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
  192. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  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
  195. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  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
  216. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  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
  225. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  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
  229. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  230. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  231. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  232. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  233. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
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  236. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  237. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  238. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  239. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  240. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  241. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  242. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  243. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  244. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  246. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  247. data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  249. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  250. data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
  252. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  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
  259. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
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  376. data/spec/connection_interpreter_spec.rb +284 -0
  377. data/spec/contig_printer_spec.rb +291 -0
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  381. data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
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  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
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  399. data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
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  401. data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
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  411. data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
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  413. data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
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  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
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  423. data/spec/data/explore/1/a.fa +2 -0
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  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
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  431. data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
  432. data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
  433. data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
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  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
  446. data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
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  450. data/spec/data/gapfilling/3/with_gaps.fa +4 -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
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  489. data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
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  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
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  497. data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
  498. data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
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  502. data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
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  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
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  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
@@ -0,0 +1,11 @@
1
+ unit ZLibConst;
2
+
3
+ interface
4
+
5
+ resourcestring
6
+ sTargetBufferTooSmall = 'ZLib error: target buffer may be too small';
7
+ sInvalidStreamOp = 'Invalid stream operation';
8
+
9
+ implementation
10
+
11
+ end.
@@ -0,0 +1,76 @@
1
+
2
+ Overview
3
+ ========
4
+
5
+ This directory contains an update to the ZLib interface unit,
6
+ distributed by Borland as a Delphi supplemental component.
7
+
8
+ The original ZLib unit is Copyright (c) 1997,99 Borland Corp.,
9
+ and is based on zlib version 1.0.4. There are a series of bugs
10
+ and security problems associated with that old zlib version, and
11
+ we recommend the users to update their ZLib unit.
12
+
13
+
14
+ Summary of modifications
15
+ ========================
16
+
17
+ - Improved makefile, adapted to zlib version 1.2.1.
18
+
19
+ - Some field types from TZStreamRec are changed from Integer to
20
+ Longint, for consistency with the zlib.h header, and for 64-bit
21
+ readiness.
22
+
23
+ - The zlib_version constant is updated.
24
+
25
+ - The new Z_RLE strategy has its corresponding symbolic constant.
26
+
27
+ - The allocation and deallocation functions and function types
28
+ (TAlloc, TFree, zlibAllocMem and zlibFreeMem) are now cdecl,
29
+ and _malloc and _free are added as C RTL stubs. As a result,
30
+ the original C sources of zlib can be compiled out of the box,
31
+ and linked to the ZLib unit.
32
+
33
+
34
+ Suggestions for improvements
35
+ ============================
36
+
37
+ Currently, the ZLib unit provides only a limited wrapper around
38
+ the zlib library, and much of the original zlib functionality is
39
+ missing. Handling compressed file formats like ZIP/GZIP or PNG
40
+ cannot be implemented without having this functionality.
41
+ Applications that handle these formats are either using their own,
42
+ duplicated code, or not using the ZLib unit at all.
43
+
44
+ Here are a few suggestions:
45
+
46
+ - Checksum class wrappers around adler32() and crc32(), similar
47
+ to the Java classes that implement the java.util.zip.Checksum
48
+ interface.
49
+
50
+ - The ability to read and write raw deflate streams, without the
51
+ zlib stream header and trailer. Raw deflate streams are used
52
+ in the ZIP file format.
53
+
54
+ - The ability to read and write gzip streams, used in the GZIP
55
+ file format, and normally produced by the gzip program.
56
+
57
+ - The ability to select a different compression strategy, useful
58
+ to PNG and MNG image compression, and to multimedia compression
59
+ in general. Besides the compression level
60
+
61
+ TCompressionLevel = (clNone, clFastest, clDefault, clMax);
62
+
63
+ which, in fact, could have used the 'z' prefix and avoided
64
+ TColor-like symbols
65
+
66
+ TCompressionLevel = (zcNone, zcFastest, zcDefault, zcMax);
67
+
68
+ there could be a compression strategy
69
+
70
+ TCompressionStrategy = (zsDefault, zsFiltered, zsHuffmanOnly, zsRle);
71
+
72
+ - ZIP and GZIP stream handling via TStreams.
73
+
74
+
75
+ --
76
+ Cosmin Truta <cosmint@cs.ubbcluj.ro>
@@ -0,0 +1,93 @@
1
+ # Makefile for zlib
2
+ # For use with Delphi and C++ Builder under Win32
3
+ # Updated for zlib 1.2.x by Cosmin Truta
4
+
5
+ # ------------ Borland C++ ------------
6
+
7
+ # This project uses the Delphi (fastcall/register) calling convention:
8
+ LOC = -DZEXPORT=__fastcall -DZEXPORTVA=__cdecl
9
+
10
+ CC = bcc32
11
+ LD = bcc32
12
+ AR = tlib
13
+ # do not use "-pr" in CFLAGS
14
+ CFLAGS = -a -d -k- -O2 $(LOC)
15
+ LDFLAGS =
16
+
17
+
18
+ # variables
19
+ ZLIB_LIB = zlib.lib
20
+
21
+ OBJ1 = adler32.obj compress.obj crc32.obj deflate.obj gzio.obj infback.obj
22
+ OBJ2 = inffast.obj inflate.obj inftrees.obj trees.obj uncompr.obj zutil.obj
23
+ OBJP1 = +adler32.obj+compress.obj+crc32.obj+deflate.obj+gzio.obj+infback.obj
24
+ OBJP2 = +inffast.obj+inflate.obj+inftrees.obj+trees.obj+uncompr.obj+zutil.obj
25
+
26
+
27
+ # targets
28
+ all: $(ZLIB_LIB) example.exe minigzip.exe
29
+
30
+ .c.obj:
31
+ $(CC) -c $(CFLAGS) $*.c
32
+
33
+ adler32.obj: adler32.c zlib.h zconf.h
34
+
35
+ compress.obj: compress.c zlib.h zconf.h
36
+
37
+ crc32.obj: crc32.c zlib.h zconf.h crc32.h
38
+
39
+ deflate.obj: deflate.c deflate.h zutil.h zlib.h zconf.h
40
+
41
+ gzio.obj: gzio.c zutil.h zlib.h zconf.h
42
+
43
+ infback.obj: infback.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
44
+ inffast.h inffixed.h
45
+
46
+ inffast.obj: inffast.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
47
+ inffast.h
48
+
49
+ inflate.obj: inflate.c zutil.h zlib.h zconf.h inftrees.h inflate.h \
50
+ inffast.h inffixed.h
51
+
52
+ inftrees.obj: inftrees.c zutil.h zlib.h zconf.h inftrees.h
53
+
54
+ trees.obj: trees.c zutil.h zlib.h zconf.h deflate.h trees.h
55
+
56
+ uncompr.obj: uncompr.c zlib.h zconf.h
57
+
58
+ zutil.obj: zutil.c zutil.h zlib.h zconf.h
59
+
60
+ example.obj: example.c zlib.h zconf.h
61
+
62
+ minigzip.obj: minigzip.c zlib.h zconf.h
63
+
64
+
65
+ # For the sake of the old Borland make,
66
+ # the command line is cut to fit in the MS-DOS 128 byte limit:
67
+ $(ZLIB_LIB): $(OBJ1) $(OBJ2)
68
+ -del $(ZLIB_LIB)
69
+ $(AR) $(ZLIB_LIB) $(OBJP1)
70
+ $(AR) $(ZLIB_LIB) $(OBJP2)
71
+
72
+
73
+ # testing
74
+ test: example.exe minigzip.exe
75
+ example
76
+ echo hello world | minigzip | minigzip -d
77
+
78
+ example.exe: example.obj $(ZLIB_LIB)
79
+ $(LD) $(LDFLAGS) example.obj $(ZLIB_LIB)
80
+
81
+ minigzip.exe: minigzip.obj $(ZLIB_LIB)
82
+ $(LD) $(LDFLAGS) minigzip.obj $(ZLIB_LIB)
83
+
84
+
85
+ # cleanup
86
+ clean:
87
+ -del *.obj
88
+ -del *.exe
89
+ -del *.lib
90
+ -del *.tds
91
+ -del zlib.bak
92
+ -del foo.gz
93
+
@@ -0,0 +1,33 @@
1
+ <?xml version="1.0" encoding="utf-8" ?>
2
+ <project name="DotZLib" default="build" basedir="./DotZLib">
3
+ <description>A .Net wrapper library around ZLib1.dll</description>
4
+
5
+ <property name="nunit.location" value="c:/program files/NUnit V2.1/bin" />
6
+ <property name="build.root" value="bin" />
7
+
8
+ <property name="debug" value="true" />
9
+ <property name="nunit" value="true" />
10
+
11
+ <property name="build.folder" value="${build.root}/debug/" if="${debug}" />
12
+ <property name="build.folder" value="${build.root}/release/" unless="${debug}" />
13
+
14
+ <target name="clean" description="Remove all generated files">
15
+ <delete dir="${build.root}" failonerror="false" />
16
+ </target>
17
+
18
+ <target name="build" description="compiles the source code">
19
+
20
+ <mkdir dir="${build.folder}" />
21
+ <csc target="library" output="${build.folder}DotZLib.dll" debug="${debug}">
22
+ <references basedir="${nunit.location}">
23
+ <includes if="${nunit}" name="nunit.framework.dll" />
24
+ </references>
25
+ <sources>
26
+ <includes name="*.cs" />
27
+ <excludes name="UnitTests.cs" unless="${nunit}" />
28
+ </sources>
29
+ <arg value="/d:nunit" if="${nunit}" />
30
+ </csc>
31
+ </target>
32
+
33
+ </project>
@@ -0,0 +1,21 @@
1
+ Microsoft Visual Studio Solution File, Format Version 8.00
2
+ Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "DotZLib", "DotZLib\DotZLib.csproj", "{BB1EE0B1-1808-46CB-B786-949D91117FC5}"
3
+ ProjectSection(ProjectDependencies) = postProject
4
+ EndProjectSection
5
+ EndProject
6
+ Global
7
+ GlobalSection(SolutionConfiguration) = preSolution
8
+ Debug = Debug
9
+ Release = Release
10
+ EndGlobalSection
11
+ GlobalSection(ProjectConfiguration) = postSolution
12
+ {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.ActiveCfg = Debug|.NET
13
+ {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Debug.Build.0 = Debug|.NET
14
+ {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.ActiveCfg = Release|.NET
15
+ {BB1EE0B1-1808-46CB-B786-949D91117FC5}.Release.Build.0 = Release|.NET
16
+ EndGlobalSection
17
+ GlobalSection(ExtensibilityGlobals) = postSolution
18
+ EndGlobalSection
19
+ GlobalSection(ExtensibilityAddIns) = postSolution
20
+ EndGlobalSection
21
+ EndGlobal
@@ -0,0 +1,58 @@
1
+ using System.Reflection;
2
+ using System.Runtime.CompilerServices;
3
+
4
+ //
5
+ // General Information about an assembly is controlled through the following
6
+ // set of attributes. Change these attribute values to modify the information
7
+ // associated with an assembly.
8
+ //
9
+ [assembly: AssemblyTitle("DotZLib")]
10
+ [assembly: AssemblyDescription(".Net bindings for ZLib compression dll 1.2.x")]
11
+ [assembly: AssemblyConfiguration("")]
12
+ [assembly: AssemblyCompany("Henrik Ravn")]
13
+ [assembly: AssemblyProduct("")]
14
+ [assembly: AssemblyCopyright("(c) 2004 by Henrik Ravn")]
15
+ [assembly: AssemblyTrademark("")]
16
+ [assembly: AssemblyCulture("")]
17
+
18
+ //
19
+ // Version information for an assembly consists of the following four values:
20
+ //
21
+ // Major Version
22
+ // Minor Version
23
+ // Build Number
24
+ // Revision
25
+ //
26
+ // You can specify all the values or you can default the Revision and Build Numbers
27
+ // by using the '*' as shown below:
28
+
29
+ [assembly: AssemblyVersion("1.0.*")]
30
+
31
+ //
32
+ // In order to sign your assembly you must specify a key to use. Refer to the
33
+ // Microsoft .NET Framework documentation for more information on assembly signing.
34
+ //
35
+ // Use the attributes below to control which key is used for signing.
36
+ //
37
+ // Notes:
38
+ // (*) If no key is specified, the assembly is not signed.
39
+ // (*) KeyName refers to a key that has been installed in the Crypto Service
40
+ // Provider (CSP) on your machine. KeyFile refers to a file which contains
41
+ // a key.
42
+ // (*) If the KeyFile and the KeyName values are both specified, the
43
+ // following processing occurs:
44
+ // (1) If the KeyName can be found in the CSP, that key is used.
45
+ // (2) If the KeyName does not exist and the KeyFile does exist, the key
46
+ // in the KeyFile is installed into the CSP and used.
47
+ // (*) In order to create a KeyFile, you can use the sn.exe (Strong Name) utility.
48
+ // When specifying the KeyFile, the location of the KeyFile should be
49
+ // relative to the project output directory which is
50
+ // %Project Directory%\obj\<configuration>. For example, if your KeyFile is
51
+ // located in the project directory, you would specify the AssemblyKeyFile
52
+ // attribute as [assembly: AssemblyKeyFile("..\\..\\mykey.snk")]
53
+ // (*) Delay Signing is an advanced option - see the Microsoft .NET Framework
54
+ // documentation for more information on this.
55
+ //
56
+ [assembly: AssemblyDelaySign(false)]
57
+ [assembly: AssemblyKeyFile("")]
58
+ [assembly: AssemblyKeyName("")]
@@ -0,0 +1,202 @@
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.Runtime.InteropServices;
10
+ using System.Text;
11
+
12
+
13
+ namespace DotZLib
14
+ {
15
+ #region ChecksumGeneratorBase
16
+ /// <summary>
17
+ /// Implements the common functionality needed for all <see cref="ChecksumGenerator"/>s
18
+ /// </summary>
19
+ /// <example></example>
20
+ public abstract class ChecksumGeneratorBase : ChecksumGenerator
21
+ {
22
+ /// <summary>
23
+ /// The value of the current checksum
24
+ /// </summary>
25
+ protected uint _current;
26
+
27
+ /// <summary>
28
+ /// Initializes a new instance of the checksum generator base - the current checksum is
29
+ /// set to zero
30
+ /// </summary>
31
+ public ChecksumGeneratorBase()
32
+ {
33
+ _current = 0;
34
+ }
35
+
36
+ /// <summary>
37
+ /// Initializes a new instance of the checksum generator basewith a specified value
38
+ /// </summary>
39
+ /// <param name="initialValue">The value to set the current checksum to</param>
40
+ public ChecksumGeneratorBase(uint initialValue)
41
+ {
42
+ _current = initialValue;
43
+ }
44
+
45
+ /// <summary>
46
+ /// Resets the current checksum to zero
47
+ /// </summary>
48
+ public void Reset() { _current = 0; }
49
+
50
+ /// <summary>
51
+ /// Gets the current checksum value
52
+ /// </summary>
53
+ public uint Value { get { return _current; } }
54
+
55
+ /// <summary>
56
+ /// Updates the current checksum with part of an array of bytes
57
+ /// </summary>
58
+ /// <param name="data">The data to update the checksum with</param>
59
+ /// <param name="offset">Where in <c>data</c> to start updating</param>
60
+ /// <param name="count">The number of bytes from <c>data</c> to use</param>
61
+ /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
62
+ /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
63
+ /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
64
+ /// <remarks>All the other <c>Update</c> methods are implmeneted in terms of this one.
65
+ /// This is therefore the only method a derived class has to implement</remarks>
66
+ public abstract void Update(byte[] data, int offset, int count);
67
+
68
+ /// <summary>
69
+ /// Updates the current checksum with an array of bytes.
70
+ /// </summary>
71
+ /// <param name="data">The data to update the checksum with</param>
72
+ public void Update(byte[] data)
73
+ {
74
+ Update(data, 0, data.Length);
75
+ }
76
+
77
+ /// <summary>
78
+ /// Updates the current checksum with the data from a string
79
+ /// </summary>
80
+ /// <param name="data">The string to update the checksum with</param>
81
+ /// <remarks>The characters in the string are converted by the UTF-8 encoding</remarks>
82
+ public void Update(string data)
83
+ {
84
+ Update(Encoding.UTF8.GetBytes(data));
85
+ }
86
+
87
+ /// <summary>
88
+ /// Updates the current checksum with the data from a string, using a specific encoding
89
+ /// </summary>
90
+ /// <param name="data">The string to update the checksum with</param>
91
+ /// <param name="encoding">The encoding to use</param>
92
+ public void Update(string data, Encoding encoding)
93
+ {
94
+ Update(encoding.GetBytes(data));
95
+ }
96
+
97
+ }
98
+ #endregion
99
+
100
+ #region CRC32
101
+ /// <summary>
102
+ /// Implements a CRC32 checksum generator
103
+ /// </summary>
104
+ public sealed class CRC32Checksum : ChecksumGeneratorBase
105
+ {
106
+ #region DLL imports
107
+
108
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
109
+ private static extern uint crc32(uint crc, int data, uint length);
110
+
111
+ #endregion
112
+
113
+ /// <summary>
114
+ /// Initializes a new instance of the CRC32 checksum generator
115
+ /// </summary>
116
+ public CRC32Checksum() : base() {}
117
+
118
+ /// <summary>
119
+ /// Initializes a new instance of the CRC32 checksum generator with a specified value
120
+ /// </summary>
121
+ /// <param name="initialValue">The value to set the current checksum to</param>
122
+ public CRC32Checksum(uint initialValue) : base(initialValue) {}
123
+
124
+ /// <summary>
125
+ /// Updates the current checksum with part of an array of bytes
126
+ /// </summary>
127
+ /// <param name="data">The data to update the checksum with</param>
128
+ /// <param name="offset">Where in <c>data</c> to start updating</param>
129
+ /// <param name="count">The number of bytes from <c>data</c> to use</param>
130
+ /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
131
+ /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
132
+ /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
133
+ public override void Update(byte[] data, int offset, int count)
134
+ {
135
+ if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
136
+ if ((offset+count) > data.Length) throw new ArgumentException();
137
+ GCHandle hData = GCHandle.Alloc(data, GCHandleType.Pinned);
138
+ try
139
+ {
140
+ _current = crc32(_current, hData.AddrOfPinnedObject().ToInt32()+offset, (uint)count);
141
+ }
142
+ finally
143
+ {
144
+ hData.Free();
145
+ }
146
+ }
147
+
148
+ }
149
+ #endregion
150
+
151
+ #region Adler
152
+ /// <summary>
153
+ /// Implements a checksum generator that computes the Adler checksum on data
154
+ /// </summary>
155
+ public sealed class AdlerChecksum : ChecksumGeneratorBase
156
+ {
157
+ #region DLL imports
158
+
159
+ [DllImport("ZLIB1.dll", CallingConvention=CallingConvention.Cdecl)]
160
+ private static extern uint adler32(uint adler, int data, uint length);
161
+
162
+ #endregion
163
+
164
+ /// <summary>
165
+ /// Initializes a new instance of the Adler checksum generator
166
+ /// </summary>
167
+ public AdlerChecksum() : base() {}
168
+
169
+ /// <summary>
170
+ /// Initializes a new instance of the Adler checksum generator with a specified value
171
+ /// </summary>
172
+ /// <param name="initialValue">The value to set the current checksum to</param>
173
+ public AdlerChecksum(uint initialValue) : base(initialValue) {}
174
+
175
+ /// <summary>
176
+ /// Updates the current checksum with part of an array of bytes
177
+ /// </summary>
178
+ /// <param name="data">The data to update the checksum with</param>
179
+ /// <param name="offset">Where in <c>data</c> to start updating</param>
180
+ /// <param name="count">The number of bytes from <c>data</c> to use</param>
181
+ /// <exception cref="ArgumentException">The sum of offset and count is larger than the length of <c>data</c></exception>
182
+ /// <exception cref="NullReferenceException"><c>data</c> is a null reference</exception>
183
+ /// <exception cref="ArgumentOutOfRangeException">Offset or count is negative.</exception>
184
+ public override void Update(byte[] data, int offset, int count)
185
+ {
186
+ if (offset < 0 || count < 0) throw new ArgumentOutOfRangeException();
187
+ if ((offset+count) > data.Length) throw new ArgumentException();
188
+ GCHandle hData = GCHandle.Alloc(data, GCHandleType.Pinned);
189
+ try
190
+ {
191
+ _current = adler32(_current, hData.AddrOfPinnedObject().ToInt32()+offset, (uint)count);
192
+ }
193
+ finally
194
+ {
195
+ hData.Free();
196
+ }
197
+ }
198
+
199
+ }
200
+ #endregion
201
+
202
+ }