zlib. Please try to reproduce the problem with a small program and send
62
+ the corresponding source to us at zlib@gzip.org . Do not send
63
+ multi-megabyte data files without prior agreement.
64
+
65
+ 9. Why do I get "undefined reference to gzputc"?
66
+
67
+ If "make test" produces something like
68
+
69
+ example.o(.text+0x154): undefined reference to `gzputc'
70
+
71
+ check that you don't have old files libz.* in /usr/lib, /usr/local/lib or
72
+ /usr/X11R6/lib. Remove any old versions, then do "make install".
73
+
74
+ 10. I need a Delphi interface to zlib.
75
+
76
+ See the contrib/delphi directory in the zlib distribution.
77
+
78
+ 11. Can zlib handle .zip archives?
79
+
80
+ Not by itself, no. See the directory contrib/minizip in the zlib
81
+ distribution.
82
+
83
+ 12. Can zlib handle .Z files?
84
+
85
+ No, sorry. You have to spawn an uncompress or gunzip subprocess, or adapt
86
+ the code of uncompress on your own.
87
+
88
+ 13. How can I make a Unix shared library?
89
+
90
+ make clean
91
+ ./configure -s
92
+ make
93
+
94
+ 14. How do I install a shared zlib library on Unix?
95
+
96
+ After the above, then:
97
+
98
+ make install
99
+
100
+ However, many flavors of Unix come with a shared zlib already installed.
101
+ Before going to the trouble of compiling a shared version of zlib and
102
+ trying to install it, you may want to check if it's already there! If you
103
+ can #include <zlib.h>, it's there. The -lz option will probably link to it.
104
+
105
+ 15. I have a question about OttoPDF.
106
+
107
+ We are not the authors of OttoPDF. The real author is on the OttoPDF web
108
+ site: Joel Hainley, jhainley@myndkryme.com.
109
+
110
+ 16. Can zlib decode Flate data in an Adobe PDF file?
111
+
112
+ Yes. See http://www.fastio.com/ (ClibPDF), or http://www.pdflib.com/ .
113
+ To modify PDF forms, see http://sourceforge.net/projects/acroformtool/ .
114
+
115
+ 17. Why am I getting this "register_frame_info not found" error on Solaris?
116
+
117
+ After installing zlib 1.1.4 on Solaris 2.6, running applications using zlib
118
+ generates an error such as:
119
+
120
+ ld.so.1: rpm: fatal: relocation error: file /usr/local/lib/libz.so:
121
+ symbol __register_frame_info: referenced symbol not found
122
+
123
+ The symbol __register_frame_info is not part of zlib, it is generated by
124
+ the C compiler (cc or gcc). You must recompile applications using zlib
125
+ which have this problem. This problem is specific to Solaris. See
126
+ http://www.sunfreeware.com for Solaris versions of zlib and applications
127
+ using zlib.
128
+
129
+ 18. Why does gzip give an error on a file I make with compress/deflate?
130
+
131
+ The compress and deflate functions produce data in the zlib format, which
132
+ is different and incompatible with the gzip format. The gz* functions in
133
+ zlib on the other hand use the gzip format. Both the zlib and gzip
134
+ formats use the same compressed data format internally, but have different
135
+ headers and trailers around the compressed data.
136
+
137
+ 19. Ok, so why are there two different formats?
138
+
139
+ The gzip format was designed to retain the directory information about
140
+ a single file, such as the name and last modification date. The zlib
141
+ format on the other hand was designed for in-memory and communication
142
+ channel applications, and has a much more compact header and trailer and
143
+ uses a faster integrity check than gzip.
144
+
145
+ 20. Well that's nice, but how do I make a gzip file in memory?
146
+
147
+ You can request that deflate write the gzip format instead of the zlib
148
+ format using deflateInit2(). You can also request that inflate decode
149
+ the gzip format using inflateInit2(). Read zlib.h for more details.
150
+
151
+ 21. Is zlib thread-safe?
152
+
153
+ Yes. However any library routines that zlib uses and any application-
154
+ provided memory allocation routines must also be thread-safe. zlib's gz*
155
+ functions use stdio library routines, and most of zlib's functions use the
156
+ library memory allocation routines by default. zlib's Init functions allow
157
+ for the application to provide custom memory allocation routines.
158
+
159
+ Of course, you should only operate on any given zlib or gzip stream from a
160
+ single thread at a time.
161
+
162
+ 22. Can I use zlib in my commercial application?
163
+
164
+ Yes. Please read the license in zlib.h.
165
+
166
+ 23. Is zlib under the GNU license?
167
+
168
+ No. Please read the license in zlib.h.
169
+
170
+ 24. The license says that altered source versions must be "plainly marked". So
171
+ what exactly do I need to do to meet that requirement?
172
+
173
+ You need to change the ZLIB_VERSION and ZLIB_VERNUM #defines in zlib.h. In
174
+ particular, the final version number needs to be changed to "f", and an
175
+ identification string should be appended to ZLIB_VERSION. Version numbers
176
+ x.x.x.f are reserved for modifications to zlib by others than the zlib
177
+ maintainers. For example, if the version of the base zlib you are altering
178
+ is "1.2.3.4", then in zlib.h you should change ZLIB_VERNUM to 0x123f, and
179
+ ZLIB_VERSION to something like "1.2.3.f-zachary-mods-v3". You can also
180
+ update the version strings in deflate.c and inftrees.c.
181
+
182
+ For altered source distributions, you should also note the origin and
183
+ nature of the changes in zlib.h, as well as in ChangeLog and README, along
184
+ with the dates of the alterations. The origin should include at least your
185
+ name (or your company's name), and an email address to contact for help or
186
+ issues with the library.
187
+
188
+ Note that distributing a compiled zlib library along with zlib.h and
189
+ zconf.h is also a source distribution, and so you should change
190
+ ZLIB_VERSION and ZLIB_VERNUM and note the origin and nature of the changes
191
+ in zlib.h as you would for a full source distribution.
192
+
193
+ 25. Will zlib work on a big-endian or little-endian architecture, and can I
194
+ exchange compressed data between them?
195
+
196
+ Yes and yes.
197
+
198
+ 26. Will zlib work on a 64-bit machine?
199
+
200
+ It should. It has been tested on 64-bit machines, and has no dependence
201
+ on any data types being limited to 32-bits in length. If you have any
202
+ difficulties, please provide a complete problem report to zlib@gzip.org
203
+
204
+ 27. Will zlib decompress data from the PKWare Data Compression Library?
205
+
206
+ No. The PKWare DCL uses a completely different compressed data format
207
+ than does PKZIP and zlib. However, you can look in zlib's contrib/blast
208
+ directory for a possible solution to your problem.
209
+
210
+ 28. Can I access data randomly in a compressed stream?
211
+
212
+ No, not without some preparation. If when compressing you periodically
213
+ use Z_FULL_FLUSH, carefully write all the pending data at those points,
214
+ and keep an index of those locations, then you can start decompression
215
+ at those points. You have to be careful to not use Z_FULL_FLUSH too
216
+ often, since it can significantly degrade compression.
217
+
218
+ 29. Does zlib work on MVS, OS/390, CICS, etc.?
219
+
220
+ We don't know for sure. We have heard occasional reports of success on
221
+ these systems. If you do use it on one of these, please provide us with
222
+ a report, instructions, and patches that we can reference when we get
223
+ these questions. Thanks.
224
+
225
+ 30. Is there some simpler, easier to read version of inflate I can look at
226
+ to understand the deflate format?
227
+
228
+ First off, you should read RFC 1951. Second, yes. Look in zlib's
229
+ contrib/puff directory.
230
+
231
+ 31. Does zlib infringe on any patents?
232
+
233
+ As far as we know, no. In fact, that was originally the whole point behind
234
+ zlib. Look here for some more information:
235
+
236
+ http://www.gzip.org/#faq11
237
+
238
+ 32. Can zlib work with greater than 4 GB of data?
239
+
240
+ Yes. inflate() and deflate() will process any amount of data correctly.
241
+ Each call of inflate() or deflate() is limited to input and output chunks
242
+ of the maximum value that can be stored in the compiler's "unsigned int"
243
+ type, but there is no limit to the number of chunks. Note however that the
244
+ strm.total_in and strm_total_out counters may be limited to 4 GB. These
245
+ counters are provided as a convenience and are not used internally by
246
+ inflate() or deflate(). The application can easily set up its own counters
247
+ updated after each call of inflate() or deflate() to count beyond 4 GB.
248
+ compress() and uncompress() may be limited to 4 GB, since they operate in a
249
+ single call. gzseek() and gztell() may be limited to 4 GB depending on how
250
+ zlib is compiled. See the zlibCompileFlags() function in zlib.h.
251
+
252
+ The word "may" appears several times above since there is a 4 GB limit
253
+ only if the compiler's "long" type is 32 bits. If the compiler's "long"
254
+ type is 64 bits, then the limit is 16 exabytes.
255
+
256
+ 33. Does zlib have any security vulnerabilities?
257
+
258
+ The only one that we are aware of is potentially in gzprintf(). If zlib
259
+ is compiled to use sprintf() or vsprintf(), then there is no protection
260
+ against a buffer overflow of a 4K string space, other than the caller of
261
+ gzprintf() assuring that the output will not exceed 4K. On the other
262
+ hand, if zlib is compiled to use snprintf() or vsnprintf(), which should
263
+ normally be the case, then there is no vulnerability. The ./configure
264
+ script will display warnings if an insecure variation of sprintf() will
265
+ be used by gzprintf(). Also the zlibCompileFlags() function will return
266
+ information on what variant of sprintf() is used by gzprintf().
267
+
268
+ If you don't have snprintf() or vsnprintf() and would like one, you can
269
+ find a portable implementation here:
270
+
271
+ http://www.ijs.si/software/snprintf/
272
+
273
+ Note that you should be using the most recent version of zlib. Versions
274
+ 1.1.3 and before were subject to a double-free vulnerability.
275
+
276
+ 34. Is there a Java version of zlib?
277
+
278
+ Probably what you want is to use zlib in Java. zlib is already included
279
+ as part of the Java SDK in the java.util.zip package. If you really want
280
+ a version of zlib written in the Java language, look on the zlib home
281
+ page for links: http://www.zlib.org/
282
+
283
+ 35. I get this or that compiler or source-code scanner warning when I crank it
284
+ up to maximally-pedantic. Can't you guys write proper code?
285
+
286
+ Many years ago, we gave up attempting to avoid warnings on every compiler
287
+ in the universe. It just got to be a waste of time, and some compilers
288
+ were downright silly. So now, we simply make sure that the code always
289
+ works.
290
+
291
+ 36. Valgrind (or some similar memory access checker) says that deflate is
292
+ performing a conditional jump that depends on an uninitialized value.
293
+ Isn't that a bug?
294
+
295
+ No. That is intentional for performance reasons, and the output of
296
+ deflate is not affected. This only started showing up recently since
297
+ zlib 1.2.x uses malloc() by default for allocations, whereas earlier
298
+ versions used calloc(), which zeros out the allocated memory.
299
+
300
+ 37. Will zlib read the (insert any ancient or arcane format here) compressed
301
+ data format?
302
+
303
+ Probably not. Look in the comp.compression FAQ for pointers to various
304
+ formats and associated software.
305
+
306
+ 38. How can I encrypt/decrypt zip files with zlib?
307
+
308
+ zlib doesn't support encryption. The original PKZIP encryption is very weak
309
+ and can be broken with freely available programs. To get strong encryption,
310
+ use GnuPG, http://www.gnupg.org/ , which already includes zlib compression.
311
+ For PKZIP compatible "encryption", look at http://www.info-zip.org/
312
+
313
+ 39. What's the difference between the "gzip" and "deflate" HTTP 1.1 encodings?
314
+
315
+ "gzip" is the gzip format, and "deflate" is the zlib format. They should
316
+ probably have called the second one "zlib" instead to avoid confusion
317
+ with the raw deflate compressed data format. While the HTTP 1.1 RFC 2616
318
+ correctly points to the zlib specification in RFC 1950 for the "deflate"
319
+ transfer encoding, there have been reports of servers and browsers that
320
+ incorrectly produce or expect raw deflate data per the deflate
321
+ specficiation in RFC 1951, most notably Microsoft. So even though the
322
+ "deflate" transfer encoding using the zlib format would be the more
323
+ efficient approach (and in fact exactly what the zlib format was designed
324
+ for), using the "gzip" transfer encoding is probably more reliable due to
325
+ an unfortunate choice of name on the part of the HTTP 1.1 authors.
326
+
327
+ Bottom line: use the gzip format for HTTP 1.1 encoding.
328
+
329
+ 40. Does zlib support the new "Deflate64" format introduced by PKWare?
330
+
331
+ No. PKWare has apparently decided to keep that format proprietary, since
332
+ they have not documented it as they have previous compression formats.
333
+ In any case, the compression improvements are so modest compared to other
334
+ more modern approaches, that it's not worth the effort to implement.
335
+
336
+ 41. Can you please sign these lengthy legal documents and fax them back to us
337
+ so that we can use your software in our product?
338
+
339
+ No. Go away. Shoo.
@@ -0,0 +1,51 @@
1
+ ChangeLog history of changes
2
+ FAQ Frequently Asked Questions about zlib
3
+ INDEX this file
4
+ Makefile makefile for Unix (generated by configure)
5
+ Makefile.in makefile for Unix (template for configure)
6
+ README guess what
7
+ algorithm.txt description of the (de)compression algorithm
8
+ configure configure script for Unix
9
+ zconf.in.h template for zconf.h (used by configure)
10
+
11
+ amiga/ makefiles for Amiga SAS C
12
+ as400/ makefiles for IBM AS/400
13
+ msdos/ makefiles for MSDOS
14
+ old/ makefiles for various architectures and zlib documentation
15
+ files that have not yet been updated for zlib 1.2.x
16
+ projects/ projects for various Integrated Development Environments
17
+ qnx/ makefiles for QNX
18
+ win32/ makefiles for Windows
19
+
20
+ zlib public header files (must be kept):
21
+ zconf.h
22
+ zlib.h
23
+
24
+ private source files used to build the zlib library:
25
+ adler32.c
26
+ compress.c
27
+ crc32.c
28
+ crc32.h
29
+ deflate.c
30
+ deflate.h
31
+ gzio.c
32
+ infback.c
33
+ inffast.c
34
+ inffast.h
35
+ inffixed.h
36
+ inflate.c
37
+ inflate.h
38
+ inftrees.c
39
+ inftrees.h
40
+ trees.c
41
+ trees.h
42
+ uncompr.c
43
+ zutil.c
44
+ zutil.h
45
+
46
+ source files for sample programs:
47
+ example.c
48
+ minigzip.c
49
+
50
+ unsupported contribution by third parties
51
+ See contrib/README.contrib
@@ -0,0 +1,154 @@
1
+ # Makefile for zlib
2
+ # Copyright (C) 1995-2005 Jean-loup Gailly.
3
+ # For conditions of distribution and use, see copyright notice in zlib.h
4
+
5
+ # To compile and test, type:
6
+ # ./configure; make test
7
+ # The call of configure is optional if you don't have special requirements
8
+ # If you wish to build zlib as a shared library, use: ./configure -s
9
+
10
+ # To use the asm code, type:
11
+ # cp contrib/asm?86/match.S ./match.S
12
+ # make LOC=-DASMV OBJA=match.o
13
+
14
+ # To install /usr/local/lib/libz.* and /usr/local/include/zlib.h, type:
15
+ # make install
16
+ # To install in $HOME instead of /usr/local, use:
17
+ # make install prefix=$HOME
18
+
19
+ CC=gcc
20
+
21
+ CFLAGS=-O3 -DUSE_MMAP
22
+ #CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
23
+ #CFLAGS=-g -DDEBUG
24
+ #CFLAGS=-O3 -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
25
+ # -Wstrict-prototypes -Wmissing-prototypes
26
+
27
+ LDFLAGS=-L. libz.a
28
+ LDSHARED=gcc
29
+ CPP=gcc -E
30
+
31
+ LIBS=libz.a
32
+ SHAREDLIB=libz.so
33
+ SHAREDLIBV=libz.so.1.2.3
34
+ SHAREDLIBM=libz.so.1
35
+
36
+ AR=ar rc
37
+ RANLIB=ranlib
38
+ TAR=tar
39
+ SHELL=/bin/sh
40
+ EXE=
41
+
42
+ prefix =/usr/local
43
+ exec_prefix =${prefix}
44
+ libdir =${exec_prefix}/lib
45
+ includedir =${prefix}/include
46
+ mandir =${prefix}/share/man
47
+ man3dir = ${mandir}/man3
48
+
49
+ OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
50
+ zutil.o inflate.o infback.o inftrees.o inffast.o
51
+
52
+ OBJA =
53
+ # to use the asm code: make OBJA=match.o
54
+
55
+ TEST_OBJS = example.o minigzip.o
56
+
57
+ all: example$(EXE) minigzip$(EXE)
58
+
59
+ check: test
60
+ test: all
61
+ @LD_LIBRARY_PATH=.:$(LD_LIBRARY_PATH) ; export LD_LIBRARY_PATH; \
62
+ echo hello world | ./minigzip | ./minigzip -d || \
63
+ echo ' *** minigzip test FAILED ***' ; \
64
+ if ./example; then \
65
+ echo ' *** zlib test OK ***'; \
66
+ else \
67
+ echo ' *** zlib test FAILED ***'; \
68
+ fi
69
+
70
+ libz.a: $(OBJS) $(OBJA)
71
+ $(AR) $@ $(OBJS) $(OBJA)
72
+ -@ ($(RANLIB) $@ || true) >/dev/null 2>&1
73
+
74
+ match.o: match.S
75
+ $(CPP) match.S > _match.s
76
+ $(CC) -c _match.s
77
+ mv _match.o match.o
78
+ rm -f _match.s
79
+
80
+ $(SHAREDLIBV): $(OBJS)
81
+ $(LDSHARED) -o $@ $(OBJS)
82
+ rm -f $(SHAREDLIB) $(SHAREDLIBM)
83
+ ln -s $@ $(SHAREDLIB)
84
+ ln -s $@ $(SHAREDLIBM)
85
+
86
+ example$(EXE): example.o $(LIBS)
87
+ $(CC) $(CFLAGS) -o $@ example.o $(LDFLAGS)
88
+
89
+ minigzip$(EXE): minigzip.o $(LIBS)
90
+ $(CC) $(CFLAGS) -o $@ minigzip.o $(LDFLAGS)
91
+
92
+ install: $(LIBS)
93
+ -@if [ ! -d $(exec_prefix) ]; then mkdir -p $(exec_prefix); fi
94
+ -@if [ ! -d $(includedir) ]; then mkdir -p $(includedir); fi
95
+ -@if [ ! -d $(libdir) ]; then mkdir -p $(libdir); fi
96
+ -@if [ ! -d $(man3dir) ]; then mkdir -p $(man3dir); fi
97
+ cp zlib.h zconf.h $(includedir)
98
+ chmod 644 $(includedir)/zlib.h $(includedir)/zconf.h
99
+ cp $(LIBS) $(libdir)
100
+ cd $(libdir); chmod 755 $(LIBS)
101
+ -@(cd $(libdir); $(RANLIB) libz.a || true) >/dev/null 2>&1
102
+ cd $(libdir); if test -f $(SHAREDLIBV); then \
103
+ rm -f $(SHAREDLIB) $(SHAREDLIBM); \
104
+ ln -s $(SHAREDLIBV) $(SHAREDLIB); \
105
+ ln -s $(SHAREDLIBV) $(SHAREDLIBM); \
106
+ (ldconfig || true) >/dev/null 2>&1; \
107
+ fi
108
+ cp zlib.3 $(man3dir)
109
+ chmod 644 $(man3dir)/zlib.3
110
+ # The ranlib in install is needed on NeXTSTEP which checks file times
111
+ # ldconfig is for Linux
112
+
113
+ uninstall:
114
+ cd $(includedir); \
115
+ cd $(libdir); rm -f libz.a; \
116
+ if test -f $(SHAREDLIBV); then \
117
+ rm -f $(SHAREDLIBV) $(SHAREDLIB) $(SHAREDLIBM); \
118
+ fi
119
+ cd $(man3dir); rm -f zlib.3
120
+
121
+ mostlyclean: clean
122
+ clean:
123
+ rm -f *.o *~ example$(EXE) minigzip$(EXE) \
124
+ libz.* foo.gz so_locations \
125
+ _match.s maketree contrib/infback9/*.o
126
+
127
+ maintainer-clean: distclean
128
+ distclean: clean
129
+ cp -p Makefile.in Makefile
130
+ cp -p zconf.in.h zconf.h
131
+ rm -f .DS_Store
132
+
133
+ tags:
134
+ etags *.[ch]
135
+
136
+ depend:
137
+ makedepend -- $(CFLAGS) -- *.[ch]
138
+
139
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
140
+
141
+ adler32.o: zlib.h zconf.h
142
+ compress.o: zlib.h zconf.h
143
+ crc32.o: crc32.h zlib.h zconf.h
144
+ deflate.o: deflate.h zutil.h zlib.h zconf.h
145
+ example.o: zlib.h zconf.h
146
+ gzio.o: zutil.h zlib.h zconf.h
147
+ inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
148
+ inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
149
+ infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
150
+ inftrees.o: zutil.h zlib.h zconf.h inftrees.h
151
+ minigzip.o: zlib.h zconf.h
152
+ trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
153
+ uncompr.o: zlib.h zconf.h
154
+ zutil.o: zutil.h zlib.h zconf.h