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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  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
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  292. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
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  325. data/lib/assembly/bubbly_assembler.rb +842 -0
  326. data/lib/assembly/c_probe_node_finder.rb +38 -0
  327. data/lib/assembly/connection_interpreter.rb +350 -0
  328. data/lib/assembly/contig_printer.rb +400 -0
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  332. data/lib/assembly/fluffer.rb +253 -0
  333. data/lib/assembly/graph_explorer.rb +85 -0
  334. data/lib/assembly/graph_generator.rb +315 -0
  335. data/lib/assembly/height_finder.rb +355 -0
  336. data/lib/assembly/hybrid_velvet_graph.rb +70 -0
  337. data/lib/assembly/input_genome.rb +182 -0
  338. data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
  339. data/lib/assembly/node_finder.rb +171 -0
  340. data/lib/assembly/oriented_node_trail.rb +507 -0
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  344. data/lib/assembly/read_input.rb +79 -0
  345. data/lib/assembly/read_to_node.rb +37 -0
  346. data/lib/assembly/scaffold_breaker.rb +126 -0
  347. data/lib/assembly/sequence_hasher.rb +71 -0
  348. data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
  349. data/lib/assembly/single_coherent_wanderer.rb +261 -0
  350. data/lib/assembly/single_ended_assembler.rb +441 -0
  351. data/lib/assembly/velvet_c_binding.rb +54 -0
  352. data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
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  357. data/lib/finishm/fluff.rb +122 -0
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  359. data/lib/finishm/orfs_finder.rb +88 -0
  360. data/lib/finishm/path_counter.rb +90 -0
  361. data/lib/finishm/primers.rb +425 -0
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  372. data/spec/all_orfs_spec.rb +443 -0
  373. data/spec/assemble_spec.rb +186 -0
  374. data/spec/bubbly_assembler_spec.rb +707 -0
  375. data/spec/c_node_finder_spec.rb +58 -0
  376. data/spec/connection_interpreter_spec.rb +284 -0
  377. data/spec/contig_printer_spec.rb +291 -0
  378. data/spec/coverage_based_graph_filter_spec.rb +102 -0
  379. data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
  380. data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
  381. data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
  382. data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
  383. data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
  384. data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
  385. data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
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  387. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
  388. data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
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  390. data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
  391. data/spec/data/assembly_visualiser/Graph +46 -0
  392. data/spec/data/assembly_visualiser/start_kmers1 +2 -0
  393. data/spec/data/bands.csv +1 -0
  394. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
  395. data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
  396. data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
  397. data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
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  399. data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
  400. data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
  401. data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
  402. data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
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  409. data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
  410. data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
  411. data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
  412. data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
  413. data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
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  416. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
  417. data/spec/data/contig_printer/1/seq.node12.fa +4 -0
  418. data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
  419. data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
  420. data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
  421. data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
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  423. data/spec/data/explore/1/a.fa +2 -0
  424. data/spec/data/explore/1/seq1_and_a.fa +3 -0
  425. data/spec/data/explore/1/seq2.fa +2 -0
  426. data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
  427. data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
  428. data/spec/data/fluff/1/seq1.fa +2 -0
  429. data/spec/data/fluff/1/seq2.fa +2 -0
  430. data/spec/data/gapfilling/1/reads.fa +171 -0
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  436. data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
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  439. data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
  440. data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
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  445. data/spec/data/gapfilling/2/with_gaps.fa +4 -0
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  448. data/spec/data/gapfilling/3/reference_part1.fa +4 -0
  449. data/spec/data/gapfilling/3/reference_part2.fa +4 -0
  450. data/spec/data/gapfilling/3/with_gaps.fa +4 -0
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  460. data/spec/data/gapfilling/6/random2.fa +28 -0
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  464. data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
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  466. data/spec/data/kmers_count1.csv +2 -0
  467. data/spec/data/kmers_count2.csv +3 -0
  468. data/spec/data/out +3 -0
  469. data/spec/data/positive_latching_pair.fa +2 -0
  470. data/spec/data/primers.csv +4 -0
  471. data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
  472. data/spec/data/read_selection_by_kmer/input.fasta +6 -0
  473. data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
  474. data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
  475. data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
  476. data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
  477. data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
  478. data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
  479. data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
  480. data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
  481. data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
  482. data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
  483. data/spec/data/t/details.txt +5 -0
  484. data/spec/data/t/details.txt.srt +5 -0
  485. data/spec/data/t/location.txt +3 -0
  486. data/spec/data/t/location.txt.srt +3 -0
  487. data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
  488. data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
  489. data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
  490. data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
  491. data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
  492. data/spec/data/tweak/3_variant/answer.fa +2 -0
  493. data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
  494. data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
  495. data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
  496. data/spec/data/velvet_test_trails/Assem/Graph +17 -0
  497. data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
  498. data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
  499. data/spec/data/velvet_test_trails/Assem/Log +35 -0
  500. data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
  501. data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
  502. data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
  503. data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
  504. data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
  505. data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
  506. data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
  507. data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
  508. data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
  509. data/spec/data/velvet_test_trails/read1.fa +2 -0
  510. data/spec/data/velvet_test_trails/reads.fa +50 -0
  511. data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
  512. data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
  513. data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
  514. data/spec/data/visualise/1/LastGraph +6695 -0
  515. data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
  516. data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
  517. data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
  518. data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
  519. data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
  520. data/spec/data/wander/1/random1.fa +2 -0
  521. data/spec/data/wander/1/random1.sammy.fa +804 -0
  522. data/spec/depth_first_search_spec.rb +190 -0
  523. data/spec/dijkstra_spec.rb +143 -0
  524. data/spec/explore_spec.rb +29 -0
  525. data/spec/fluffer_spec.rb +155 -0
  526. data/spec/gapfiller_spec.rb +107 -0
  527. data/spec/graph_explorer_spec.rb +475 -0
  528. data/spec/graph_generator_spec.rb +99 -0
  529. data/spec/height_finder_spec.rb +306 -0
  530. data/spec/kmer_abundance_pattern_spec.rb +56 -0
  531. data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
  532. data/spec/kmer_profile_finder_spec.rb +38 -0
  533. data/spec/kmers_count_tabulate_spec.rb +120 -0
  534. data/spec/oriented_node_trail_spec.rb +221 -0
  535. data/spec/paired_end_neighbours_spec.rb +126 -0
  536. data/spec/paths_between_nodes_spec.rb +349 -0
  537. data/spec/priner_spec.rb +7 -0
  538. data/spec/read_input_spec.rb +23 -0
  539. data/spec/read_selection_by_kmer_spec.rb +166 -0
  540. data/spec/read_to_node_spec.rb +35 -0
  541. data/spec/roundup_spec.rb +366 -0
  542. data/spec/scaffold_breaker_spec.rb +144 -0
  543. data/spec/sequence_spec.rb +43 -0
  544. data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
  545. data/spec/single_coherent_wanderer_spec.rb +120 -0
  546. data/spec/single_ended_assembler_spec.rb +398 -0
  547. data/spec/spec_helper.rb +310 -0
  548. data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
  549. data/spec/visualise_spec.rb +105 -0
  550. data/spec/wander_spec.rb +119 -0
  551. data/spec/watch_for_changes.sh +16 -0
  552. data/validation/fasta_compare.rb +72 -0
  553. data/validation/gapfill_simulate_perfect.rb +108 -0
  554. metadata +899 -0
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc ADDED
@@ -0,0 +1,32 @@
1
+ #include <windows.h>
2
+
3
+ #define IDR_VERSION1 1
4
+ IDR_VERSION1 VERSIONINFO MOVEABLE IMPURE LOADONCALL DISCARDABLE
5
+ FILEVERSION 1,2,3,0
6
+ PRODUCTVERSION 1,2,3,0
7
+ FILEFLAGSMASK VS_FFI_FILEFLAGSMASK
8
+ FILEFLAGS 0
9
+ FILEOS VOS_DOS_WINDOWS32
10
+ FILETYPE VFT_DLL
11
+ FILESUBTYPE 0 // not used
12
+ BEGIN
13
+ BLOCK "StringFileInfo"
14
+ BEGIN
15
+ BLOCK "040904E4"
16
+ //language ID = U.S. English, char set = Windows, Multilingual
17
+
18
+ BEGIN
19
+ VALUE "FileDescription", "zlib data compression library\0"
20
+ VALUE "FileVersion", "1.2.3.0\0"
21
+ VALUE "InternalName", "zlib\0"
22
+ VALUE "OriginalFilename", "zlib.dll\0"
23
+ VALUE "ProductName", "ZLib.DLL\0"
24
+ VALUE "Comments","DLL support by Alessandro Iacopetti & Gilles Vollant\0"
25
+ VALUE "LegalCopyright", "(C) 1995-2003 Jean-loup Gailly & Mark Adler\0"
26
+ END
27
+ END
28
+ BLOCK "VarFileInfo"
29
+ BEGIN
30
+ VALUE "Translation", 0x0409, 1252
31
+ END
32
+ END
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj ADDED
@@ -0,0 +1,246 @@
1
+ <?xml version="1.0" encoding = "Windows-1252"?>
2
+ <VisualStudioProject
3
+ ProjectType="Visual C++"
4
+ Version="7.00"
5
+ Name="zlibstat"
6
+ SccProjectName=""
7
+ SccLocalPath="">
8
+ <Platforms>
9
+ <Platform
10
+ Name="Win32"/>
11
+ </Platforms>
12
+ <Configurations>
13
+ <Configuration
14
+ Name="Debug|Win32"
15
+ OutputDirectory=".\zlibstatDebug"
16
+ IntermediateDirectory=".\zlibstatDebug"
17
+ ConfigurationType="4"
18
+ UseOfMFC="0"
19
+ ATLMinimizesCRunTimeLibraryUsage="FALSE">
20
+ <Tool
21
+ Name="VCCLCompilerTool"
22
+ Optimization="0"
23
+ AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
24
+ PreprocessorDefinitions="WIN32;ZLIB_WINAPI"
25
+ ExceptionHandling="FALSE"
26
+ RuntimeLibrary="5"
27
+ PrecompiledHeaderFile=".\zlibstatDebug/zlibstat.pch"
28
+ AssemblerListingLocation=".\zlibstatDebug/"
29
+ ObjectFile=".\zlibstatDebug/"
30
+ ProgramDataBaseFileName=".\zlibstatDebug/"
31
+ WarningLevel="3"
32
+ SuppressStartupBanner="TRUE"
33
+ DebugInformationFormat="1"/>
34
+ <Tool
35
+ Name="VCCustomBuildTool"/>
36
+ <Tool
37
+ Name="VCLibrarianTool"
38
+ AdditionalOptions="/NODEFAULTLIB "
39
+ OutputFile=".\zlibstatDebug\zlibstat.lib"
40
+ SuppressStartupBanner="TRUE"/>
41
+ <Tool
42
+ Name="VCMIDLTool"/>
43
+ <Tool
44
+ Name="VCPostBuildEventTool"/>
45
+ <Tool
46
+ Name="VCPreBuildEventTool"/>
47
+ <Tool
48
+ Name="VCPreLinkEventTool"/>
49
+ <Tool
50
+ Name="VCResourceCompilerTool"
51
+ Culture="1036"/>
52
+ <Tool
53
+ Name="VCWebServiceProxyGeneratorTool"/>
54
+ </Configuration>
55
+ <Configuration
56
+ Name="ReleaseAxp|Win32"
57
+ OutputDirectory=".\zlibsta0"
58
+ IntermediateDirectory=".\zlibsta0"
59
+ ConfigurationType="4"
60
+ UseOfMFC="0"
61
+ ATLMinimizesCRunTimeLibraryUsage="FALSE">
62
+ <Tool
63
+ Name="VCCLCompilerTool"
64
+ InlineFunctionExpansion="1"
65
+ AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
66
+ PreprocessorDefinitions="WIN32;ZLIB_WINAPI"
67
+ StringPooling="TRUE"
68
+ ExceptionHandling="FALSE"
69
+ RuntimeLibrary="4"
70
+ EnableFunctionLevelLinking="TRUE"
71
+ PrecompiledHeaderFile=".\zlibsta0/zlibstat.pch"
72
+ AssemblerListingLocation=".\zlibsta0/"
73
+ ObjectFile=".\zlibsta0/"
74
+ ProgramDataBaseFileName=".\zlibsta0/"
75
+ WarningLevel="3"
76
+ SuppressStartupBanner="TRUE"/>
77
+ <Tool
78
+ Name="VCCustomBuildTool"/>
79
+ <Tool
80
+ Name="VCLibrarianTool"
81
+ AdditionalOptions="/NODEFAULTLIB "
82
+ OutputFile=".\zlibsta0\zlibstat.lib"
83
+ SuppressStartupBanner="TRUE"/>
84
+ <Tool
85
+ Name="VCMIDLTool"/>
86
+ <Tool
87
+ Name="VCPostBuildEventTool"/>
88
+ <Tool
89
+ Name="VCPreBuildEventTool"/>
90
+ <Tool
91
+ Name="VCPreLinkEventTool"/>
92
+ <Tool
93
+ Name="VCResourceCompilerTool"/>
94
+ <Tool
95
+ Name="VCWebServiceProxyGeneratorTool"/>
96
+ </Configuration>
97
+ <Configuration
98
+ Name="Release|Win32"
99
+ OutputDirectory=".\zlibstat"
100
+ IntermediateDirectory=".\zlibstat"
101
+ ConfigurationType="4"
102
+ UseOfMFC="0"
103
+ ATLMinimizesCRunTimeLibraryUsage="FALSE">
104
+ <Tool
105
+ Name="VCCLCompilerTool"
106
+ InlineFunctionExpansion="1"
107
+ AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
108
+ PreprocessorDefinitions="WIN32;ZLIB_WINAPI;ASMV;ASMINF"
109
+ StringPooling="TRUE"
110
+ ExceptionHandling="FALSE"
111
+ RuntimeLibrary="4"
112
+ EnableFunctionLevelLinking="TRUE"
113
+ PrecompiledHeaderFile=".\zlibstat/zlibstat.pch"
114
+ AssemblerListingLocation=".\zlibstat/"
115
+ ObjectFile=".\zlibstat/"
116
+ ProgramDataBaseFileName=".\zlibstat/"
117
+ WarningLevel="3"
118
+ SuppressStartupBanner="TRUE"/>
119
+ <Tool
120
+ Name="VCCustomBuildTool"/>
121
+ <Tool
122
+ Name="VCLibrarianTool"
123
+ AdditionalOptions="..\..\masmx86\gvmat32.obj ..\..\masmx86\inffas32.obj /NODEFAULTLIB "
124
+ OutputFile=".\zlibstat\zlibstat.lib"
125
+ SuppressStartupBanner="TRUE"/>
126
+ <Tool
127
+ Name="VCMIDLTool"/>
128
+ <Tool
129
+ Name="VCPostBuildEventTool"/>
130
+ <Tool
131
+ Name="VCPreBuildEventTool"/>
132
+ <Tool
133
+ Name="VCPreLinkEventTool"/>
134
+ <Tool
135
+ Name="VCResourceCompilerTool"
136
+ Culture="1036"/>
137
+ <Tool
138
+ Name="VCWebServiceProxyGeneratorTool"/>
139
+ </Configuration>
140
+ <Configuration
141
+ Name="ReleaseWithoutAsm|Win32"
142
+ OutputDirectory="zlibstatWithoutAsm"
143
+ IntermediateDirectory="zlibstatWithoutAsm"
144
+ ConfigurationType="4"
145
+ UseOfMFC="0"
146
+ ATLMinimizesCRunTimeLibraryUsage="FALSE">
147
+ <Tool
148
+ Name="VCCLCompilerTool"
149
+ InlineFunctionExpansion="1"
150
+ AdditionalIncludeDirectories="..\..\..;..\..\masmx86"
151
+ PreprocessorDefinitions="WIN32;ZLIB_WINAPI"
152
+ StringPooling="TRUE"
153
+ ExceptionHandling="FALSE"
154
+ RuntimeLibrary="4"
155
+ EnableFunctionLevelLinking="TRUE"
156
+ PrecompiledHeaderFile=".\zlibstat/zlibstat.pch"
157
+ AssemblerListingLocation=".\zlibstatWithoutAsm/"
158
+ ObjectFile=".\zlibstatWithoutAsm/"
159
+ ProgramDataBaseFileName=".\zlibstatWithoutAsm/"
160
+ WarningLevel="3"
161
+ SuppressStartupBanner="TRUE"/>
162
+ <Tool
163
+ Name="VCCustomBuildTool"/>
164
+ <Tool
165
+ Name="VCLibrarianTool"
166
+ AdditionalOptions=" /NODEFAULTLIB "
167
+ OutputFile=".\zlibstatWithoutAsm\zlibstat.lib"
168
+ SuppressStartupBanner="TRUE"/>
169
+ <Tool
170
+ Name="VCMIDLTool"/>
171
+ <Tool
172
+ Name="VCPostBuildEventTool"/>
173
+ <Tool
174
+ Name="VCPreBuildEventTool"/>
175
+ <Tool
176
+ Name="VCPreLinkEventTool"/>
177
+ <Tool
178
+ Name="VCResourceCompilerTool"
179
+ Culture="1036"/>
180
+ <Tool
181
+ Name="VCWebServiceProxyGeneratorTool"/>
182
+ </Configuration>
183
+ </Configurations>
184
+ <Files>
185
+ <Filter
186
+ Name="Source Files"
187
+ Filter="">
188
+ <File
189
+ RelativePath="..\..\..\adler32.c">
190
+ </File>
191
+ <File
192
+ RelativePath="..\..\..\compress.c">
193
+ </File>
194
+ <File
195
+ RelativePath="..\..\..\crc32.c">
196
+ </File>
197
+ <File
198
+ RelativePath="..\..\..\deflate.c">
199
+ </File>
200
+ <File
201
+ RelativePath="..\..\masmx86\gvmat32c.c">
202
+ </File>
203
+ <File
204
+ RelativePath="..\..\..\gzio.c">
205
+ </File>
206
+ <File
207
+ RelativePath="..\..\..\infback.c">
208
+ </File>
209
+ <File
210
+ RelativePath="..\..\..\inffast.c">
211
+ </File>
212
+ <File
213
+ RelativePath="..\..\..\inflate.c">
214
+ </File>
215
+ <File
216
+ RelativePath="..\..\..\inftrees.c">
217
+ </File>
218
+ <File
219
+ RelativePath="..\..\minizip\ioapi.c">
220
+ </File>
221
+ <File
222
+ RelativePath="..\..\..\trees.c">
223
+ </File>
224
+ <File
225
+ RelativePath="..\..\..\uncompr.c">
226
+ </File>
227
+ <File
228
+ RelativePath="..\..\minizip\unzip.c">
229
+ </File>
230
+ <File
231
+ RelativePath="..\..\minizip\zip.c">
232
+ </File>
233
+ <File
234
+ RelativePath=".\zlib.rc">
235
+ </File>
236
+ <File
237
+ RelativePath=".\zlibvc.def">
238
+ </File>
239
+ <File
240
+ RelativePath="..\..\..\zutil.c">
241
+ </File>
242
+ </Filter>
243
+ </Files>
244
+ <Globals>
245
+ </Globals>
246
+ </VisualStudioProject>
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def ADDED
@@ -0,0 +1,92 @@
1
+
2
+ VERSION 1.23
3
+
4
+ HEAPSIZE 1048576,8192
5
+
6
+ EXPORTS
7
+ adler32 @1
8
+ compress @2
9
+ crc32 @3
10
+ deflate @4
11
+ deflateCopy @5
12
+ deflateEnd @6
13
+ deflateInit2_ @7
14
+ deflateInit_ @8
15
+ deflateParams @9
16
+ deflateReset @10
17
+ deflateSetDictionary @11
18
+ gzclose @12
19
+ gzdopen @13
20
+ gzerror @14
21
+ gzflush @15
22
+ gzopen @16
23
+ gzread @17
24
+ gzwrite @18
25
+ inflate @19
26
+ inflateEnd @20
27
+ inflateInit2_ @21
28
+ inflateInit_ @22
29
+ inflateReset @23
30
+ inflateSetDictionary @24
31
+ inflateSync @25
32
+ uncompress @26
33
+ zlibVersion @27
34
+ gzprintf @28
35
+ gzputc @29
36
+ gzgetc @30
37
+ gzseek @31
38
+ gzrewind @32
39
+ gztell @33
40
+ gzeof @34
41
+ gzsetparams @35
42
+ zError @36
43
+ inflateSyncPoint @37
44
+ get_crc_table @38
45
+ compress2 @39
46
+ gzputs @40
47
+ gzgets @41
48
+ inflateCopy @42
49
+ inflateBackInit_ @43
50
+ inflateBack @44
51
+ inflateBackEnd @45
52
+ compressBound @46
53
+ deflateBound @47
54
+ gzclearerr @48
55
+ gzungetc @49
56
+ zlibCompileFlags @50
57
+ deflatePrime @51
58
+
59
+ unzOpen @61
60
+ unzClose @62
61
+ unzGetGlobalInfo @63
62
+ unzGetCurrentFileInfo @64
63
+ unzGoToFirstFile @65
64
+ unzGoToNextFile @66
65
+ unzOpenCurrentFile @67
66
+ unzReadCurrentFile @68
67
+ unzOpenCurrentFile3 @69
68
+ unztell @70
69
+ unzeof @71
70
+ unzCloseCurrentFile @72
71
+ unzGetGlobalComment @73
72
+ unzStringFileNameCompare @74
73
+ unzLocateFile @75
74
+ unzGetLocalExtrafield @76
75
+ unzOpen2 @77
76
+ unzOpenCurrentFile2 @78
77
+ unzOpenCurrentFilePassword @79
78
+
79
+ zipOpen @80
80
+ zipOpenNewFileInZip @81
81
+ zipWriteInFileInZip @82
82
+ zipCloseFileInZip @83
83
+ zipClose @84
84
+ zipOpenNewFileInZip2 @86
85
+ zipCloseFileInZipRaw @87
86
+ zipOpen2 @88
87
+ zipOpenNewFileInZip3 @89
88
+
89
+ unzGetFilePos @100
90
+ unzGoToFilePos @101
91
+
92
+ fill_win32_filefunc @110
data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln ADDED
@@ -0,0 +1,78 @@
1
+ Microsoft Visual Studio Solution File, Format Version 7.00
2
+ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "zlibstat", "zlibstat.vcproj", "{745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}"
3
+ EndProject
4
+ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "zlibvc", "zlibvc.vcproj", "{8FD826F8-3739-44E6-8CC8-997122E53B8D}"
5
+ EndProject
6
+ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "minizip", "minizip.vcproj", "{48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}"
7
+ EndProject
8
+ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "miniunz", "miniunz.vcproj", "{C52F9E7B-498A-42BE-8DB4-85A15694382A}"
9
+ EndProject
10
+ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "testZlibDll", "testzlib.vcproj", "{AA6666AA-E09F-4135-9C0C-4FE50C3C654C}"
11
+ EndProject
12
+ Global
13
+ GlobalSection(SolutionConfiguration) = preSolution
14
+ ConfigName.0 = Debug
15
+ ConfigName.1 = Release
16
+ ConfigName.2 = ReleaseAxp
17
+ ConfigName.3 = ReleaseWithoutAsm
18
+ ConfigName.4 = ReleaseWithoutCrtdll
19
+ EndGlobalSection
20
+ GlobalSection(ProjectDependencies) = postSolution
21
+ EndGlobalSection
22
+ GlobalSection(ProjectConfiguration) = postSolution
23
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug.ActiveCfg = Debug|Win32
24
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Debug.Build.0 = Debug|Win32
25
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release.ActiveCfg = Release|Win32
26
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.Release.Build.0 = Release|Win32
27
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseAxp.ActiveCfg = ReleaseAxp|Win32
28
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseAxp.Build.0 = ReleaseAxp|Win32
29
+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm.ActiveCfg = ReleaseWithoutAsm|Win32
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+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutAsm.Build.0 = ReleaseWithoutAsm|Win32
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+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutCrtdll.ActiveCfg = ReleaseAxp|Win32
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+ {745DEC58-EBB3-47A9-A9B8-4C6627C01BF8}.ReleaseWithoutCrtdll.Build.0 = ReleaseAxp|Win32
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+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Debug.ActiveCfg = Debug|Win32
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+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Debug.Build.0 = Debug|Win32
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+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Release.ActiveCfg = Release|Win32
36
+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.Release.Build.0 = Release|Win32
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+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseAxp.Build.0 = ReleaseAxp|Win32
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+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutAsm.Build.0 = ReleaseWithoutAsm|Win32
41
+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutCrtdll.ActiveCfg = ReleaseWithoutCrtdll|Win32
42
+ {8FD826F8-3739-44E6-8CC8-997122E53B8D}.ReleaseWithoutCrtdll.Build.0 = ReleaseWithoutCrtdll|Win32
43
+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.Debug.ActiveCfg = Debug|Win32
44
+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.Debug.Build.0 = Debug|Win32
45
+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.Release.ActiveCfg = Release|Win32
46
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47
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+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.ReleaseAxp.Build.0 = Release|Win32
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+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm.ActiveCfg = Release|Win32
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+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutAsm.Build.0 = Release|Win32
51
+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutCrtdll.ActiveCfg = Release|Win32
52
+ {48CDD9DC-E09F-4135-9C0C-4FE50C3C654B}.ReleaseWithoutCrtdll.Build.0 = Release|Win32
53
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.Debug.ActiveCfg = Debug|Win32
54
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.Debug.Build.0 = Debug|Win32
55
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56
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.Release.Build.0 = Release|Win32
57
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58
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.ReleaseAxp.Build.0 = Release|Win32
59
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.ReleaseWithoutAsm.ActiveCfg = Release|Win32
60
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.ReleaseWithoutAsm.Build.0 = Release|Win32
61
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.ReleaseWithoutCrtdll.ActiveCfg = Release|Win32
62
+ {C52F9E7B-498A-42BE-8DB4-85A15694382A}.ReleaseWithoutCrtdll.Build.0 = Release|Win32
63
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.Debug.ActiveCfg = Debug|Win32
64
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.Debug.Build.0 = Debug|Win32
65
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.Release.ActiveCfg = Release|Win32
66
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.Release.Build.0 = Release|Win32
67
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseAxp.ActiveCfg = Release|Win32
68
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseAxp.Build.0 = Release|Win32
69
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseWithoutAsm.ActiveCfg = Release|Win32
70
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseWithoutAsm.Build.0 = Release|Win32
71
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseWithoutCrtdll.ActiveCfg = Release|Win32
72
+ {AA6666AA-E09F-4135-9C0C-4FE50C3C654C}.ReleaseWithoutCrtdll.Build.0 = Release|Win32
73
+ EndGlobalSection
74
+ GlobalSection(ExtensibilityGlobals) = postSolution
75
+ EndGlobalSection
76
+ GlobalSection(ExtensibilityAddIns) = postSolution
77
+ EndGlobalSection
78
+ EndGlobal