finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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+ # Makefile for zlib
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+ # Borland C++ for Win32
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+ #
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+ # Updated for zlib 1.2.x by Cosmin Truta, 11-Mar-2003
5
+ # Last updated: 28-Aug-2003
6
+ #
7
+ # Usage:
8
+ # make -f win32/Makefile.bor
9
+ # make -f win32/Makefile.bor LOCAL_ZLIB=-DASMV OBJA=match.obj OBJPA=+match.obj
10
+
11
+ # ------------ Borland C++ ------------
12
+
13
+ # Optional nonstandard preprocessor flags (e.g. -DMAX_MEM_LEVEL=7)
14
+ # should be added to the environment via "set LOCAL_ZLIB=-DFOO" or
15
+ # added to the declaration of LOC here:
16
+ LOC = $(LOCAL_ZLIB)
17
+
18
+ CC = bcc32
19
+ AS = bcc32
20
+ LD = bcc32
21
+ AR = tlib
22
+ CFLAGS = -a -d -k- -O2 $(LOC)
23
+ ASFLAGS = $(LOC)
24
+ LDFLAGS = $(LOC)
25
+
26
+
27
+ # variables
28
+ ZLIB_LIB = zlib.lib
29
+
30
+ OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
31
+ OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
32
+ #OBJA =
33
+ OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
34
+ OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
35
+ #OBJPA=
36
+
37
+
38
+ # targets
39
+ all: $(ZLIB_LIB) example.exe minigzip.exe
40
+
41
+ .c.obj:
42
+ $(CC) -c $(CFLAGS) $<
43
+
44
+ .asm.obj:
45
+ $(AS) -c $(ASFLAGS) $<
46
+
47
+ adler32.obj: adler32.c zlib.h zconf.h
48
+
49
+ compress.obj: compress.c zlib.h zconf.h
50
+
51
+ crc32.obj: crc32.c zlib.h zconf.h crc32.h
52
+
53
+ deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
54
+
55
+ gzio.obj: gzio.c zutil.h zlib.h zconf.h
56
+
57
+ infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
58
+ inffast.h inffixed.h
59
+
60
+ inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
61
+ inffast.h
62
+
63
+ inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
64
+ inffast.h inffixed.h
65
+
66
+ inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
67
+
68
+ trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
69
+
70
+ uncompr.obj: uncompr.c zlib.h zconf.h
71
+
72
+ zutil.obj: zutil.c zutil.h zlib.h zconf.h
73
+
74
+ example.obj: example.c zlib.h zconf.h
75
+
76
+ minigzip.obj: minigzip.c zlib.h zconf.h
77
+
78
+
79
+ # For the sake of the old Borland make,
80
+ # the command line is cut to fit in the MS-DOS 128 byte limit:
81
+ $(ZLIB_LIB): $(OBJ1) $(OBJ2) $(OBJA)
82
+ -del $(ZLIB_LIB)
83
+ $(AR) $(ZLIB_LIB) $(OBJP1)
84
+ $(AR) $(ZLIB_LIB) $(OBJP2)
85
+ $(AR) $(ZLIB_LIB) $(OBJPA)
86
+
87
+
88
+ # testing
89
+ test: example.exe minigzip.exe
90
+ example
91
+ echo hello world | minigzip | minigzip -d
92
+
93
+ example.exe: example.obj $(ZLIB_LIB)
94
+ $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
95
+
96
+ minigzip.exe: minigzip.obj $(ZLIB_LIB)
97
+ $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
98
+
99
+
100
+ # cleanup
101
+ clean:
102
+ -del *.obj
103
+ -del *.lib
104
+ -del *.exe
105
+ -del *.tds
106
+ -del zlib.bak
107
+ -del foo.gz
@@ -0,0 +1,69 @@
1
+ # Makefile for zlib. Modified for emx/rsxnt by Chr. Spieler, 6/16/98.
2
+ # Copyright (C) 1995-1998 Jean-loup Gailly.
3
+ # For conditions of distribution and use, see copyright notice in zlib.h
4
+
5
+ # To compile, or to compile and test, type:
6
+ #
7
+ # make -fmakefile.emx; make test -fmakefile.emx
8
+ #
9
+
10
+ CC=gcc -Zwin32
11
+
12
+ #CFLAGS=-MMD -O
13
+ #CFLAGS=-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7
14
+ #CFLAGS=-MMD -g -DDEBUG
15
+ CFLAGS=-MMD -O3 $(BUTT) -Wall -Wwrite-strings -Wpointer-arith -Wconversion \
16
+ -Wstrict-prototypes -Wmissing-prototypes
17
+
18
+ # If cp.exe is available, replace "copy /Y" with "cp -fp" .
19
+ CP=copy /Y
20
+ # If gnu install.exe is available, replace $(CP) with ginstall.
21
+ INSTALL=$(CP)
22
+ # The default value of RM is "rm -f." If "rm.exe" is found, comment out:
23
+ RM=del
24
+ LDLIBS=-L. -lzlib
25
+ LD=$(CC) -s -o
26
+ LDSHARED=$(CC)
27
+
28
+ INCL=zlib.h zconf.h
29
+ LIBS=zlib.a
30
+
31
+ AR=ar rcs
32
+
33
+ prefix=/usr/local
34
+ exec_prefix = $(prefix)
35
+
36
+ OBJS = adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o \
37
+ zutil.o inflate.o infback.o inftrees.o inffast.o
38
+
39
+ TEST_OBJS = example.o minigzip.o
40
+
41
+ all: example.exe minigzip.exe
42
+
43
+ test: all
44
+ ./example
45
+ echo hello world | .\minigzip | .\minigzip -d
46
+
47
+ %.o : %.c
48
+ $(CC) $(CFLAGS) -c $< -o $@
49
+
50
+ zlib.a: $(OBJS)
51
+ $(AR) $@ $(OBJS)
52
+
53
+ %.exe : %.o $(LIBS)
54
+ $(LD) $@ $< $(LDLIBS)
55
+
56
+
57
+ .PHONY : clean
58
+
59
+ clean:
60
+ $(RM) *.d
61
+ $(RM) *.o
62
+ $(RM) *.exe
63
+ $(RM) zlib.a
64
+ $(RM) foo.gz
65
+
66
+ DEPS := $(wildcard *.d)
67
+ ifneq ($(DEPS),)
68
+ include $(DEPS)
69
+ endif
@@ -0,0 +1,141 @@
1
+ # Makefile for zlib, derived from Makefile.dj2.
2
+ # Modified for mingw32 by C. Spieler, 6/16/98.
3
+ # Updated for zlib 1.2.x by Christian Spieler and Cosmin Truta, Mar-2003.
4
+ # Last updated: 1-Aug-2003.
5
+ # Tested under Cygwin and MinGW.
6
+
7
+ # Copyright (C) 1995-2003 Jean-loup Gailly.
8
+ # For conditions of distribution and use, see copyright notice in zlib.h
9
+
10
+ # To compile, or to compile and test, type:
11
+ #
12
+ # make -fmakefile.gcc; make test testdll -fmakefile.gcc
13
+ #
14
+ # To use the asm code, type:
15
+ # cp contrib/asm?86/match.S ./match.S
16
+ # make LOC=-DASMV OBJA=match.o -fmakefile.gcc
17
+ #
18
+ # To install libz.a, zconf.h and zlib.h in the system directories, type:
19
+ #
20
+ # make install -fmakefile.gcc
21
+
22
+ # Note:
23
+ # If the platform is *not* MinGW (e.g. it is Cygwin or UWIN),
24
+ # the DLL name should be changed from "zlib1.dll".
25
+
26
+ STATICLIB = libz.a
27
+ SHAREDLIB = zlib1.dll
28
+ IMPLIB = libzdll.a
29
+
30
+ #LOC = -DASMV
31
+ #LOC = -DDEBUG -g
32
+
33
+ CC = gcc
34
+ CFLAGS = $(LOC) -O3 -Wall
35
+
36
+ AS = $(CC)
37
+ ASFLAGS = $(LOC) -Wall
38
+
39
+ LD = $(CC)
40
+ LDFLAGS = $(LOC) -s
41
+
42
+ AR = ar
43
+ ARFLAGS = rcs
44
+
45
+ RC = windres
46
+ RCFLAGS = --define GCC_WINDRES
47
+
48
+ CP = cp -fp
49
+ # If GNU install is available, replace $(CP) with install.
50
+ INSTALL = $(CP)
51
+ RM = rm -f
52
+
53
+ prefix = /usr/local
54
+ exec_prefix = $(prefix)
55
+
56
+ OBJS = adler32.o compress.o crc32.o deflate.o gzio.o infback.o \
57
+ inffast.o inflate.o inftrees.o trees.o uncompr.o zutil.o
58
+ OBJA =
59
+
60
+ all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) example minigzip example_d minigzip_d
61
+
62
+ test: example minigzip
63
+ ./example
64
+ echo hello world | ./minigzip | ./minigzip -d
65
+
66
+ testdll: example_d minigzip_d
67
+ ./example_d
68
+ echo hello world | ./minigzip_d | ./minigzip_d -d
69
+
70
+ .c.o:
71
+ $(CC) $(CFLAGS) -c -o $@ $<
72
+
73
+ .S.o:
74
+ $(AS) $(ASFLAGS) -c -o $@ $<
75
+
76
+ $(STATICLIB): $(OBJS) $(OBJA)
77
+ $(AR) $(ARFLAGS) $@ $(OBJS) $(OBJA)
78
+
79
+ $(IMPLIB): $(SHAREDLIB)
80
+
81
+ $(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlibrc.o
82
+ dllwrap --driver-name $(CC) --def win32/zlib.def \
83
+ --implib $(IMPLIB) -o $@ $(OBJS) $(OBJA) zlibrc.o
84
+ strip $@
85
+
86
+ example: example.o $(STATICLIB)
87
+ $(LD) $(LDFLAGS) -o $@ example.o $(STATICLIB)
88
+
89
+ minigzip: minigzip.o $(STATICLIB)
90
+ $(LD) $(LDFLAGS) -o $@ minigzip.o $(STATICLIB)
91
+
92
+ example_d: example.o $(IMPLIB)
93
+ $(LD) $(LDFLAGS) -o $@ example.o $(IMPLIB)
94
+
95
+ minigzip_d: minigzip.o $(IMPLIB)
96
+ $(LD) $(LDFLAGS) -o $@ minigzip.o $(IMPLIB)
97
+
98
+ zlibrc.o: win32/zlib1.rc
99
+ $(RC) $(RCFLAGS) -o $@ win32/zlib1.rc
100
+
101
+
102
+ # INCLUDE_PATH and LIBRARY_PATH must be set.
103
+
104
+ .PHONY: install uninstall clean
105
+
106
+ install: zlib.h zconf.h $(LIB)
107
+ -@if not exist $(INCLUDE_PATH)/nul mkdir $(INCLUDE_PATH)
108
+ -@if not exist $(LIBRARY_PATH)/nul mkdir $(LIBRARY_PATH)
109
+ -$(INSTALL) zlib.h $(INCLUDE_PATH)
110
+ -$(INSTALL) zconf.h $(INCLUDE_PATH)
111
+ -$(INSTALL) $(STATICLIB) $(LIBRARY_PATH)
112
+ -$(INSTALL) $(IMPLIB) $(LIBRARY_PATH)
113
+
114
+ uninstall:
115
+ -$(RM) $(INCLUDE_PATH)/zlib.h
116
+ -$(RM) $(INCLUDE_PATH)/zconf.h
117
+ -$(RM) $(LIBRARY_PATH)/$(STATICLIB)
118
+ -$(RM) $(LIBRARY_PATH)/$(IMPLIB)
119
+
120
+ clean:
121
+ -$(RM) $(STATICLIB)
122
+ -$(RM) $(SHAREDLIB)
123
+ -$(RM) $(IMPLIB)
124
+ -$(RM) *.o
125
+ -$(RM) *.exe
126
+ -$(RM) foo.gz
127
+
128
+ adler32.o: zlib.h zconf.h
129
+ compress.o: zlib.h zconf.h
130
+ crc32.o: crc32.h zlib.h zconf.h
131
+ deflate.o: deflate.h zutil.h zlib.h zconf.h
132
+ example.o: zlib.h zconf.h
133
+ gzio.o: zutil.h zlib.h zconf.h
134
+ inffast.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
135
+ inflate.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
136
+ infback.o: zutil.h zlib.h zconf.h inftrees.h inflate.h inffast.h
137
+ inftrees.o: zutil.h zlib.h zconf.h inftrees.h
138
+ minigzip.o: zlib.h zconf.h
139
+ trees.o: deflate.h zutil.h zlib.h zconf.h trees.h
140
+ uncompr.o: zlib.h zconf.h
141
+ zutil.o: zutil.h zlib.h zconf.h
@@ -0,0 +1,126 @@
1
+ # Makefile for zlib -- Microsoft (Visual) C
2
+ #
3
+ # Authors:
4
+ # Cosmin Truta, 11-Mar-2003
5
+ # Christian Spieler, 19-Mar-2003
6
+ #
7
+ # Last updated:
8
+ # Cosmin Truta, 27-Aug-2003
9
+ #
10
+ # Usage:
11
+ # nmake -f win32/Makefile.msc (standard build)
12
+ # nmake -f win32/Makefile.msc LOC=-DFOO (nonstandard build)
13
+ # nmake -f win32/Makefile.msc LOC=-DASMV OBJA=match.obj (use ASM code)
14
+
15
+
16
+ # optional build flags
17
+ LOC =
18
+
19
+
20
+ # variables
21
+ STATICLIB = zlib.lib
22
+ SHAREDLIB = zlib1.dll
23
+ IMPLIB = zdll.lib
24
+
25
+ CC = cl
26
+ AS = ml
27
+ LD = link
28
+ AR = lib
29
+ RC = rc
30
+ CFLAGS = -nologo -MD -O2 $(LOC)
31
+ ASFLAGS = -coff
32
+ LDFLAGS = -nologo -release
33
+ ARFLAGS = -nologo
34
+ RCFLAGS = /dWIN32 /r
35
+
36
+ OBJS = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj \
37
+ inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
38
+ OBJA =
39
+
40
+
41
+ # targets
42
+ all: $(STATICLIB) $(SHAREDLIB) $(IMPLIB) \
43
+ example.exe minigzip.exe example_d.exe minigzip_d.exe
44
+
45
+ $(STATICLIB): $(OBJS) $(OBJA)
46
+ $(AR) $(ARFLAGS) -out:$@ $(OBJS) $(OBJA)
47
+
48
+ $(IMPLIB): $(SHAREDLIB)
49
+
50
+ $(SHAREDLIB): win32/zlib.def $(OBJS) $(OBJA) zlib1.res
51
+ $(LD) $(LDFLAGS) -def:win32/zlib.def -dll -implib:$(IMPLIB) \
52
+ -out:$@ $(OBJS) $(OBJA) zlib1.res
53
+
54
+ example.exe: example.obj $(STATICLIB)
55
+ $(LD) $(LDFLAGS) example.obj $(STATICLIB)
56
+
57
+ minigzip.exe: minigzip.obj $(STATICLIB)
58
+ $(LD) $(LDFLAGS) minigzip.obj $(STATICLIB)
59
+
60
+ example_d.exe: example.obj $(IMPLIB)
61
+ $(LD) $(LDFLAGS) -out:$@ example.obj $(IMPLIB)
62
+
63
+ minigzip_d.exe: minigzip.obj $(IMPLIB)
64
+ $(LD) $(LDFLAGS) -out:$@ minigzip.obj $(IMPLIB)
65
+
66
+ .c.obj:
67
+ $(CC) -c $(CFLAGS) $<
68
+
69
+ .asm.obj:
70
+ $(AS) -c $(ASFLAGS) $<
71
+
72
+ adler32.obj: adler32.c zlib.h zconf.h
73
+
74
+ compress.obj: compress.c zlib.h zconf.h
75
+
76
+ crc32.obj: crc32.c zlib.h zconf.h crc32.h
77
+
78
+ deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
79
+
80
+ gzio.obj: gzio.c zutil.h zlib.h zconf.h
81
+
82
+ infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
83
+ inffast.h inffixed.h
84
+
85
+ inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
86
+ inffast.h
87
+
88
+ inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
89
+ inffast.h inffixed.h
90
+
91
+ inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
92
+
93
+ trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
94
+
95
+ uncompr.obj: uncompr.c zlib.h zconf.h
96
+
97
+ zutil.obj: zutil.c zutil.h zlib.h zconf.h
98
+
99
+ example.obj: example.c zlib.h zconf.h
100
+
101
+ minigzip.obj: minigzip.c zlib.h zconf.h
102
+
103
+ zlib1.res: win32/zlib1.rc
104
+ $(RC) $(RCFLAGS) /fo$@ win32/zlib1.rc
105
+
106
+
107
+ # testing
108
+ test: example.exe minigzip.exe
109
+ example
110
+ echo hello world | minigzip | minigzip -d
111
+
112
+ testdll: example_d.exe minigzip_d.exe
113
+ example_d
114
+ echo hello world | minigzip_d | minigzip_d -d
115
+
116
+
117
+ # cleanup
118
+ clean:
119
+ -del $(STATICLIB)
120
+ -del $(SHAREDLIB)
121
+ -del $(IMPLIB)
122
+ -del *.obj
123
+ -del *.res
124
+ -del *.exp
125
+ -del *.exe
126
+ -del foo.gz
@@ -0,0 +1,3 @@
1
+
2
+ To build zlib using the Microsoft Visual C++ environment,
3
+ use the appropriate project from the projects/ directory.