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 +1,274 @@
1
+ //
2
+ // � Copyright Henrik Ravn 2004
3
+ //
4
+ // Use, modification and distribution are subject to the Boost Software License, Version 1.0.
5
+ // (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
6
+ //
7
+
8
+ using System;
9
+ using System.Collections;
10
+ using System.IO;
11
+
12
+ // uncomment the define below to include unit tests
13
+ //#define nunit
14
+ #if nunit
15
+ using NUnit.Framework;
16
+
17
+ // Unit tests for the DotZLib class library
18
+ // ----------------------------------------
19
+ //
20
+ // Use this with NUnit 2 from http://www.nunit.org
21
+ //
22
+
23
+ namespace DotZLibTests
24
+ {
25
+ using DotZLib;
26
+
27
+ // helper methods
28
+ internal class Utils
29
+ {
30
+ public static bool byteArrEqual( byte[] lhs, byte[] rhs )
31
+ {
32
+ if (lhs.Length != rhs.Length)
33
+ return false;
34
+ for (int i = lhs.Length-1; i >= 0; --i)
35
+ if (lhs[i] != rhs[i])
36
+ return false;
37
+ return true;
38
+ }
39
+
40
+ }
41
+
42
+
43
+ [TestFixture]
44
+ public class CircBufferTests
45
+ {
46
+ #region Circular buffer tests
47
+ [Test]
48
+ public void SinglePutGet()
49
+ {
50
+ CircularBuffer buf = new CircularBuffer(10);
51
+ Assert.AreEqual( 0, buf.Size );
52
+ Assert.AreEqual( -1, buf.Get() );
53
+
54
+ Assert.IsTrue(buf.Put( 1 ));
55
+ Assert.AreEqual( 1, buf.Size );
56
+ Assert.AreEqual( 1, buf.Get() );
57
+ Assert.AreEqual( 0, buf.Size );
58
+ Assert.AreEqual( -1, buf.Get() );
59
+ }
60
+
61
+ [Test]
62
+ public void BlockPutGet()
63
+ {
64
+ CircularBuffer buf = new CircularBuffer(10);
65
+ byte[] arr = {1,2,3,4,5,6,7,8,9,10};
66
+ Assert.AreEqual( 10, buf.Put(arr,0,10) );
67
+ Assert.AreEqual( 10, buf.Size );
68
+ Assert.IsFalse( buf.Put(11) );
69
+ Assert.AreEqual( 1, buf.Get() );
70
+ Assert.IsTrue( buf.Put(11) );
71
+
72
+ byte[] arr2 = (byte[])arr.Clone();
73
+ Assert.AreEqual( 9, buf.Get(arr2,1,9) );
74
+ Assert.IsTrue( Utils.byteArrEqual(arr,arr2) );
75
+ }
76
+
77
+ #endregion
78
+ }
79
+
80
+ [TestFixture]
81
+ public class ChecksumTests
82
+ {
83
+ #region CRC32 Tests
84
+ [Test]
85
+ public void CRC32_Null()
86
+ {
87
+ CRC32Checksum crc32 = new CRC32Checksum();
88
+ Assert.AreEqual( 0, crc32.Value );
89
+
90
+ crc32 = new CRC32Checksum(1);
91
+ Assert.AreEqual( 1, crc32.Value );
92
+
93
+ crc32 = new CRC32Checksum(556);
94
+ Assert.AreEqual( 556, crc32.Value );
95
+ }
96
+
97
+ [Test]
98
+ public void CRC32_Data()
99
+ {
100
+ CRC32Checksum crc32 = new CRC32Checksum();
101
+ byte[] data = { 1,2,3,4,5,6,7 };
102
+ crc32.Update(data);
103
+ Assert.AreEqual( 0x70e46888, crc32.Value );
104
+
105
+ crc32 = new CRC32Checksum();
106
+ crc32.Update("penguin");
107
+ Assert.AreEqual( 0x0e5c1a120, crc32.Value );
108
+
109
+ crc32 = new CRC32Checksum(1);
110
+ crc32.Update("penguin");
111
+ Assert.AreEqual(0x43b6aa94, crc32.Value);
112
+
113
+ }
114
+ #endregion
115
+
116
+ #region Adler tests
117
+
118
+ [Test]
119
+ public void Adler_Null()
120
+ {
121
+ AdlerChecksum adler = new AdlerChecksum();
122
+ Assert.AreEqual(0, adler.Value);
123
+
124
+ adler = new AdlerChecksum(1);
125
+ Assert.AreEqual( 1, adler.Value );
126
+
127
+ adler = new AdlerChecksum(556);
128
+ Assert.AreEqual( 556, adler.Value );
129
+ }
130
+
131
+ [Test]
132
+ public void Adler_Data()
133
+ {
134
+ AdlerChecksum adler = new AdlerChecksum(1);
135
+ byte[] data = { 1,2,3,4,5,6,7 };
136
+ adler.Update(data);
137
+ Assert.AreEqual( 0x5b001d, adler.Value );
138
+
139
+ adler = new AdlerChecksum();
140
+ adler.Update("penguin");
141
+ Assert.AreEqual(0x0bcf02f6, adler.Value );
142
+
143
+ adler = new AdlerChecksum(1);
144
+ adler.Update("penguin");
145
+ Assert.AreEqual(0x0bd602f7, adler.Value);
146
+
147
+ }
148
+ #endregion
149
+ }
150
+
151
+ [TestFixture]
152
+ public class InfoTests
153
+ {
154
+ #region Info tests
155
+ [Test]
156
+ public void Info_Version()
157
+ {
158
+ Info info = new Info();
159
+ Assert.AreEqual("1.2.3", Info.Version);
160
+ Assert.AreEqual(32, info.SizeOfUInt);
161
+ Assert.AreEqual(32, info.SizeOfULong);
162
+ Assert.AreEqual(32, info.SizeOfPointer);
163
+ Assert.AreEqual(32, info.SizeOfOffset);
164
+ }
165
+ #endregion
166
+ }
167
+
168
+ [TestFixture]
169
+ public class DeflateInflateTests
170
+ {
171
+ #region Deflate tests
172
+ [Test]
173
+ public void Deflate_Init()
174
+ {
175
+ using (Deflater def = new Deflater(CompressLevel.Default))
176
+ {
177
+ }
178
+ }
179
+
180
+ private ArrayList compressedData = new ArrayList();
181
+ private uint adler1;
182
+
183
+ private ArrayList uncompressedData = new ArrayList();
184
+ private uint adler2;
185
+
186
+ public void CDataAvail(byte[] data, int startIndex, int count)
187
+ {
188
+ for (int i = 0; i < count; ++i)
189
+ compressedData.Add(data[i+startIndex]);
190
+ }
191
+
192
+ [Test]
193
+ public void Deflate_Compress()
194
+ {
195
+ compressedData.Clear();
196
+
197
+ byte[] testData = new byte[35000];
198
+ for (int i = 0; i < testData.Length; ++i)
199
+ testData[i] = 5;
200
+
201
+ using (Deflater def = new Deflater((CompressLevel)5))
202
+ {
203
+ def.DataAvailable += new DataAvailableHandler(CDataAvail);
204
+ def.Add(testData);
205
+ def.Finish();
206
+ adler1 = def.Checksum;
207
+ }
208
+ }
209
+ #endregion
210
+
211
+ #region Inflate tests
212
+ [Test]
213
+ public void Inflate_Init()
214
+ {
215
+ using (Inflater inf = new Inflater())
216
+ {
217
+ }
218
+ }
219
+
220
+ private void DDataAvail(byte[] data, int startIndex, int count)
221
+ {
222
+ for (int i = 0; i < count; ++i)
223
+ uncompressedData.Add(data[i+startIndex]);
224
+ }
225
+
226
+ [Test]
227
+ public void Inflate_Expand()
228
+ {
229
+ uncompressedData.Clear();
230
+
231
+ using (Inflater inf = new Inflater())
232
+ {
233
+ inf.DataAvailable += new DataAvailableHandler(DDataAvail);
234
+ inf.Add((byte[])compressedData.ToArray(typeof(byte)));
235
+ inf.Finish();
236
+ adler2 = inf.Checksum;
237
+ }
238
+ Assert.AreEqual( adler1, adler2 );
239
+ }
240
+ #endregion
241
+ }
242
+
243
+ [TestFixture]
244
+ public class GZipStreamTests
245
+ {
246
+ #region GZipStream test
247
+ [Test]
248
+ public void GZipStream_WriteRead()
249
+ {
250
+ using (GZipStream gzOut = new GZipStream("gzstream.gz", CompressLevel.Best))
251
+ {
252
+ BinaryWriter writer = new BinaryWriter(gzOut);
253
+ writer.Write("hi there");
254
+ writer.Write(Math.PI);
255
+ writer.Write(42);
256
+ }
257
+
258
+ using (GZipStream gzIn = new GZipStream("gzstream.gz"))
259
+ {
260
+ BinaryReader reader = new BinaryReader(gzIn);
261
+ string s = reader.ReadString();
262
+ Assert.AreEqual("hi there",s);
263
+ double d = reader.ReadDouble();
264
+ Assert.AreEqual(Math.PI, d);
265
+ int i = reader.ReadInt32();
266
+ Assert.AreEqual(42,i);
267
+ }
268
+
269
+ }
270
+ #endregion
271
+ }
272
+ }
273
+
274
+ #endif
@@ -0,0 +1,23 @@
1
+ Boost Software License - Version 1.0 - August 17th, 2003
2
+
3
+ Permission is hereby granted, free of charge, to any person or organization
4
+ obtaining a copy of the software and accompanying documentation covered by
5
+ this license (the "Software") to use, reproduce, display, distribute,
6
+ execute, and transmit the Software, and to prepare derivative works of the
7
+ Software, and to permit third-parties to whom the Software is furnished to
8
+ do so, all subject to the following:
9
+
10
+ The copyright notices in the Software and this entire statement, including
11
+ the above license grant, this restriction and the following disclaimer,
12
+ must be included in all copies of the Software, in whole or in part, and
13
+ all derivative works of the Software, unless such copies or derivative
14
+ works are solely in the form of machine-executable object code generated by
15
+ a source language processor.
16
+
17
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
20
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
21
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
22
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23
+ DEALINGS IN THE SOFTWARE.
@@ -0,0 +1,58 @@
1
+ This directory contains a .Net wrapper class library for the ZLib1.dll
2
+
3
+ The wrapper includes support for inflating/deflating memory buffers,
4
+ .Net streaming wrappers for the gz streams part of zlib, and wrappers
5
+ for the checksum parts of zlib. See DotZLib/UnitTests.cs for examples.
6
+
7
+ Directory structure:
8
+ --------------------
9
+
10
+ LICENSE_1_0.txt - License file.
11
+ readme.txt - This file.
12
+ DotZLib.chm - Class library documentation
13
+ DotZLib.build - NAnt build file
14
+ DotZLib.sln - Microsoft Visual Studio 2003 solution file
15
+
16
+ DotZLib\*.cs - Source files for the class library
17
+
18
+ Unit tests:
19
+ -----------
20
+ The file DotZLib/UnitTests.cs contains unit tests for use with NUnit 2.1 or higher.
21
+ To include unit tests in the build, define nunit before building.
22
+
23
+
24
+ Build instructions:
25
+ -------------------
26
+
27
+ 1. Using Visual Studio.Net 2003:
28
+ Open DotZLib.sln in VS.Net and build from there. Output file (DotZLib.dll)
29
+ will be found ./DotZLib/bin/release or ./DotZLib/bin/debug, depending on
30
+ you are building the release or debug version of the library. Check
31
+ DotZLib/UnitTests.cs for instructions on how to include unit tests in the
32
+ build.
33
+
34
+ 2. Using NAnt:
35
+ Open a command prompt with access to the build environment and run nant
36
+ in the same directory as the DotZLib.build file.
37
+ You can define 2 properties on the nant command-line to control the build:
38
+ debug={true|false} to toggle between release/debug builds (default=true).
39
+ nunit={true|false} to include or esclude unit tests (default=true).
40
+ Also the target clean will remove binaries.
41
+ Output file (DotZLib.dll) will be found in either ./DotZLib/bin/release
42
+ or ./DotZLib/bin/debug, depending on whether you are building the release
43
+ or debug version of the library.
44
+
45
+ Examples:
46
+ nant -D:debug=false -D:nunit=false
47
+ will build a release mode version of the library without unit tests.
48
+ nant
49
+ will build a debug version of the library with unit tests
50
+ nant clean
51
+ will remove all previously built files.
52
+
53
+
54
+ ---------------------------------
55
+ Copyright (c) Henrik Ravn 2004
56
+
57
+ Use, modification and distribution are subject to the Boost Software License, Version 1.0.
58
+ (See accompanying file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
@@ -0,0 +1 @@
1
+ See infback9.h for what this is and how to use it.
@@ -0,0 +1,608 @@
1
+ /* infback9.c -- inflate deflate64 data using a call-back interface
2
+ * Copyright (C) 1995-2003 Mark Adler
3
+ * For conditions of distribution and use, see copyright notice in zlib.h
4
+ */
5
+
6
+ #include "zutil.h"
7
+ #include "infback9.h"
8
+ #include "inftree9.h"
9
+ #include "inflate9.h"
10
+
11
+ #define WSIZE 65536UL
12
+
13
+ /*
14
+ strm provides memory allocation functions in zalloc and zfree, or
15
+ Z_NULL to use the library memory allocation functions.
16
+
17
+ window is a user-supplied window and output buffer that is 64K bytes.
18
+ */
19
+ int ZEXPORT inflateBack9Init_(strm, window, version, stream_size)
20
+ z_stream FAR *strm;
21
+ unsigned char FAR *window;
22
+ const char *version;
23
+ int stream_size;
24
+ {
25
+ struct inflate_state FAR *state;
26
+
27
+ if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
28
+ stream_size != (int)(sizeof(z_stream)))
29
+ return Z_VERSION_ERROR;
30
+ if (strm == Z_NULL || window == Z_NULL)
31
+ return Z_STREAM_ERROR;
32
+ strm->msg = Z_NULL; /* in case we return an error */
33
+ if (strm->zalloc == (alloc_func)0) {
34
+ strm->zalloc = zcalloc;
35
+ strm->opaque = (voidpf)0;
36
+ }
37
+ if (strm->zfree == (free_func)0) strm->zfree = zcfree;
38
+ state = (struct inflate_state FAR *)ZALLOC(strm, 1,
39
+ sizeof(struct inflate_state));
40
+ if (state == Z_NULL) return Z_MEM_ERROR;
41
+ Tracev((stderr, "inflate: allocated\n"));
42
+ strm->state = (voidpf)state;
43
+ state->window = window;
44
+ return Z_OK;
45
+ }
46
+
47
+ /*
48
+ Build and output length and distance decoding tables for fixed code
49
+ decoding.
50
+ */
51
+ #ifdef MAKEFIXED
52
+ #include <stdio.h>
53
+
54
+ void makefixed9(void)
55
+ {
56
+ unsigned sym, bits, low, size;
57
+ code *next, *lenfix, *distfix;
58
+ struct inflate_state state;
59
+ code fixed[544];
60
+
61
+ /* literal/length table */
62
+ sym = 0;
63
+ while (sym < 144) state.lens[sym++] = 8;
64
+ while (sym < 256) state.lens[sym++] = 9;
65
+ while (sym < 280) state.lens[sym++] = 7;
66
+ while (sym < 288) state.lens[sym++] = 8;
67
+ next = fixed;
68
+ lenfix = next;
69
+ bits = 9;
70
+ inflate_table9(LENS, state.lens, 288, &(next), &(bits), state.work);
71
+
72
+ /* distance table */
73
+ sym = 0;
74
+ while (sym < 32) state.lens[sym++] = 5;
75
+ distfix = next;
76
+ bits = 5;
77
+ inflate_table9(DISTS, state.lens, 32, &(next), &(bits), state.work);
78
+
79
+ /* write tables */
80
+ puts(" /* inffix9.h -- table for decoding deflate64 fixed codes");
81
+ puts(" * Generated automatically by makefixed9().");
82
+ puts(" */");
83
+ puts("");
84
+ puts(" /* WARNING: this file should *not* be used by applications.");
85
+ puts(" It is part of the implementation of this library and is");
86
+ puts(" subject to change. Applications should only use zlib.h.");
87
+ puts(" */");
88
+ puts("");
89
+ size = 1U << 9;
90
+ printf(" static const code lenfix[%u] = {", size);
91
+ low = 0;
92
+ for (;;) {
93
+ if ((low % 6) == 0) printf("\n ");
94
+ printf("{%u,%u,%d}", lenfix[low].op, lenfix[low].bits,
95
+ lenfix[low].val);
96
+ if (++low == size) break;
97
+ putchar(',');
98
+ }
99
+ puts("\n };");
100
+ size = 1U << 5;
101
+ printf("\n static const code distfix[%u] = {", size);
102
+ low = 0;
103
+ for (;;) {
104
+ if ((low % 5) == 0) printf("\n ");
105
+ printf("{%u,%u,%d}", distfix[low].op, distfix[low].bits,
106
+ distfix[low].val);
107
+ if (++low == size) break;
108
+ putchar(',');
109
+ }
110
+ puts("\n };");
111
+ }
112
+ #endif /* MAKEFIXED */
113
+
114
+ /* Macros for inflateBack(): */
115
+
116
+ /* Clear the input bit accumulator */
117
+ #define INITBITS() \
118
+ do { \
119
+ hold = 0; \
120
+ bits = 0; \
121
+ } while (0)
122
+
123
+ /* Assure that some input is available. If input is requested, but denied,
124
+ then return a Z_BUF_ERROR from inflateBack(). */
125
+ #define PULL() \
126
+ do { \
127
+ if (have == 0) { \
128
+ have = in(in_desc, &next); \
129
+ if (have == 0) { \
130
+ next = Z_NULL; \
131
+ ret = Z_BUF_ERROR; \
132
+ goto inf_leave; \
133
+ } \
134
+ } \
135
+ } while (0)
136
+
137
+ /* Get a byte of input into the bit accumulator, or return from inflateBack()
138
+ with an error if there is no input available. */
139
+ #define PULLBYTE() \
140
+ do { \
141
+ PULL(); \
142
+ have--; \
143
+ hold += (unsigned long)(*next++) << bits; \
144
+ bits += 8; \
145
+ } while (0)
146
+
147
+ /* Assure that there are at least n bits in the bit accumulator. If there is
148
+ not enough available input to do that, then return from inflateBack() with
149
+ an error. */
150
+ #define NEEDBITS(n) \
151
+ do { \
152
+ while (bits < (unsigned)(n)) \
153
+ PULLBYTE(); \
154
+ } while (0)
155
+
156
+ /* Return the low n bits of the bit accumulator (n <= 16) */
157
+ #define BITS(n) \
158
+ ((unsigned)hold & ((1U << (n)) - 1))
159
+
160
+ /* Remove n bits from the bit accumulator */
161
+ #define DROPBITS(n) \
162
+ do { \
163
+ hold >>= (n); \
164
+ bits -= (unsigned)(n); \
165
+ } while (0)
166
+
167
+ /* Remove zero to seven bits as needed to go to a byte boundary */
168
+ #define BYTEBITS() \
169
+ do { \
170
+ hold >>= bits & 7; \
171
+ bits -= bits & 7; \
172
+ } while (0)
173
+
174
+ /* Assure that some output space is available, by writing out the window
175
+ if it's full. If the write fails, return from inflateBack() with a
176
+ Z_BUF_ERROR. */
177
+ #define ROOM() \
178
+ do { \
179
+ if (left == 0) { \
180
+ put = window; \
181
+ left = WSIZE; \
182
+ wrap = 1; \
183
+ if (out(out_desc, put, (unsigned)left)) { \
184
+ ret = Z_BUF_ERROR; \
185
+ goto inf_leave; \
186
+ } \
187
+ } \
188
+ } while (0)
189
+
190
+ /*
191
+ strm provides the memory allocation functions and window buffer on input,
192
+ and provides information on the unused input on return. For Z_DATA_ERROR
193
+ returns, strm will also provide an error message.
194
+
195
+ in() and out() are the call-back input and output functions. When
196
+ inflateBack() needs more input, it calls in(). When inflateBack() has
197
+ filled the window with output, or when it completes with data in the
198
+ window, it calls out() to write out the data. The application must not
199
+ change the provided input until in() is called again or inflateBack()
200
+ returns. The application must not change the window/output buffer until
201
+ inflateBack() returns.
202
+
203
+ in() and out() are called with a descriptor parameter provided in the
204
+ inflateBack() call. This parameter can be a structure that provides the
205
+ information required to do the read or write, as well as accumulated
206
+ information on the input and output such as totals and check values.
207
+
208
+ in() should return zero on failure. out() should return non-zero on
209
+ failure. If either in() or out() fails, than inflateBack() returns a
210
+ Z_BUF_ERROR. strm->next_in can be checked for Z_NULL to see whether it
211
+ was in() or out() that caused in the error. Otherwise, inflateBack()
212
+ returns Z_STREAM_END on success, Z_DATA_ERROR for an deflate format
213
+ error, or Z_MEM_ERROR if it could not allocate memory for the state.
214
+ inflateBack() can also return Z_STREAM_ERROR if the input parameters
215
+ are not correct, i.e. strm is Z_NULL or the state was not initialized.
216
+ */
217
+ int ZEXPORT inflateBack9(strm, in, in_desc, out, out_desc)
218
+ z_stream FAR *strm;
219
+ in_func in;
220
+ void FAR *in_desc;
221
+ out_func out;
222
+ void FAR *out_desc;
223
+ {
224
+ struct inflate_state FAR *state;
225
+ unsigned char FAR *next; /* next input */
226
+ unsigned char FAR *put; /* next output */
227
+ unsigned have; /* available input */
228
+ unsigned long left; /* available output */
229
+ inflate_mode mode; /* current inflate mode */
230
+ int lastblock; /* true if processing last block */
231
+ int wrap; /* true if the window has wrapped */
232
+ unsigned long write; /* window write index */
233
+ unsigned char FAR *window; /* allocated sliding window, if needed */
234
+ unsigned long hold; /* bit buffer */
235
+ unsigned bits; /* bits in bit buffer */
236
+ unsigned extra; /* extra bits needed */
237
+ unsigned long length; /* literal or length of data to copy */
238
+ unsigned long offset; /* distance back to copy string from */
239
+ unsigned long copy; /* number of stored or match bytes to copy */
240
+ unsigned char FAR *from; /* where to copy match bytes from */
241
+ code const FAR *lencode; /* starting table for length/literal codes */
242
+ code const FAR *distcode; /* starting table for distance codes */
243
+ unsigned lenbits; /* index bits for lencode */
244
+ unsigned distbits; /* index bits for distcode */
245
+ code this; /* current decoding table entry */
246
+ code last; /* parent table entry */
247
+ unsigned len; /* length to copy for repeats, bits to drop */
248
+ int ret; /* return code */
249
+ static const unsigned short order[19] = /* permutation of code lengths */
250
+ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
251
+ #include "inffix9.h"
252
+
253
+ /* Check that the strm exists and that the state was initialized */
254
+ if (strm == Z_NULL || strm->state == Z_NULL)
255
+ return Z_STREAM_ERROR;
256
+ state = (struct inflate_state FAR *)strm->state;
257
+
258
+ /* Reset the state */
259
+ strm->msg = Z_NULL;
260
+ mode = TYPE;
261
+ lastblock = 0;
262
+ write = 0;
263
+ wrap = 0;
264
+ window = state->window;
265
+ next = strm->next_in;
266
+ have = next != Z_NULL ? strm->avail_in : 0;
267
+ hold = 0;
268
+ bits = 0;
269
+ put = window;
270
+ left = WSIZE;
271
+ lencode = Z_NULL;
272
+ distcode = Z_NULL;
273
+
274
+ /* Inflate until end of block marked as last */
275
+ for (;;)
276
+ switch (mode) {
277
+ case TYPE:
278
+ /* determine and dispatch block type */
279
+ if (lastblock) {
280
+ BYTEBITS();
281
+ mode = DONE;
282
+ break;
283
+ }
284
+ NEEDBITS(3);
285
+ lastblock = BITS(1);
286
+ DROPBITS(1);
287
+ switch (BITS(2)) {
288
+ case 0: /* stored block */
289
+ Tracev((stderr, "inflate: stored block%s\n",
290
+ lastblock ? " (last)" : ""));
291
+ mode = STORED;
292
+ break;
293
+ case 1: /* fixed block */
294
+ lencode = lenfix;
295
+ lenbits = 9;
296
+ distcode = distfix;
297
+ distbits = 5;
298
+ Tracev((stderr, "inflate: fixed codes block%s\n",
299
+ lastblock ? " (last)" : ""));
300
+ mode = LEN; /* decode codes */
301
+ break;
302
+ case 2: /* dynamic block */
303
+ Tracev((stderr, "inflate: dynamic codes block%s\n",
304
+ lastblock ? " (last)" : ""));
305
+ mode = TABLE;
306
+ break;
307
+ case 3:
308
+ strm->msg = (char *)"invalid block type";
309
+ mode = BAD;
310
+ }
311
+ DROPBITS(2);
312
+ break;
313
+
314
+ case STORED:
315
+ /* get and verify stored block length */
316
+ BYTEBITS(); /* go to byte boundary */
317
+ NEEDBITS(32);
318
+ if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
319
+ strm->msg = (char *)"invalid stored block lengths";
320
+ mode = BAD;
321
+ break;
322
+ }
323
+ length = (unsigned)hold & 0xffff;
324
+ Tracev((stderr, "inflate: stored length %lu\n",
325
+ length));
326
+ INITBITS();
327
+
328
+ /* copy stored block from input to output */
329
+ while (length != 0) {
330
+ copy = length;
331
+ PULL();
332
+ ROOM();
333
+ if (copy > have) copy = have;
334
+ if (copy > left) copy = left;
335
+ zmemcpy(put, next, copy);
336
+ have -= copy;
337
+ next += copy;
338
+ left -= copy;
339
+ put += copy;
340
+ length -= copy;
341
+ }
342
+ Tracev((stderr, "inflate: stored end\n"));
343
+ mode = TYPE;
344
+ break;
345
+
346
+ case TABLE:
347
+ /* get dynamic table entries descriptor */
348
+ NEEDBITS(14);
349
+ state->nlen = BITS(5) + 257;
350
+ DROPBITS(5);
351
+ state->ndist = BITS(5) + 1;
352
+ DROPBITS(5);
353
+ state->ncode = BITS(4) + 4;
354
+ DROPBITS(4);
355
+ if (state->nlen > 286) {
356
+ strm->msg = (char *)"too many length symbols";
357
+ mode = BAD;
358
+ break;
359
+ }
360
+ Tracev((stderr, "inflate: table sizes ok\n"));
361
+
362
+ /* get code length code lengths (not a typo) */
363
+ state->have = 0;
364
+ while (state->have < state->ncode) {
365
+ NEEDBITS(3);
366
+ state->lens[order[state->have++]] = (unsigned short)BITS(3);
367
+ DROPBITS(3);
368
+ }
369
+ while (state->have < 19)
370
+ state->lens[order[state->have++]] = 0;
371
+ state->next = state->codes;
372
+ lencode = (code const FAR *)(state->next);
373
+ lenbits = 7;
374
+ ret = inflate_table9(CODES, state->lens, 19, &(state->next),
375
+ &(lenbits), state->work);
376
+ if (ret) {
377
+ strm->msg = (char *)"invalid code lengths set";
378
+ mode = BAD;
379
+ break;
380
+ }
381
+ Tracev((stderr, "inflate: code lengths ok\n"));
382
+
383
+ /* get length and distance code code lengths */
384
+ state->have = 0;
385
+ while (state->have < state->nlen + state->ndist) {
386
+ for (;;) {
387
+ this = lencode[BITS(lenbits)];
388
+ if ((unsigned)(this.bits) <= bits) break;
389
+ PULLBYTE();
390
+ }
391
+ if (this.val < 16) {
392
+ NEEDBITS(this.bits);
393
+ DROPBITS(this.bits);
394
+ state->lens[state->have++] = this.val;
395
+ }
396
+ else {
397
+ if (this.val == 16) {
398
+ NEEDBITS(this.bits + 2);
399
+ DROPBITS(this.bits);
400
+ if (state->have == 0) {
401
+ strm->msg = (char *)"invalid bit length repeat";
402
+ mode = BAD;
403
+ break;
404
+ }
405
+ len = (unsigned)(state->lens[state->have - 1]);
406
+ copy = 3 + BITS(2);
407
+ DROPBITS(2);
408
+ }
409
+ else if (this.val == 17) {
410
+ NEEDBITS(this.bits + 3);
411
+ DROPBITS(this.bits);
412
+ len = 0;
413
+ copy = 3 + BITS(3);
414
+ DROPBITS(3);
415
+ }
416
+ else {
417
+ NEEDBITS(this.bits + 7);
418
+ DROPBITS(this.bits);
419
+ len = 0;
420
+ copy = 11 + BITS(7);
421
+ DROPBITS(7);
422
+ }
423
+ if (state->have + copy > state->nlen + state->ndist) {
424
+ strm->msg = (char *)"invalid bit length repeat";
425
+ mode = BAD;
426
+ break;
427
+ }
428
+ while (copy--)
429
+ state->lens[state->have++] = (unsigned short)len;
430
+ }
431
+ }
432
+
433
+ /* handle error breaks in while */
434
+ if (mode == BAD) break;
435
+
436
+ /* build code tables */
437
+ state->next = state->codes;
438
+ lencode = (code const FAR *)(state->next);
439
+ lenbits = 9;
440
+ ret = inflate_table9(LENS, state->lens, state->nlen,
441
+ &(state->next), &(lenbits), state->work);
442
+ if (ret) {
443
+ strm->msg = (char *)"invalid literal/lengths set";
444
+ mode = BAD;
445
+ break;
446
+ }
447
+ distcode = (code const FAR *)(state->next);
448
+ distbits = 6;
449
+ ret = inflate_table9(DISTS, state->lens + state->nlen,
450
+ state->ndist, &(state->next), &(distbits),
451
+ state->work);
452
+ if (ret) {
453
+ strm->msg = (char *)"invalid distances set";
454
+ mode = BAD;
455
+ break;
456
+ }
457
+ Tracev((stderr, "inflate: codes ok\n"));
458
+ mode = LEN;
459
+
460
+ case LEN:
461
+ /* get a literal, length, or end-of-block code */
462
+ for (;;) {
463
+ this = lencode[BITS(lenbits)];
464
+ if ((unsigned)(this.bits) <= bits) break;
465
+ PULLBYTE();
466
+ }
467
+ if (this.op && (this.op & 0xf0) == 0) {
468
+ last = this;
469
+ for (;;) {
470
+ this = lencode[last.val +
471
+ (BITS(last.bits + last.op) >> last.bits)];
472
+ if ((unsigned)(last.bits + this.bits) <= bits) break;
473
+ PULLBYTE();
474
+ }
475
+ DROPBITS(last.bits);
476
+ }
477
+ DROPBITS(this.bits);
478
+ length = (unsigned)this.val;
479
+
480
+ /* process literal */
481
+ if (this.op == 0) {
482
+ Tracevv((stderr, this.val >= 0x20 && this.val < 0x7f ?
483
+ "inflate: literal '%c'\n" :
484
+ "inflate: literal 0x%02x\n", this.val));
485
+ ROOM();
486
+ *put++ = (unsigned char)(length);
487
+ left--;
488
+ mode = LEN;
489
+ break;
490
+ }
491
+
492
+ /* process end of block */
493
+ if (this.op & 32) {
494
+ Tracevv((stderr, "inflate: end of block\n"));
495
+ mode = TYPE;
496
+ break;
497
+ }
498
+
499
+ /* invalid code */
500
+ if (this.op & 64) {
501
+ strm->msg = (char *)"invalid literal/length code";
502
+ mode = BAD;
503
+ break;
504
+ }
505
+
506
+ /* length code -- get extra bits, if any */
507
+ extra = (unsigned)(this.op) & 31;
508
+ if (extra != 0) {
509
+ NEEDBITS(extra);
510
+ length += BITS(extra);
511
+ DROPBITS(extra);
512
+ }
513
+ Tracevv((stderr, "inflate: length %lu\n", length));
514
+
515
+ /* get distance code */
516
+ for (;;) {
517
+ this = distcode[BITS(distbits)];
518
+ if ((unsigned)(this.bits) <= bits) break;
519
+ PULLBYTE();
520
+ }
521
+ if ((this.op & 0xf0) == 0) {
522
+ last = this;
523
+ for (;;) {
524
+ this = distcode[last.val +
525
+ (BITS(last.bits + last.op) >> last.bits)];
526
+ if ((unsigned)(last.bits + this.bits) <= bits) break;
527
+ PULLBYTE();
528
+ }
529
+ DROPBITS(last.bits);
530
+ }
531
+ DROPBITS(this.bits);
532
+ if (this.op & 64) {
533
+ strm->msg = (char *)"invalid distance code";
534
+ mode = BAD;
535
+ break;
536
+ }
537
+ offset = (unsigned)this.val;
538
+
539
+ /* get distance extra bits, if any */
540
+ extra = (unsigned)(this.op) & 15;
541
+ if (extra != 0) {
542
+ NEEDBITS(extra);
543
+ offset += BITS(extra);
544
+ DROPBITS(extra);
545
+ }
546
+ if (offset > WSIZE - (wrap ? 0: left)) {
547
+ strm->msg = (char *)"invalid distance too far back";
548
+ mode = BAD;
549
+ break;
550
+ }
551
+ Tracevv((stderr, "inflate: distance %lu\n", offset));
552
+
553
+ /* copy match from window to output */
554
+ do {
555
+ ROOM();
556
+ copy = WSIZE - offset;
557
+ if (copy < left) {
558
+ from = put + copy;
559
+ copy = left - copy;
560
+ }
561
+ else {
562
+ from = put - offset;
563
+ copy = left;
564
+ }
565
+ if (copy > length) copy = length;
566
+ length -= copy;
567
+ left -= copy;
568
+ do {
569
+ *put++ = *from++;
570
+ } while (--copy);
571
+ } while (length != 0);
572
+ break;
573
+
574
+ case DONE:
575
+ /* inflate stream terminated properly -- write leftover output */
576
+ ret = Z_STREAM_END;
577
+ if (left < WSIZE) {
578
+ if (out(out_desc, window, (unsigned)(WSIZE - left)))
579
+ ret = Z_BUF_ERROR;
580
+ }
581
+ goto inf_leave;
582
+
583
+ case BAD:
584
+ ret = Z_DATA_ERROR;
585
+ goto inf_leave;
586
+
587
+ default: /* can't happen, but makes compilers happy */
588
+ ret = Z_STREAM_ERROR;
589
+ goto inf_leave;
590
+ }
591
+
592
+ /* Return unused input */
593
+ inf_leave:
594
+ strm->next_in = next;
595
+ strm->avail_in = have;
596
+ return ret;
597
+ }
598
+
599
+ int ZEXPORT inflateBack9End(strm)
600
+ z_stream FAR *strm;
601
+ {
602
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
603
+ return Z_STREAM_ERROR;
604
+ ZFREE(strm, strm->state);
605
+ strm->state = Z_NULL;
606
+ Tracev((stderr, "inflate: end\n"));
607
+ return Z_OK;
608
+ }