finishm 0.0.1

Sign up to get free protection for your applications and to get access to all the features.
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
  234. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.sln +78 -0
  235. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.vcproj +445 -0
  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
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
  262. data/ext/src/third-party/zlib-1.2.3/examples/zran.c +404 -0
  263. data/ext/src/third-party/zlib-1.2.3/gzio.c +1026 -0
  264. data/ext/src/third-party/zlib-1.2.3/gzio.o +0 -0
  265. data/ext/src/third-party/zlib-1.2.3/infback.c +623 -0
  266. data/ext/src/third-party/zlib-1.2.3/infback.o +0 -0
  267. data/ext/src/third-party/zlib-1.2.3/inffast.c +318 -0
  268. data/ext/src/third-party/zlib-1.2.3/inffast.h +11 -0
  269. data/ext/src/third-party/zlib-1.2.3/inffast.o +0 -0
  270. data/ext/src/third-party/zlib-1.2.3/inffixed.h +94 -0
  271. data/ext/src/third-party/zlib-1.2.3/inflate.c +1368 -0
  272. data/ext/src/third-party/zlib-1.2.3/inflate.h +115 -0
  273. data/ext/src/third-party/zlib-1.2.3/inflate.o +0 -0
  274. data/ext/src/third-party/zlib-1.2.3/inftrees.c +329 -0
  275. data/ext/src/third-party/zlib-1.2.3/inftrees.h +55 -0
  276. data/ext/src/third-party/zlib-1.2.3/inftrees.o +0 -0
  277. data/ext/src/third-party/zlib-1.2.3/libz.a +0 -0
  278. data/ext/src/third-party/zlib-1.2.3/make_vms.com +461 -0
  279. data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
  280. data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
  281. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
  282. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
  283. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
  284. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
  285. data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
  286. data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
  287. data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
  288. data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
  289. data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
  290. data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
  291. data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
  292. data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
  293. data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
  294. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
  295. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
  296. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
  297. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
  298. data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
  299. data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
  300. data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
  301. data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
  302. data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
  303. data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
  304. data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
  305. data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
  306. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
  307. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
  308. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
  309. data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
  310. data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
  311. data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
  312. data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
  313. data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
  314. data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
  315. data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
  316. data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
  317. data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
  318. data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
  319. data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
  320. data/lib/assembly/a_b_visualiser.rb +169 -0
  321. data/lib/assembly/acyclic_connection_finder.rb +81 -0
  322. data/lib/assembly/all_orfs.rb +615 -0
  323. data/lib/assembly/bad_format_writer.rb +46 -0
  324. data/lib/assembly/bam_probe_read_selector.rb +48 -0
  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
  329. data/lib/assembly/coverage_based_graph_filter.rb +68 -0
  330. data/lib/assembly/depth_first_search.rb +63 -0
  331. data/lib/assembly/dijkstra.rb +216 -0
  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
  341. data/lib/assembly/paired_end_assembler.rb +53 -0
  342. data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
  343. data/lib/assembly/probed_graph.rb +105 -0
  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
  353. data/lib/external/VERSION +1 -0
  354. data/lib/finishm/assemble.rb +224 -0
  355. data/lib/finishm/explore.rb +217 -0
  356. data/lib/finishm/finisher.rb +303 -0
  357. data/lib/finishm/fluff.rb +122 -0
  358. data/lib/finishm/gapfiller.rb +325 -0
  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
  362. data/lib/finishm/primers_check.rb +176 -0
  363. data/lib/finishm/roundup.rb +344 -0
  364. data/lib/finishm/sequence.rb +142 -0
  365. data/lib/finishm/visualise.rb +430 -0
  366. data/lib/finishm/wander.rb +270 -0
  367. data/lib/kmer_abundance_pattern.rb +79 -0
  368. data/lib/kmer_multi_abundance_file.rb +48 -0
  369. data/lib/oligo_designer.rb +88 -0
  370. data/lib/priner.rb +66 -0
  371. data/spec/acyclic_connection_finder_spec.rb +551 -0
  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
  386. data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
  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
  389. data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
  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
  398. data/spec/data/c_probe_node_finder/1/Log +756 -0
  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
  403. data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
  404. data/spec/data/contig_printer/1/contigs.fa +4 -0
  405. data/spec/data/contig_printer/1/seq.fa +2408 -0
  406. data/spec/data/contig_printer/1/seq.fa.svg +153 -0
  407. data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
  408. data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
  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
  414. data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
  415. data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
  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
  422. data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
  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
  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
  434. data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
  435. data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
  436. data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
  437. data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
  438. data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
  439. data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
  440. data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
  441. data/spec/data/gapfilling/2/reference.fa +2 -0
  442. data/spec/data/gapfilling/2/reference_part1.fa +4 -0
  443. data/spec/data/gapfilling/2/reference_part2.fa +4 -0
  444. data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
  445. data/spec/data/gapfilling/2/with_gaps.fa +4 -0
  446. data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
  447. data/spec/data/gapfilling/3/reads.fa.gz +0 -0
  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
  451. data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
  452. data/spec/data/gapfilling/4/reads.fa.gz +0 -0
  453. data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
  454. data/spec/data/gapfilling/5/answer.fna +2 -0
  455. data/spec/data/gapfilling/5/gappy.fna +2 -0
  456. data/spec/data/gapfilling/5/reads.fa +17961 -0
  457. data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
  458. data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
  459. data/spec/data/gapfilling/6/random1.fa +28 -0
  460. data/spec/data/gapfilling/6/random2.fa +28 -0
  461. data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
  462. data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
  463. data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
  464. data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
  465. data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
  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/spec/data/assembly_visualiser/Graph ADDED
@@ -0,0 +1,46 @@
1
+ 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 @@
1
+ >probe0 1 0
2
+ >probe1 2 0
3
+ >probe0 3 0
4
+ >probe1 4 0
5
+ >probe0 5 0
6
+ >probe1 6 0
7
+ >probe0 7 0
8
+ >probe1 8 0
9
+ >probe0 9 0
10
+ >probe1 10 0
11
+ >probe0 11 0
12
+ >probe1 12 0
13
+ >probe0 13 0
14
+ >probe1 14 0
15
+ >probe0 15 0
16
+ >probe1 16 0
17
+ >probe0 17 0
18
+ >probe1 18 0
19
+ >probe0 19 0
20
+ >probe1 20 0
21
+ >probe0 21 0
22
+ >probe1 22 0
23
+ >probe0 23 0
24
+ >probe1 24 0
25
+ >probe0 25 0
26
+ >probe1 26 0
27
+ >probe0 27 0
28
+ >probe1 28 0
29
+ >probe0 29 0
30
+ >probe1 30 0
31
+ >probe0 31 0
32
+ >probe1 32 0
33
+ >probe0 33 0
34
+ >probe1 34 0
35
+ >probe0 35 0
36
+ >probe1 36 0
37
+ >probe0 37 0
38
+ >probe1 38 0
39
+ >probe0 39 0
40
+ >probe1 40 0
41
+ >probe0 41 0
42
+ >probe1 42 0
43
+ >probe0 43 0
44
+ >probe1 44 0
45
+ >probe0 45 0
46
+ >probe1 46 0
47
+ >probe0 47 0
48
+ >probe1 48 0
49
+ >probe0 49 0
50
+ >probe1 50 0
51
+ >probe0 51 0
52
+ >probe1 52 0
53
+ >probe0 53 0
54
+ >probe1 54 0
55
+ >probe0 55 0
56
+ >probe1 56 0
57
+ >probe0 57 0
58
+ >probe1 58 0
59
+ >probe0 59 0
60
+ >probe1 60 0
61
+ >probe0 61 0
62
+ >probe1 62 0
63
+ >probe0 63 0
64
+ >probe1 64 0
65
+ >probe0 65 0
66
+ >probe1 66 0
67
+ >probe0 67 0
68
+ >probe1 68 0
69
+ >probe0 69 0
70
+ >probe1 70 0
71
+ >probe0 71 0
72
+ >probe1 72 0
73
+ >probe0 73 0
74
+ >probe1 74 0
75
+ >probe0 75 0
76
+ >probe1 76 0
77
+ >probe0 77 0
78
+ >probe1 78 0
79
+ >probe0 79 0
80
+ >probe1 80 0
81
+ >probe0 81 0
82
+ >probe1 82 0
83
+ >probe0 83 0
84
+ >probe1 84 0
85
+ >probe0 85 0
86
+ >probe1 86 0
87
+ >probe0 87 0
88
+ >probe1 88 0
89
+ >probe0 89 0
90
+ >probe1 90 0
91
+ >probe0 91 0
92
+ >probe1 92 0
93
+ >probe0 93 0
94
+ >probe1 94 0
95
+ >probe0 95 0
96
+ >probe1 96 0
97
+ >probe0 97 0
98
+ >probe1 98 0
99
+ >probe0 99 0
100
+ >probe1 100 0
101
+ >1_1 101 0
102
+ >1_2 102 0
103
+ >2_1 103 0
104
+ >2_2 104 0
105
+ >3_1 105 0
106
+ >3_2 106 0
107
+ >4_1 107 0
108
+ >4_2 108 0
109
+ >5_1 109 0
110
+ >5_2 110 0
111
+ >6_1 111 0
112
+ >6_2 112 0
113
+ >7_1 113 0
114
+ >7_2 114 0
115
+ >8_1 115 0
116
+ >8_2 116 0
117
+ >9_1 117 0
118
+ >9_2 118 0
119
+ >10_1 119 0
120
+ >10_2 120 0
121
+ >11_1 121 0
122
+ >11_2 122 0
123
+ >12_1 123 0
124
+ >12_2 124 0
125
+ >13_1 125 0
126
+ >13_2 126 0
127
+ >14_1 127 0
128
+ >14_2 128 0
129
+ >15_1 129 0
130
+ >15_2 130 0
131
+ >16_1 131 0
132
+ >16_2 132 0
133
+ >17_1 133 0
134
+ >17_2 134 0
135
+ >18_1 135 0
136
+ >18_2 136 0
137
+ >19_1 137 0
138
+ >19_2 138 0
139
+ >20_1 139 0
140
+ >20_2 140 0
141
+ >21_1 141 0
142
+ >21_2 142 0
143
+ >22_1 143 0
144
+ >22_2 144 0
145
+ >23_1 145 0
146
+ >23_2 146 0
147
+ >24_1 147 0
148
+ >24_2 148 0
149
+ >25_1 149 0
150
+ >25_2 150 0
151
+ >26_1 151 0
152
+ >26_2 152 0
153
+ >27_1 153 0
154
+ >27_2 154 0
155
+ >28_1 155 0
156
+ >28_2 156 0
157
+ >29_1 157 0
158
+ >29_2 158 0
159
+ >30_1 159 0
160
+ >30_2 160 0
161
+ >31_1 161 0
162
+ >31_2 162 0
163
+ >32_1 163 0
164
+ >32_2 164 0
165
+ >33_1 165 0
166
+ >33_2 166 0
167
+ >34_1 167 0
168
+ >34_2 168 0
169
+ >35_1 169 0
170
+ >35_2 170 0
171
+ >36_1 171 0
172
+ >36_2 172 0
173
+ >37_1 173 0
174
+ >37_2 174 0
175
+ >38_1 175 0
176
+ >38_2 176 0
177
+ >39_1 177 0
178
+ >39_2 178 0
179
+ >40_1 179 0
180
+ >40_2 180 0
181
+ >41_1 181 0
182
+ >41_2 182 0
183
+ >42_1 183 0
184
+ >42_2 184 0
185
+ >43_1 185 0
186
+ >43_2 186 0
187
+ >44_1 187 0
188
+ >44_2 188 0
189
+ >45_1 189 0
190
+ >45_2 190 0
191
+ >46_1 191 0
192
+ >46_2 192 0
193
+ >47_1 193 0
194
+ >47_2 194 0
195
+ >48_1 195 0
196
+ >48_2 196 0
197
+ >49_1 197 0
198
+ >49_2 198 0
199
+ >50_1 199 0
200
+ >50_2 200 0
201
+ >51_1 201 0
202
+ >51_2 202 0
203
+ >52_1 203 0
204
+ >52_2 204 0
205
+ >53_1 205 0
206
+ >53_2 206 0
207
+ >54_1 207 0
208
+ >54_2 208 0
209
+ >55_1 209 0
210
+ >55_2 210 0
211
+ >56_1 211 0
212
+ >56_2 212 0
213
+ >57_1 213 0
214
+ >57_2 214 0
215
+ >58_1 215 0
216
+ >58_2 216 0
217
+ >59_1 217 0
218
+ >59_2 218 0
219
+ >60_1 219 0
220
+ >60_2 220 0
221
+ >61_1 221 0
222
+ >61_2 222 0
223
+ >62_1 223 0
224
+ >62_2 224 0
225
+ >63_1 225 0
226
+ >63_2 226 0
227
+ >64_1 227 0
228
+ >64_2 228 0
229
+ >65_1 229 0
230
+ >65_2 230 0
231
+ >66_1 231 0
232
+ >66_2 232 0
233
+ >67_1 233 0
234
+ >67_2 234 0
235
+ >68_1 235 0
236
+ >68_2 236 0
237
+ >69_1 237 0
238
+ >69_2 238 0
239
+ >70_1 239 0
240
+ >70_2 240 0
241
+ >71_1 241 0
242
+ >71_2 242 0
243
+ >72_1 243 0
244
+ >72_2 244 0
245
+ >73_1 245 0
246
+ >73_2 246 0
247
+ >74_1 247 0
248
+ >74_2 248 0
249
+ >75_1 249 0
250
+ >75_2 250 0
251
+ >76_1 251 0
252
+ >76_2 252 0
253
+ >77_1 253 0
254
+ >77_2 254 0
255
+ >78_1 255 0
256
+ >78_2 256 0
257
+ >79_1 257 0
258
+ >79_2 258 0
259
+ >80_1 259 0
260
+ >80_2 260 0
261
+ >81_1 261 0
262
+ >81_2 262 0
263
+ >82_1 263 0
264
+ >82_2 264 0
265
+ >83_1 265 0
266
+ >83_2 266 0
267
+ >84_1 267 0
268
+ >84_2 268 0
269
+ >85_1 269 0
270
+ >85_2 270 0
271
+ >86_1 271 0
272
+ >86_2 272 0
273
+ >87_1 273 0
274
+ >87_2 274 0
275
+ >88_1 275 0
276
+ >88_2 276 0
277
+ >89_1 277 0
278
+ >89_2 278 0
279
+ >90_1 279 0
280
+ >90_2 280 0
281
+ >91_1 281 0
282
+ >91_2 282 0
283
+ >92_1 283 0
284
+ >92_2 284 0
285
+ >93_1 285 0
286
+ >93_2 286 0
287
+ >94_1 287 0
288
+ >94_2 288 0
289
+ >95_1 289 0
290
+ >95_2 290 0
291
+ >96_1 291 0
292
+ >96_2 292 0
293
+ >97_1 293 0
294
+ >97_2 294 0
295
+ >98_1 295 0
296
+ >98_2 296 0
297
+ >99_1 297 0
298
+ >99_2 298 0
299
+ >100_1 299 0
300
+ >100_2 300 0
301
+ >101_1 301 0
302
+ >101_2 302 0
303
+ >102_1 303 0
304
+ >102_2 304 0
305
+ >103_1 305 0
306
+ >103_2 306 0
307
+ >104_1 307 0
308
+ >104_2 308 0
309
+ >105_1 309 0
310
+ >105_2 310 0
311
+ >106_1 311 0
312
+ >106_2 312 0
313
+ >107_1 313 0
314
+ >107_2 314 0
315
+ >108_1 315 0
316
+ >108_2 316 0
317
+ >109_1 317 0
318
+ >109_2 318 0
319
+ >110_1 319 0
320
+ >110_2 320 0
321
+ >111_1 321 0
322
+ >111_2 322 0
323
+ >112_1 323 0
324
+ >112_2 324 0
325
+ >113_1 325 0
326
+ >113_2 326 0
327
+ >114_1 327 0
328
+ >114_2 328 0
329
+ >115_1 329 0
330
+ >115_2 330 0
331
+ >116_1 331 0
332
+ >116_2 332 0
333
+ >117_1 333 0
334
+ >117_2 334 0
335
+ >118_1 335 0
336
+ >118_2 336 0
337
+ >119_1 337 0
338
+ >119_2 338 0
339
+ >120_1 339 0
340
+ >120_2 340 0
341
+ >121_1 341 0
342
+ >121_2 342 0
343
+ >122_1 343 0
344
+ >122_2 344 0
345
+ >123_1 345 0
346
+ >123_2 346 0
347
+ >124_1 347 0
348
+ >124_2 348 0
349
+ >125_1 349 0
350
+ >125_2 350 0
351
+ >126_1 351 0
352
+ >126_2 352 0
353
+ >127_1 353 0
354
+ >127_2 354 0
355
+ >128_1 355 0
356
+ >128_2 356 0
357
+ >129_1 357 0
358
+ >129_2 358 0
359
+ >130_1 359 0
360
+ >130_2 360 0
361
+ >131_1 361 0
362
+ >131_2 362 0
363
+ >132_1 363 0
364
+ >132_2 364 0
365
+ >133_1 365 0
366
+ >133_2 366 0
367
+ >134_1 367 0
368
+ >134_2 368 0
369
+ >135_1 369 0
370
+ >135_2 370 0
371
+ >136_1 371 0
372
+ >136_2 372 0
373
+ >137_1 373 0
374
+ >137_2 374 0
375
+ >138_1 375 0
376
+ >138_2 376 0
377
+ >139_1 377 0
378
+ >139_2 378 0
379
+ >140_1 379 0
380
+ >140_2 380 0
381
+ >141_1 381 0
382
+ >141_2 382 0
383
+ >142_1 383 0
384
+ >142_2 384 0
385
+ >143_1 385 0
386
+ >143_2 386 0
387
+ >144_1 387 0
388
+ >144_2 388 0
389
+ >145_1 389 0
390
+ >145_2 390 0
391
+ >146_1 391 0
392
+ >146_2 392 0
393
+ >147_1 393 0
394
+ >147_2 394 0
395
+ >148_1 395 0
396
+ >148_2 396 0
397
+ >149_1 397 0
398
+ >149_2 398 0
399
+ >150_1 399 0
400
+ >150_2 400 0
401
+ >151_1 401 0
402
+ >151_2 402 0
403
+ >152_1 403 0
404
+ >152_2 404 0
405
+ >153_1 405 0
406
+ >153_2 406 0
407
+ >154_1 407 0
408
+ >154_2 408 0
409
+ >155_1 409 0
410
+ >155_2 410 0
411
+ >156_1 411 0
412
+ >156_2 412 0
413
+ >157_1 413 0
414
+ >157_2 414 0
415
+ >158_1 415 0
416
+ >158_2 416 0
417
+ >159_1 417 0
418
+ >159_2 418 0
419
+ >160_1 419 0
420
+ >160_2 420 0
421
+ >161_1 421 0
422
+ >161_2 422 0
423
+ >162_1 423 0
424
+ >162_2 424 0
425
+ >163_1 425 0
426
+ >163_2 426 0
427
+ >164_1 427 0
428
+ >164_2 428 0
429
+ >165_1 429 0
430
+ >165_2 430 0
431
+ >166_1 431 0
432
+ >166_2 432 0
433
+ >167_1 433 0
434
+ >167_2 434 0
435
+ >168_1 435 0
436
+ >168_2 436 0
437
+ >169_1 437 0
438
+ >169_2 438 0
439
+ >170_1 439 0
440
+ >170_2 440 0
441
+ >171_1 441 0
442
+ >171_2 442 0
443
+ >172_1 443 0
444
+ >172_2 444 0
445
+ >173_1 445 0
446
+ >173_2 446 0
447
+ >174_1 447 0
448
+ >174_2 448 0
449
+ >175_1 449 0
450
+ >175_2 450 0
451
+ >176_1 451 0
452
+ >176_2 452 0
453
+ >177_1 453 0
454
+ >177_2 454 0
455
+ >178_1 455 0
456
+ >178_2 456 0
457
+ >179_1 457 0
458
+ >179_2 458 0
459
+ >180_1 459 0
460
+ >180_2 460 0
461
+ >181_1 461 0
462
+ >181_2 462 0
463
+ >182_1 463 0
464
+ >182_2 464 0
465
+ >183_1 465 0
466
+ >183_2 466 0
467
+ >184_1 467 0
468
+ >184_2 468 0
469
+ >185_1 469 0
470
+ >185_2 470 0
471
+ >186_1 471 0
472
+ >186_2 472 0
473
+ >187_1 473 0
474
+ >187_2 474 0
475
+ >188_1 475 0
476
+ >188_2 476 0
477
+ >189_1 477 0
478
+ >189_2 478 0
479
+ >190_1 479 0
480
+ >190_2 480 0
481
+ >191_1 481 0
482
+ >191_2 482 0
483
+ >192_1 483 0
484
+ >192_2 484 0
485
+ >193_1 485 0
486
+ >193_2 486 0
487
+ >194_1 487 0
488
+ >194_2 488 0
489
+ >195_1 489 0
490
+ >195_2 490 0
491
+ >196_1 491 0
492
+ >196_2 492 0
493
+ >197_1 493 0
494
+ >197_2 494 0
495
+ >198_1 495 0
496
+ >198_2 496 0
497
+ >199_1 497 0
498
+ >199_2 498 0
499
+ >200_1 499 0
500
+ >200_2 500 0
501
+ >201_1 501 0
502
+ >201_2 502 0
503
+ >1_1 503 0
504
+ >1_2 504 0
505
+ >2_1 505 0
506
+ >2_2 506 0
507
+ >3_1 507 0
508
+ >3_2 508 0
509
+ >4_1 509 0
510
+ >4_2 510 0
511
+ >5_1 511 0
512
+ >5_2 512 0
513
+ >6_1 513 0
514
+ >6_2 514 0
515
+ >7_1 515 0
516
+ >7_2 516 0
517
+ >8_1 517 0
518
+ >8_2 518 0
519
+ >9_1 519 0
520
+ >9_2 520 0
521
+ >10_1 521 0
522
+ >10_2 522 0
523
+ >11_1 523 0
524
+ >11_2 524 0
525
+ >12_1 525 0
526
+ >12_2 526 0
527
+ >13_1 527 0
528
+ >13_2 528 0
529
+ >14_1 529 0
530
+ >14_2 530 0
531
+ >15_1 531 0
532
+ >15_2 532 0
533
+ >16_1 533 0
534
+ >16_2 534 0
535
+ >17_1 535 0
536
+ >17_2 536 0
537
+ >18_1 537 0
538
+ >18_2 538 0
539
+ >19_1 539 0
540
+ >19_2 540 0
541
+ >20_1 541 0
542
+ >20_2 542 0
543
+ >21_1 543 0
544
+ >21_2 544 0