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
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data/spec/data/assembly_visualiser/Graph ADDED
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+ 11 161 101 1
2
+ NODE 1 533 3299 3299 0 0
3
+ TCCAGATAGCCTTTTCAAAAATAGCCTGCTGTTCATTAGTAAATGCTTCCAGGATTATACCTCCTTGCCGTATTATTCCATATATTCCCAGTCATAGTTATACCGCGTTGCTGTGATCGATTCTTTTACAGATGGACCTTCGAACCTGTACCTCTGCTTTGTGCAGACGAAGTCTGAGAAACCTGCAAGGAAGTTATCGTACATATTGACAGTTTTTCCCAGAAGTTAATCTGGGCTTGCGTATTCAGGTTTAATCTCTACATCTATGTGCCATCCTGGATGATGCCTCAAGGAAGACACTGCTGGCGCGAGTTTACAACAATAGATACCGAGAACAGCAAGAAGGTCATTGTTCGCAGAGCGCACCGTAGGTGACCAGATGGTAGAGAGGTATTGGATGATCTGTCCCTTAAGAGAGCTTATTATGGATCACGGAAGCGAGTTCGGTGCCCATCGGAGAGATGAGAATGGGAATTGGGATGGTGAATTTAAGCAGCATATAATGAATTTAGAAATTAAACCAATCCTGGCAC
4
+ GTGATCCATAATAAGCTCTCTTAAGGGACAGATCATCCAATACCTCTCTACCATCTGGTCACCTACGGTGCGCTCTGCGAACAATGACCTTCTTGCTGTTCTCGGTATCTATTGTTGTAAACTCGCGCCAGCAGTGTCTTCCTTGAGGCATCATCCAGGATGGCACATAGATGTAGAGATTAAACCTGAATACGCAAGCCCAGATTAACTTCTGGGAAAAACTGTCAATATGTACGATAACTTCCTTGCAGGTTTCTCAGACTTCGTCTGCACAAAGCAGAGGTACAGGTTCGAAGGTCCATCTGTAAAAGAATCGATCACAGCAACGCGGTATAACTATGACTGGGAATATATGGAATAATACGGCAAGGAGGTATAATCCTGGAAGCATTTACTAATGAACAGCAGGCTATTTTTGAAAAGGCTATCTGGAAATTCCTTGAGGAGAACAGGGAACTCGTGCTCAGGCGGCTGCTCGGGATAGATAAACTGGGGCTGTCGGCGCCAAACGAGATTACCATAGTTGTGAATGC
5
+ NODE 2 101 1161 1161 0 0
6
+ AGCTGTTTAATTTGATTTTTCCTGAAATAAACAGATCTCCTAACTCTTTAATTGATTTATAATGATATGAATTGGATAGTTTAAGCATTCCTCTCTTTTGG
7
+ TTTCCTTTTGATCACAAAAAGTTTATGAATATTTCTGATGCTACACTTCTTGCGAGATCAGGAAAGAAGGTATATGGTGCTAAAAAGCTCAAGAATTACGT
8
+ NODE 3 416 4152 4152 0 0
9
+ GCGTTATTTATTGTAAAAGAAGGTATCATCAGTTTGGCTATCATCAATTCAGATAGACTTTTATACAGGCAAGAATCACTATTTAACGGGCTTAGAAAACTTAGTAATAAGATTAATAGGTCCAAAGAAATCCATCTCCAATTGTTGGCAGTAATTGAGATGATTTCTAAAAATAAAAACCTGTTATTTCTAGATCGATTGTGTGAACGTCAGTAACAATACAATATATCCAAATGTCAGAAAAAATGCCATCATTGCATTTATCTGGGTGAGAAAACAAAGTTAATCAAAATCCTCTTATGTATTCTACCCACCATATTGCAGAATAAGAAAATTTCCAGCGCAGTGGTCGGAAGCCTCCATACATTCGGCCTAAAACTTCGGAACCTTGGTCTTTTGATAACCACTTTCCCAGC
10
+ TGGTGGGTAGAATACATAAGAGGATTTTGATTAACTTTGTTTTCTCACCCAGATAAATGCAATGATGGCATTTTTTCTGACATTTGGATATATTGTATTGTTACTGACGTTCACACAATCGATCTAGAAATAACAGGTTTTTATTTTTAGAAATCATCTCAATTACTGCCAACAATTGGAGATGGATTTCTTTGGACCTATTAATCTTATTACTAAGTTTTCTAAGCCCGTTAAATAGTGATTCTTGCCTGTATAAAAGTCTATCTGAATTGATGATAGCCAAACTGATGATACCTTCTTTTACAATAAATAACGCCCAAAAGAGAGGAATGCTTAAACTATCCAATTCATATCATTATAAATCAATTAAAGAGTTAGGAGATCTGTTTATTTCAGGAAAAATCAAATTAAACAGC
11
+ NODE 4 101 984 984 0 0
12
+ GAGTGAAGCATCCTCCGACGAATAGGAAGCTGGAGAAATGGTTTGATACTTACCGCAGATTCAGGAAATCCTTCTCCAGCTTTGATGAGTTCGTTGATTGG
13
+ CGTGCCAGGATTGGTTTAATTTCTAAATTCATTATATGCTGCTTAAATTCACCATCCCAATTCCCATTCTCATCTCTCCGATGGGCACCGAACTCGCTTCC
14
+ NODE 5 489 5988 5988 0 0
15
+ TATAACAATCGACTTCATACTAGATTTTTAGAAACTCTGCTGTCTCAGACCTGATTCTCTCCTCCTGCCCTATCAGCAAGTGACCGCCGCTTCCCAGTCCGATAAACCTCGCACCTGGTATGTGTTGTGCAGTGTATTGAGCGCCAATAAATGTATTATACGGGTCATCAACCACGCTGATCACCAGCGTCGGCGCAGTAATACTTTCAAGTGGATAACGATCGAGTGAGGAGGTAATATTCGCATCGTTTAACAAGCCTGGTAGCCGCATACTGATTGGCAGCAGCATCTGCATGAGTTCAGACAGCTGCTCCTCTTGCGCAGGCGTGAGCCTGGCCTGCACCTCTGAAGGTACGCCGAGCAGAGACATCACGCTTGATCGGGCCACTCTCATCGCCAGCCAGATAGCAAAATCCGACCTTATGACTTTTAACATCAAGTCTGAAGCCGGGGAAGGCTGAGCCGGTGATGGAGGCGGAGGCGCATAGG
16
+ AGTGGCCCGATCAAGCGTGATGTCTCTGCTCGGCGTACCTTCAGAGGTGCAGGCCAGGCTCACGCCTGCGCAAGAGGAGCAGCTGTCTGAACTCATGCAGATGCTGCTGCCAATCAGTATGCGGCTACCAGGCTTGTTAAACGATGCGAATATTACCTCCTCACTCGATCGTTATCCACTTGAAAGTATTACTGCGCCGACGCTGGTGATCAGCGTGGTTGATGACCCGTATAATACATTTATTGGCGCTCAATACACTGCACAACACATACCAGGTGCGAGGTTTATCGGACTGGGAAGCGGCGGTCACTTGCTGATAGGGCAGGAGGAGAGAATCAGGTCTGAGACAGCAGAGTTTCTAAAAATCTAGTATGAAGTCGATTGTTATACCAATCAACGAACTCATCAAAGCTGGAGAAGGATTTCCTGAATCTGCGGTAAGTATCAAACCATTTCTCCAGCTTCCTATTCGTCGGAGGATGCTTCACT
17
+ NODE 6 101 1024 1024 0 0
18
+ TGCATTCACAACTATGGTAATCTCGTTTGGCGCCGACAGCCCCAGTTTATCTATCCCGAGCAGCCGCCTGAGCACGAGTTCCCTGTTCTCCTCAAGGAATT
19
+ AGCTGGGAAAGTGGTTATCAAAAGACCAAGGTTCCGAAGTTTTAGGCCGAATGTATGGAGGCTTCCGACCACTGCGCTGGAAATTTTCTTATTCTGCAATA
20
+ NODE 7 211 2428 2428 0 0
21
+ GTTAGATGCTTTTTATTGTGATTAATTATCTTAAAGTCAGTGATAAAATTTAATCCGTTGGATCTTTCTATAGTAATTAATAAATCCTGCAGTACCTCATAACTTTTAGTAACGTAATTCTTGAGCTTTTTAGCACCATATACCTTCTTTCCTGATCTCGCAAGAAGTGTAGCATCAGAAATATTCATAAACTTTTTGTGATCAAAAGGAA
22
+ TACTAAAAGTTATGAGGTACTGCAGGATTTATTAATTACTATAGAAAGATCCAACGGATTAAATTTTATCACTGACTTTAAGATAATTAATCACAATAAAAAGCATCTAACAAAACCAGAAGAAATAGCCAAAGCGATTAAATCAGGCAAAATAAAGAAAAACAGTTGGTTAGTCATTGATGGAGGGTTAAAATCCAAAGAACTGTTAAAA
23
+ NODE 8 101 101 101 0 0
24
+ GGCTGTTTAATTTGATTTTTCCTGAAATAAACAGATCTCCTAACTCTTTAATTGATTTATAATGATATGAATTGGATAGTTTAAGCATTCCTCTCTTTTGG
25
+ CTTCCTTTTGATCACAAAAAGTTTATGAATATTTCTGATGCTACACTTCTTGCGAGATCAGGAAAGAAGGTATATGGTGCTAAAAAGCTCAAGAATTACGT
26
+ NODE 9 420 2738 2738 0 0
27
+ GGCAGAATATATGCATGGATAAGGGATATGATTTCCCTGACATCAAAGAGCTTGTAGAAGAATATGGCTATACCGCACATATTCGCACACGTGGAGAAGAGAAGAAAGAAAAAAAGAGATACCAGGCTACAGAGCAAGAAGATGGGTAGTAGAAAGAACACATTCATGGCTGAACAGGTTCAGAAGGTTGCTCATACGATGGGAGAAGAAAGTTGAGAATTATTCAGCACTAATTCATTTTGCATGTGCTTGGATAACATTCAGAGCAGCAGGACTTTTCGGATAGGCTCTAAAACTAAGGCAGAAGGTTTATTGTAGATAAGATGTAACTCTTATAGCCAGATTATTAACTGGCATAAGGTGGGTGGGAAATATGAACAAGAAAATTAAAAAGGTAGCTATTGCTATCTTACTTGCAAT
28
+ ATCTACAATAAACCTTCTGCCTTAGTTTTAGAGCCTATCCGAAAAGTCCTGCTGCTCTGAATGTTATCCAAGCACATGCAAAATGAATTAGTGCTGAATAATTCTCAACTTTCTTCTCCCATCGTATGAGCAACCTTCTGAACCTGTTCAGCCATGAATGTGTTCTTTCTACTACCCATCTTCTTGCTCTGTAGCCTGGTATCTCTTTTTTTCTTTCTTCTCTTCTCCACGTGTGCGAATATGTGCGGTATAGCCATATTCTTCTACAAGCTCTTTGATGTCAGGGAAATCATATCCCTTATCCATGCATATATTCTGCCTTACCTCTTCGGTGGATGGTCTTTCTACAATTATGGCATCAAGAGTACCTTTTACAAGTTTTTTATCGTGACGATTGGCTCCATCCACGGTAACTGAAAG
29
+ NODE 10 101 101 101 0 0
30
+ AGTGCCAGGATTGGTTTAATTTCTAAATTCATTATATGCTGCTTAAATTCACCATCCCAATTCCCATTCTCATCTCTCCGATGGGCACCGAACTCGCTTCC
31
+ TAGTGAAGCATCCTCCGACGAATAGGAAGCTGGAGAAATGGTTTGATACTTACCGCAGATTCAGGAAATCCTTCTCCAGCTTTGATGAGTTCGTTGATTGG
32
+ NODE 11 101 101 101 0 0
33
+ GGCTGGGAAAGTGGTTATCAAAAGACCAAGGTTCCGAAGTTTTAGGCCGAATGTATGGAGGCTTCCGACCACTGCGCTGGAAATTTTCTTATTCTGCAATA
34
+ CGCATTCACAACTATGGTAATCTCGTTTGGCGCCGACAGCCCCAGTTTATCTATCCCGAGCAGCCGCCTGAGCACGAGTTCCCTGTTCTCCTCAAGGAATT
35
+ ARC 1 -10 1
36
+ ARC 1 4 8
37
+ ARC -1 -6 10
38
+ ARC -1 11 1
39
+ ARC 2 3 10
40
+ ARC -2 -7 9
41
+ ARC 3 -11 1
42
+ ARC 3 6 12
43
+ ARC -3 -8 1
44
+ ARC 4 5 11
45
+ ARC -5 10 1
46
+ ARC 7 8 1
data/spec/data/assembly_visualiser/start_kmers1 ADDED
@@ -0,0 +1,2 @@
1
+ TTTTCAAAAATAGCCTGCTGTTCATTAGTAAATGCTTCCAGGATTAT
2
+ GACATTTGGATATATTGTATTGTTACTGACGTTCACACAATCGATCTAGAAATAACAGGTTTTTATTTT
data/spec/data/bands.csv ADDED
@@ -0,0 +1 @@
1
+ 1_2200 1,3,4
data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names ADDED
@@ -0,0 +1,544 @@
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14
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25
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96
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97
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98
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99
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100
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101
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102
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103
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108
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110
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111
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112
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113
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114
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116
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118
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120
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121
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122
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128
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129
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130
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131
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132
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133
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134
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135
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136
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137
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138
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139
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140
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141
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142
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143
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144
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145
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148
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150
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151
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152
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153
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154
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155
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156
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157
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158
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159
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160
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161
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162
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163
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164
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165
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166
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171
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180
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182
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183
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184
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185
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186
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187
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188
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189
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190
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191
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192
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193
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194
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195
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196
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197
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198
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199
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200
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201
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202
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203
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204
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205
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206
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207
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208
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209
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210
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212
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213
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214
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215
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216
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217
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218
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219
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220
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221
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222
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223
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224
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225
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226
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227
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228
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229
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230
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231
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232
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233
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234
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250
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252
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254
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255
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256
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276
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410
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411
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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426
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427
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428
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429
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430
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432
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433
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434
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436
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