finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
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  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
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  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
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  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
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  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
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  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
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  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
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  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
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  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
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  260. data/ext/src/third-party/zlib-1.2.3/examples/zlib_how.html +523 -0
  261. data/ext/src/third-party/zlib-1.2.3/examples/zpipe.c +191 -0
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  392. data/spec/data/assembly_visualiser/start_kmers1 +2 -0
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  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
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  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
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  485. data/spec/data/t/location.txt +3 -0
  486. data/spec/data/t/location.txt.srt +3 -0
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  500. data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
  501. data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -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
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  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
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  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/coverage_based_graph_filter_spec.rb ADDED
@@ -0,0 +1,102 @@
1
+ require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
2
+
3
+ #Bio::Log::CLI.logger('stderr'); Bio::Log::CLI.trace('debug'); log = Bio::Log::LoggerPlus.new('finishm'); Bio::Log::CLI.configure('finishm')
4
+
5
+ describe "coverage based graph filter" do
6
+ it 'should filter nodes by coverage' do
7
+ graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
8
+
9
+ graph.nodes.length.should == 4
10
+ cutoffer = Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter.new
11
+
12
+ deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 0)
13
+ deleted_nodes.length.should == 0
14
+ deleted_arcs.length.should == 0
15
+ graph.nodes.length.should == 4
16
+
17
+ deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 3.5)
18
+ deleted_nodes.length.should == 2
19
+ deleted_arcs.length.should == 4
20
+ graph.nodes.length.should == 2
21
+
22
+ graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
23
+ deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10)
24
+ deleted_nodes.length.should == 4
25
+ deleted_arcs.length.should == 4
26
+ graph.nodes.length.should == 0
27
+ end
28
+
29
+ it 'should respect whitelisted sequences' do
30
+ graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
31
+ graph.nodes.length.should == 4
32
+ cutoffer = Bio::AssemblyGraphAlgorithms::CoverageBasedGraphFilter.new
33
+
34
+ deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10, :whitelisted_sequences => [1])
35
+ deleted_nodes.length.should == 1
36
+ graph.nodes.length.should == 3
37
+
38
+ graph = Bio::Velvet::Graph.parse_from_file File.join(TEST_DATA_DIR, 'velvet_test_trails','Assem','LastGraph')
39
+ deleted_nodes, deleted_arcs = cutoffer.remove_low_coverage_nodes(graph, 10, :whitelisted_sequences => [1,2])
40
+ deleted_nodes.length.should == 0
41
+ deleted_arcs.length.should == 0
42
+ graph.nodes.length.should == 4
43
+ end
44
+
45
+ it 'should filter by connectivity' do
46
+ graph = GraphTesting.emit([
47
+ [1,2],
48
+ [3,4]
49
+ ])
50
+ filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
51
+ graph.nodes.length.should == 4
52
+ filter.remove_unconnected_nodes(graph,[graph.nodes[1]])
53
+ graph.nodes.length.should == 2
54
+ graph.arcs.length.should == 1
55
+
56
+ graph = GraphTesting.emit([
57
+ [1,2],
58
+ [2,3],
59
+ [3,4]
60
+ ])
61
+ filter.remove_unconnected_nodes(graph,[graph.nodes[1]])
62
+ graph.nodes.length.should == 4
63
+ end
64
+
65
+ it 'should filter by leashed connectivity' do
66
+ graph = GraphTesting.emit([
67
+ [1,2],
68
+ [3,4]
69
+ ])
70
+ filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
71
+ graph.nodes.length.should == 4
72
+ filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 5)
73
+ graph.nodes.length.should == 2 #or 1.meh.
74
+ graph.arcs.length.should == 1
75
+ end
76
+
77
+ it 'should filter by leashed connectivity 2 nodes' do
78
+ graph = GraphTesting.emit([
79
+ [1,2],
80
+ [2,3],
81
+ [3,4]
82
+ ])
83
+ graph.nodes.length.should == 4
84
+ filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
85
+ filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 15)
86
+ graph.nodes.length.should == 3#or 2.meh.
87
+
88
+ end
89
+
90
+ it 'should filter by fake leashed connectivity' do
91
+ graph = GraphTesting.emit([
92
+ [1,2],
93
+ [2,3],
94
+ [3,4]
95
+ ])
96
+ graph.nodes.length.should == 4
97
+ filter = Bio::AssemblyGraphAlgorithms::ConnectivityBasedGraphFilter.new
98
+ filter.remove_unconnected_nodes(graph,[graph.nodes[1]], :leash_length => 9999)
99
+ graph.nodes.length.should == 4
100
+
101
+ end
102
+ end
data/spec/data/acyclic_connection_finder/1/probes.fa ADDED
@@ -0,0 +1,5 @@
1
+ >probe_fwd
2
+ GCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCA
3
+ >probe_rev_revcom
4
+ ACTGGAGTCGGCGCGATCGCGGCGGTTAGTAGGCTCTTGAGTACCCATGCTTCCTCAGCTCTATGATGAACCCAGTGCCTGGGCGCCCATT
5
+
data/spec/data/acyclic_connection_finder/1/random1.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_1000
2
+ GGCAGAGCGGTAACCGACAGGCGTAATTGAAGCACCAAGCAAAGCTTAATGGCATGTGAAGCACCCCCGGTTCGTGAACAGAACCTTCGGGCGTTGGTATTCACCTTGGCACCTATACCTAGACACAGACTACGCGTTTTGAACGATTAGTATCCGCGACTTTCAGTGCCTTCTACAGGACGCAAGCTGACAGGCATACTCTACCCAAATTATGCGCGATCCCCTATCTGTACGGAGACGGGTGACCTCGTAACCTGCTATGAGAATCATCAAGAATCTGTCGGGTTAGCGACCACAACGGCCGATAGTGTTGCGATATCGGCCTAACCACGCGACTAATCGCCTACCACGACCGGTCACGACGAGACCTGCAGGTCGACATGAAGACGATGTTGTAAGGCGTAAAACTCCGACTGTGGCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCAAATGGGCGCCCAGGCACTGGGTTCATCATAGAGCTGAGGAAGCATGGGTACTCAAGAGCCTACTAACCGCCGCGATCGCGCCGACTCCAGTGCCTGTAGTTCTTCATAATAAAATAACACGTCACTTGCTCCATGTACGCGCTACGTTTGACGTTGCTAGACGGATACCAACGCCCCGGGCGATAAATGTTCCGTGGTCGCTTCTGGTAGGATGCAATTGACGATTTTCCACATGGGCTCGTATGTCCCACCGCCCTCTGGTCGAACATGCGAGCGTACACTGTCATATCCCCACTAGCGGAGCAACCGACGGACCAAACGTCTGTCGTCTGGATATGTAAGCTAACATAACTCCAATCTGATTGGCGTGCTATATATTCGAGCGAAGCCTTTTGTGTTCTCACTGGAAAGAGTGGCATTTCTGCCGCTGGAAGATTAAGATTTTAGCCTGAGGTGGCACAGTCTCTATGATTGAGGGGAAATTACGGTGTGTCC
data/spec/data/acyclic_connection_finder/1/random2.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_1000
2
+ GGCAGAGCGGTAACCGACAGGCGTAATTGAAGCACCAAGCAAAGCTTAATGGCATGTGAAGCACCCCCGGTTCGTGAACAGAACCTTCGGGCGTTGGTATTCACCTTGGCACCTATACCTAGACACAGACTACGCGTTTTGAACGATTAGTATCCGCGACTTTCAGTGCCTTCTACAGGACGCAAGCTGACAGGCATACTCTACCCAAATTATGCGCGATCCCCTATCTGTACGGAGACGGGTGACCTCGTAACCTGCTATGAGAATCATCAAGAATCTGTCGGGTTAGCGACCACAACGGCCGATAGTGTTGCGATATCGGCCTAACCACGCGACTAATCGCCTACCACGACCGGTCACGACGAGACCTGCAGGTCGACATGAAGACGATGTTGTAAGGCGTAAAACTCCGACTGTGGCATACGTATGCATGTTGCGCTGTTTGACCCGAAATGGTGCCCGGAGCAAGGCTTAGCATCCAATGCAGATAGCCCAGCTCTACTCATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAATGGGCGCCCAGGCACTGGGTTCATCATAGAGCTGAGGAAGCATGGGTACTCAAGAGCCTACTAACCGCCGCGATCGCGCCGACTCCAGTGCCTGTAGTTCTTCATAATAAAATAACACGTCACTTGCTCCATGTACGCGCTACGTTTGACGTTGCTAGACGGATACCAACGCCCCGGGCGATAAATGTTCCGTGGTCGCTTCTGGTAGGATGCAATTGACGATTTTCCACATGGGCTCGTATGTCCCACCGCCCTCTGGTCGAACATGCGAGCGTACACTGTCATATCCCCACTAGCGGAGCAACCGACGGACCAAACGTCTGTCGTCTGGATATGTAAGCTAACATAACTCCAATCTGATTGGCGTGCTATATATTCGAGCGAAGCCTTTTGTGTTCTCACTGGAAAGAGTGGCATTTCTGCCGCTGGAAGATTAAGATTTTAGCCTGAGGTGGCACAGTCTCTATGATTGAGGGGAAATTACGGTGTGTCC
data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa ADDED
@@ -0,0 +1,39 @@
1
+ >random_sequence_length_3000
2
+ TTGTAATGAGGGATCTCATAGGGCTCTTGGTAGTCACGATTCCCTCGGTTATAGTTGCAGGAGACGGGGGTTAACCGTAA
3
+ ACAAGACTCGCTTATCGCTACGACCTGCACAACTAAGCTTCGGCTGCAGCCCACCGACTGTAGAATCCGGCCCAGTCTGC
4
+ CTATGTATGGCAGCATCTTATCGGTATGACACGCCAACAATCTCCTGTACAAGAGATTATCAAGCAATCAATGAAGCATC
5
+ CACTCTTGTCTGTCGGGATGTATATGCGCGACCGTGTTAGCCTTGCGTGGTGGCATGAAACCATCGAATAGCACCACCTA
6
+ GTGCGGTGGACCTGTCCGCTCGACTACCGGCCGGTTAAGACAGCAAAGTGCACCTGACGGAATTATTACGCTGTCTACAC
7
+ GAACAAGTCTACCCCCATAATTATTGCTGGTATAACCGCTCGCTATAATTCGCGTCTGCTTTAAGGTACGGTCGGTCAAA
8
+ TGGGCGTTATCTTGATTTTTCCATATCCATCTCTCAGATCGAGCCGATACGAATGAATAATTATGCCGACCAGTTCATTA
9
+ ATTGAACCTTCCCAGAGCTTCCTTCAAAATCATTCTGAGACGGATGTTGCGCCCATGACTCCGGGGGGTTGGGTACTTGG
10
+ ATGATTCCCACGACCCCAGAGAGTCCTGACATTACGTCTCGGGTTCACAGCGAGCCAAATGGGGGCAGTCTGGTCCCGTG
11
+ ACGACCACCGATTGATTGAGACAATGAGCGTCACAACTACCAGTCAACTCGTCTGGCATAGTTACTCATCGCCACACGAT
12
+ GCTTGTCTGTTGAGTCTTGGGCCATAAATTGCTCGAGGGGGCGCTCTGCCAAAGAGAGCATGCTACTGCACGTATCTCTT
13
+ AACTATCGTACCCGATACTGATGTTGCGTCGGTTCGTGCAGACTATTACCGGAGCGAGCTGCCATACAGTGCGGTGATCT
14
+ GAAGGAGCGCCCACGCTGCTCAACCCCACCGCTATCTTTCAAGCATGCCGTGACAAATGCGAAGGCCGGACACTGCATTG
15
+ GGATAATATTTCGTACTGGCGACATATGACTACACAGCTAAAGGGGGCGACAGTTGTGATATATACCCAAATGATCTGTT
16
+ TCCCTCTTACCTTCATTACGGCCTTATCGCAGTGCTAATCCTCTGGTCTTTTACGTAAGTATGCGTAATCGGCGTTATCC
17
+ CGGCAGAACTCGATCCGGGCTGAGAGAATGATTCCAGGTACAGGATTAGAAGCCATTTGGGAAGAGAAGCGCAGGGCTAG
18
+ CACGATAATGATGTAAGAAAGAACCACTAACGTTGTATTTGACCACTGTCAACGTATAGGCAGCGAGGATCACTGTTTCA
19
+ GACCGATTTACATTCGTTAGCCGAACCGAATGCTCAGGTCGGAACTGGGTCCAGATGAACCACAATTCCGCGCTGGTAAG
20
+ GAAGTCCGTTCTTCATCCAGAGGTCCACGCCAAAGCAGTCATTATCGGGTGGGTAGTCTCCATCGTAAGCTAAGTTAAAG
21
+ ATGCAAGGTGCTTCAAGTACCTGCTCCCAGGCTAGTTTACAACTCTGGGGATAGTGTTTTACCGAGGAGGCATGCCCTAG
22
+ GTTGTGGACCATGATCGGCCCCCCCTCCCTACTGCGTTACTTTACGGCGAATGGGACACCGTAGTTTTTTGCTATAGCTA
23
+ ATCCGCAGTTCTCCCGTACGGTATACACGCGATAGCTCCGTATTAAGATCCGTGCGTTGCCACAGTACCCCGCAGGCGAC
24
+ CTACCATCCCATACCGTCCTTCGAAGATACGTAAGATCGAGCGTGAGTTTTTTTTAATGTTGCTTACTAACTTAACACGT
25
+ CGGAGGGATGCTGTGTGACGGGGGGCACAATAAATCAACCTCCGAAGCAAGACGCACCATTACCAGTGTCGCCGGGATGC
26
+ ACGTTACAACCTTTTCTATTTCTACAGACTGTGGGTATACATCCGTAAATTAATTAATCAGTATTCTGATTTAGGAAACG
27
+ TGGATCCCCTTCAAAAGTGGCAGGTATGATGGGTCCTATGCGCGTTATAAATGTAAGTTCTATGTTGCCATTAAAAGCTC
28
+ GCCAGAGACACGATACGGCGAGGACGGTTAGATGGCGTGCACCTTATGGCATCTGCGCGCAAACGGTAGAGGCAAGGAGT
29
+ TCCTATATCCCAAAAACTATTCGGGTTTTGCCTATTGCTGAGACTTACATCTCGGCTGTGATCCTCAGCTGTCAGAGGAG
30
+ TAGTGTGGCGCATTTCGTCACCTGCCCGCTGGTTAATAGAGACTCGGTCAGGTAGGAATGTTATGTTCCGGCAAATCACC
31
+ CACAAATTATACGGTGCTTAATTACTTTTTGTCGAAGGCCATCTTTCATGGGCCTGCGTTACTCAAATAAATGCGACTAG
32
+ GAGCCTCTGTACCCCGGGGGCTATCGTCAACCAACTACTGATTCAATCGTACGGCAACAGCCTTAAGAGGGTCAGGCCAA
33
+ TTCCGGGGCCCCTAGAAGTTGAACAAATGCCGGCATGTGATAATGTTTAATGTAGTCGCCACACCAAGAACGATTTAATT
34
+ GGACGGCCGAAATAAGAAGTTCAACATGTTTGCCGGTGGCGCAGGAGTCTTAGTTAGAGTTAGCGAGTGGGCTCGGTAAT
35
+ AGGTGTACGTCCCTGTAGCTAATTTCGAGACTAACTTCCTATTCCCTGTCGCCTTGATTGATGTGGTCTCAGCAACGAGT
36
+ CTTAGCTAGGGTTACCGTTTGTTGGTCTGGAATCAGGTAGGAGACGTATACAAACGGATAGTTTCACCGGAGCGCTCTCC
37
+ TGGAGCTGCTCGCGCGCACTAACTGAAATGGCGTTTGGACTGCGATGGAAGAGGAGCCGCGCTTAGGGCCTGCTCCGAAA
38
+ TGCTTCAGATCATCCACGTTCTACGGCGGACGCCGTCCTAACTTAGGTCAGGGAGTCCCGTACCGATACTACTCTAAAGC
39
+ CGGGAGTGAAGTCTAGGTACTTAAGAGCTCACGCGGGTCA
data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa ADDED
@@ -0,0 +1,39 @@
1
+ >random_sequence_length_3000
2
+ TTGTAATGAGGGATCTCATAGGGCTCTTGGTAGTCACGATTCCCTCGGTTATAGTTGCAGGAGACGGGGGTTAACCGTAA
3
+ ACAAGACTCGCTTATCGCTACGACCTGCACAACTAAGCTTCGGCTGCAGCCCACCGACTGTAGAATCCGGCCCAGTCTGC
4
+ CTATGTATGGCAGCATCTTATCGGTATGACACGCCAACAATCTCCTGTACAAGAGATTATCAAGCAATCAATGAAGCATC
5
+ CACTCTTGTCTGTCGGGATGTATATGCGCGACCGTGTTAGCCTTGCGTGGTGGCATGAAACCATCGAATAGCACCACCTA
6
+ GTGCGGTGGACCTGTCCGCTCGACTACCGGCCGGTTAAGACAGCAAAGTGCACCTGACGGAATTATTACGCTGTCTACAC
7
+ GAACAAGTCTACCCCCATAATTATTGCTGGTATAACCGCTCGCTATAATTCGCGTCTGCTTTAAGGTACGGTCGGTCAAA
8
+ TGGGCGTTATCTTGATTTTTCCATATCCATCTCTCAGATCGAGCCGATACGAATGAATAATTATGCCGACCAGTTCATTA
9
+ ATTGAACCTTCCCAGAGCTTCCTTCAAAATCATTCTGAGACGGATGTTGCGCCCATGACTCCGGGGGGTTGGGTACTTGG
10
+ ATGATTCCCACGACCCCAGAGAGTCCTGACATTACGTCTCGGGTTCACAGCGAGCCAAATGGGGGCAGTCTGGTCCCGTG
11
+ ACGACCACCGATTGATTGAGACAATGAGCGTCACAACTACCAGTCAACTCGTCTGGCATAGTTACTCATCGCCACACGAT
12
+ GCTTGTCTGTTGAGTCTTGGGCCATAAATTGCTCGAGGGGGCGCTCTGCCAAAGAGAGCATGCTACTGCACGTATCTCTT
13
+ AACTATCGTACCCGATACTGATGTTGCGTCGGTTCGTGCAGACTATTACCGGAGCGAGCTGCCATACAGTGCGGTGATCT
14
+ GAAGGAGCGCCCACGCTGCTCAACCCCACCGCTATCTTTCAAGCATGCCGTGACAAATGCGAAGGCCGGACACTGCATTG
15
+ GGATAATATTTCGTACTGGCGACATATGACTACACAGCTAAAGGGGGCGACAGTTGTGATATATACCCAAATGATCTGTT
16
+ TCCCTCTTACCTTCATTACGGCCTTATCGCAGTGCTAATCCTCTGGTCTTTTACGTAAGTATGCGTAATCGGCGTTATCC
17
+ CGGCAGAACTCGATCCGGGCTGAGAGAATGATTCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCAGGTACAGGATTAGAAGCCATTTGGGAAGAGAAGCGCAGGGCTAG
18
+ CACGATAATGATGTAAGAAAGAACCACTAACGTTGTATTTGACCACTGTCAACGTATAGGCAGCGAGGATCACTGTTTCA
19
+ GACCGATTTACATTCGTTAGCCGAACCGAATGCTCAGGTCGGAACTGGGTCCAGATGAACCACAATTCCGCGCTGGTAAG
20
+ GAAGTCCGTTCTTCATCCAGAGGTCCACGCCAAAGCAGTCATTATCGGGTGGGTAGTCTCCATCGTAAGCTAAGTTAAAG
21
+ ATGCAAGGTGCTTCAAGTACCTGCTCCCAGGCTAGTTTACAACTCTGGGGATAGTGTTTTACCGAGGAGGCATGCCCTAG
22
+ GTTGTGGACCATGATCGGCCCCCCCTCCCTACTGCGTTACTTTACGGCGAATGGGACACCGTAGTTTTTTGCTATAGCTA
23
+ ATCCGCAGTTCTCCCGTACGGTATACACGCGATAGCTCCGTATTAAGATCCGTGCGTTGCCACAGTACCCCGCAGGCGAC
24
+ CTACCATCCCATACCGTCCTTCGAAGATACGTAAGATCGAGCGTGAGTTTTTTTTAATGTTGCTTACTAACTTAACACGT
25
+ CGGAGGGATGCTGTGTGACGGGGGGCACAATAAATCAACCTCCGAAGCAAGACGCACCATTACCAGTGTCGCCGGGATGC
26
+ ACGTTACAACCTTTTCTATTTCTACAGACTGTGGGTATACATCCGTAAATTAATTAATCAGTATTCTGATTTAGGAAACG
27
+ TGGATCCCCTTCAAAAGTGGCAGGTATGATGGGTCCTATGCGCGTTATAAATGTAAGTTCTATGTTGCCATTAAAAGCTC
28
+ GCCAGAGACACGATACGGCGAGGACGGTTAGATGGCGTGCACCTTATGGCATCTGCGCGCAAACGGTAGAGGCAAGGAGT
29
+ TCCTATATCCCAAAAACTATTCGGGTTTTGCCTATTGCTGAGACTTACATCTCGGCTGTGATCCTCAGCTGTCAGAGGAG
30
+ TAGTGTGGCGCATTTCGTCACCTGCCCGCTGGTTAATAGAGACTCGGTCAGGTAGGAATGTTATGTTCCGGCAAATCACC
31
+ CACAAATTATACGGTGCTTAATTACTTTTTGTCGAAGGCCATCTTTCATGGGCCTGCGTTACTCAAATAAATGCGACTAG
32
+ GAGCCTCTGTACCCCGGGGGCTATCGTCAACCAACTACTGATTCAATCGTACGGCAACAGCCTTAAGAGGGTCAGGCCAA
33
+ TTCCGGGGCCCCTAGAAGTTGAACAAATGCCGGCATGTGATAATGTTTAATGTAGTCGCCACACCAAGAACGATTTAATT
34
+ GGACGGCCGAAATAAGAAGTTCAACATGTTTGCCGGTGGCGCAGGAGTCTTAGTTAGAGTTAGCGAGTGGGCTCGGTAAT
35
+ AGGTGTACGTCCCTGTAGCTAATTTCGAGACTAACTTCCTATTCCCTGTCGCCTTGATTGATGTGGTCTCAGCAACGAGT
36
+ CTTAGCTAGGGTTACCGTTTGTTGGTCTGGAATCAGGTAGGAGACGTATACAAACGGATAGTTTCACCGGAGCGCTCTCC
37
+ TGGAGCTGCTCGCGCGCACTAACTGAAATGGCGTTTGGACTGCGATGGAAGAGGAGCCGCGCTTAGGGCCTGCTCCGAAA
38
+ TGCTTCAGATCATCCACGTTCTACGGCGGACGCCGTCCTAACTTAGGTCAGGGAGTCCCGTACCGATACTACTCTAAAGC
39
+ CGGGAGTGAAGTCTAGGTACTTAAGAGCTCACGCGGGTCA
data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 ADDED
@@ -0,0 +1,220 @@
1
+ TTTCGGATAGGCTCTAAGAATGAAGATAATA
2
+ AAATCTGATTCAGGCGACGGATGCCTAGATT
3
+ GGATAACGTTCAGAGCTTCTGGACTTTTCGG
4
+ TCGTCCTGATTGTCCTGCATTCAGTGCCGGT
5
+ TAATAAAATCTGATTCAGGCGACGGATGCCT
6
+ ACCATCCGCCCTGGTGTGATCCCCTACGCTA
7
+ CAAGAAGCCCCGGGAGGGATTTGAACCCTCG
8
+ TTTGAACCCTCGACCTCGTCCTGATTGTCCT
9
+ ACGTTCAGAGCTTCTGGACTTTTCGGATAGG
10
+ ACCCTCGACCTCGTCCTGATTGTCCTGCATT
11
+ AGAGATACTTGACCATCCGCCCTGGTGTGAT
12
+ TTACACTTCGCATGTGCATGGATAACGTTCA
13
+ ATAAAATCTGATTCAGGCGACGGATGCCTAG
14
+ CTTCGCATGTGCATGGATAACGTTCAGAGCT
15
+ GATTCAGGCGACGGATGCCTAGATTAGCATT
16
+ TCTGGACTTTTCGGATAGGCTCTAAGAATGA
17
+ TTTTCGGATAGGCTCTAAGAATGAAGATAAT
18
+ CAGAGCTTCTGGACTTTTCGGATAGGCTCTA
19
+ ATGAAGATAATAAAATCTGATTCAGGCGACG
20
+ ATAGGCTCTAAGAATGAAGATAATAAAATCT
21
+ GAGATACTTGACCATCCGCCCTGGTGTGATC
22
+ AGAAGCCCCGGGAGGGATTTGAACCCTCGAC
23
+ CGGATGCCTAGATTAGCATTAGAGATACTTG
24
+ ACTTTTCGGATAGGCTCTAAGAATGAAGATA
25
+ GCATTAGAGATACTTGACCATCCGCCCTGGT
26
+ GCTAACTTGGCTAATAAATTTCAAGAAGCCC
27
+ TTCGGATAGGCTCTAAGAATGAAGATAATAA
28
+ CTGGTGTGATCCCCTACGCTAACTTGGCTAA
29
+ AGAGCTTCTGGACTTTTCGGATAGGCTCTAA
30
+ TAGGCTCTAAGAATGAAGATAATAAAATCTG
31
+ CATGTGCATGGATAACGTTCAGAGCTTCTGG
32
+ GCTAATAAATTTCAAGAAGCCCCGGGAGGGA
33
+ ATCCCCTACGCTAACTTGGCTAATAAATTTC
34
+ CGCCCTGGTGTGATCCCCTACGCTAACTTGG
35
+ CCCTACGCTAACTTGGCTAATAAATTTCAAG
36
+ AACTTGGCTAATAAATTTCAAGAAGCCCCGG
37
+ CCTCGTCCTGATTGTCCTGCATTCAGTGCCG
38
+ TGAAGATAATAAAATCTGATTCAGGCGACGG
39
+ AAGCCCCGGGAGGGATTTGAACCCTCGACCT
40
+ CTGGACTTTTCGGATAGGCTCTAAGAATGAA
41
+ ACTTGACCATCCGCCCTGGTGTGATCCCCTA
42
+ GATGCCTAGATTAGCATTAGAGATACTTGAC
43
+ ATCTGATTCAGGCGACGGATGCCTAGATTAG
44
+ TAAATTTCAAGAAGCCCCGGGAGGGATTTGA
45
+ GTTCAGAGCTTCTGGACTTTTCGGATAGGCT
46
+ TCCTGATTGTCCTGCATTCAGTGCCGGTTAC
47
+ TCTGATTCAGGCGACGGATGCCTAGATTAGC
48
+ CTTGGCTAATAAATTTCAAGAAGCCCCGGGA
49
+ GGCTAATAAATTTCAAGAAGCCCCGGGAGGG
50
+ CCTACGCTAACTTGGCTAATAAATTTCAAGA
51
+ AAGAAGCCCCGGGAGGGATTTGAACCCTCGA
52
+ CTTGACCATCCGCCCTGGTGTGATCCCCTAC
53
+ GTCCTGATTGTCCTGCATTCAGTGCCGGTTA
54
+ GATAACGTTCAGAGCTTCTGGACTTTTCGGA
55
+ GGATGCCTAGATTAGCATTAGAGATACTTGA
56
+ ATAACGTTCAGAGCTTCTGGACTTTTCGGAT
57
+ ATGTGCATGGATAACGTTCAGAGCTTCTGGA
58
+ TTTCAAGAAGCCCCGGGAGGGATTTGAACCC
59
+ CATTAGAGATACTTGACCATCCGCCCTGGTG
60
+ TTAGCATTAGAGATACTTGACCATCCGCCCT
61
+ ATTGTCCTGCATTCAGTGCCGGTTACCAAGG
62
+ CTCGACCTCGTCCTGATTGTCCTGCATTCAG
63
+ CCCTGGTGTGATCCCCTACGCTAACTTGGCT
64
+ GATTTGAACCCTCGACCTCGTCCTGATTGTC
65
+ AGGCTCTAAGAATGAAGATAATAAAATCTGA
66
+ TTGACCATCCGCCCTGGTGTGATCCCCTACG
67
+ CTAACTTGGCTAATAAATTTCAAGAAGCCCC
68
+ ACACTTCGCATGTGCATGGATAACGTTCAGA
69
+ CCTCGACCTCGTCCTGATTGTCCTGCATTCA
70
+ TACGCTAACTTGGCTAATAAATTTCAAGAAG
71
+ CTGATTCAGGCGACGGATGCCTAGATTAGCA
72
+ AGGCGACGGATGCCTAGATTAGCATTAGAGA
73
+ ACGCTAACTTGGCTAATAAATTTCAAGAAGC
74
+ GAAGATAATAAAATCTGATTCAGGCGACGGA
75
+ TCAAGAAGCCCCGGGAGGGATTTGAACCCTC
76
+ GACGGATGCCTAGATTAGCATTAGAGATACT
77
+ GGACTTTTCGGATAGGCTCTAAGAATGAAGA
78
+ CCGGGAGGGATTTGAACCCTCGACCTCGTCC
79
+ TCTAAGAATGAAGATAATAAAATCTGATTCA
80
+ TGCCTAGATTAGCATTAGAGATACTTGACCA
81
+ GGTGTGATCCCCTACGCTAACTTGGCTAATA
82
+ ATCCGCCCTGGTGTGATCCCCTACGCTAACT
83
+ TAACTTGGCTAATAAATTTCAAGAAGCCCCG
84
+ CGACGGATGCCTAGATTAGCATTAGAGATAC
85
+ TTCTGGACTTTTCGGATAGGCTCTAAGAATG
86
+ AGCCCCGGGAGGGATTTGAACCCTCGACCTC
87
+ CCTGCATTCAGTGCCGGTTACCAAGGACGCG
88
+ AGCATTAGAGATACTTGACCATCCGCCCTGG
89
+ AATTTCAAGAAGCCCCGGGAGGGATTTGAAC
90
+ GGATAGGCTCTAAGAATGAAGATAATAAAAT
91
+ GACTTTTCGGATAGGCTCTAAGAATGAAGAT
92
+ GATCCCCTACGCTAACTTGGCTAATAAATTT
93
+ GTGATCCCCTACGCTAACTTGGCTAATAAAT
94
+ CGCTAACTTGGCTAATAAATTTCAAGAAGCC
95
+ GAATGAAGATAATAAAATCTGATTCAGGCGA
96
+ GATAGGCTCTAAGAATGAAGATAATAAAATC
97
+ CTACGCTAACTTGGCTAATAAATTTCAAGAA
98
+ CCCTCGACCTCGTCCTGATTGTCCTGCATTC
99
+ CACTTCGCATGTGCATGGATAACGTTCAGAG
100
+ TTCAGGCGACGGATGCCTAGATTAGCATTAG
101
+ GGAGGGATTTGAACCCTCGACCTCGTCCTGA
102
+ GGGAGGGATTTGAACCCTCGACCTCGTCCTG
103
+ TCAGGCGACGGATGCCTAGATTAGCATTAGA
104
+ TAAGAATGAAGATAATAAAATCTGATTCAGG
105
+ GACCTCGTCCTGATTGTCCTGCATTCAGTGC
106
+ TACTTGACCATCCGCCCTGGTGTGATCCCCT
107
+ TCGACCTCGTCCTGATTGTCCTGCATTCAGT
108
+ ATTAGCATTAGAGATACTTGACCATCCGCCC
109
+ GATACTTGACCATCCGCCCTGGTGTGATCCC
110
+ TGTCCTGCATTCAGTGCCGGTTACCAAGGAC
111
+ GTCCTGCATTCAGTGCCGGTTACCAAGGACG
112
+ GCGACGGATGCCTAGATTAGCATTAGAGATA
113
+ GCCCTGGTGTGATCCCCTACGCTAACTTGGC
114
+ TAATAAATTTCAAGAAGCCCCGGGAGGGATT
115
+ ACGGATGCCTAGATTAGCATTAGAGATACTT
116
+ TGATTCAGGCGACGGATGCCTAGATTAGCAT
117
+ CCTGGTGTGATCCCCTACGCTAACTTGGCTA
118
+ CTTTTCGGATAGGCTCTAAGAATGAAGATAA
119
+ CCCGGGAGGGATTTGAACCCTCGACCTCGTC
120
+ AGATAATAAAATCTGATTCAGGCGACGGATG
121
+ CATCCGCCCTGGTGTGATCCCCTACGCTAAC
122
+ ATTCAGGCGACGGATGCCTAGATTAGCATTA
123
+ TCCCCTACGCTAACTTGGCTAATAAATTTCA
124
+ GGCTCTAAGAATGAAGATAATAAAATCTGAT
125
+ AAGAATGAAGATAATAAAATCTGATTCAGGC
126
+ CGACCTCGTCCTGATTGTCCTGCATTCAGTG
127
+ AAAATCTGATTCAGGCGACGGATGCCTAGAT
128
+ CGGGAGGGATTTGAACCCTCGACCTCGTCCT
129
+ CTCGTCCTGATTGTCCTGCATTCAGTGCCGG
130
+ ATTTCAAGAAGCCCCGGGAGGGATTTGAACC
131
+ ATTAGAGATACTTGACCATCCGCCCTGGTGT
132
+ CTCTAAGAATGAAGATAATAAAATCTGATTC
133
+ TGAACCCTCGACCTCGTCCTGATTGTCCTGC
134
+ GATTGTCCTGCATTCAGTGCCGGTTACCAAG
135
+ ACCTCGTCCTGATTGTCCTGCATTCAGTGCC
136
+ AATCTGATTCAGGCGACGGATGCCTAGATTA
137
+ CGGATAGGCTCTAAGAATGAAGATAATAAAA
138
+ GCTTCTGGACTTTTCGGATAGGCTCTAAGAA
139
+ AAGATAATAAAATCTGATTCAGGCGACGGAT
140
+ TAGCATTAGAGATACTTGACCATCCGCCCTG
141
+ GACCATCCGCCCTGGTGTGATCCCCTACGCT
142
+ AATAAAATCTGATTCAGGCGACGGATGCCTA
143
+ GTGCATGGATAACGTTCAGAGCTTCTGGACT
144
+ ACTTCGCATGTGCATGGATAACGTTCAGAGC
145
+ GCATGTGCATGGATAACGTTCAGAGCTTCTG
146
+ GAGGGATTTGAACCCTCGACCTCGTCCTGAT
147
+ TCCGCCCTGGTGTGATCCCCTACGCTAACTT
148
+ TTAGAGATACTTGACCATCCGCCCTGGTGTG
149
+ TGATTGTCCTGCATTCAGTGCCGGTTACCAA
150
+ GATTAGCATTAGAGATACTTGACCATCCGCC
151
+ CGTCCTGATTGTCCTGCATTCAGTGCCGGTT
152
+ CTGATTGTCCTGCATTCAGTGCCGGTTACCA
153
+ GCCTAGATTAGCATTAGAGATACTTGACCAT
154
+ AACGTTCAGAGCTTCTGGACTTTTCGGATAG
155
+ GCTCTAAGAATGAAGATAATAAAATCTGATT
156
+ GCCCCGGGAGGGATTTGAACCCTCGACCTCG
157
+ TGGATAACGTTCAGAGCTTCTGGACTTTTCG
158
+ CCATCCGCCCTGGTGTGATCCCCTACGCTAA
159
+ TAAAATCTGATTCAGGCGACGGATGCCTAGA
160
+ CCCCTACGCTAACTTGGCTAATAAATTTCAA
161
+ CTGCATTCAGTGCCGGTTACCAAGGACGCGC
162
+ GAACCCTCGACCTCGTCCTGATTGTCCTGCA
163
+ TTGAACCCTCGACCTCGTCCTGATTGTCCTG
164
+ CTAATAAATTTCAAGAAGCCCCGGGAGGGAT
165
+ GCATGGATAACGTTCAGAGCTTCTGGACTTT
166
+ AGCTTCTGGACTTTTCGGATAGGCTCTAAGA
167
+ AGATTAGCATTAGAGATACTTGACCATCCGC
168
+ TGACCATCCGCCCTGGTGTGATCCCCTACGC
169
+ TACACTTCGCATGTGCATGGATAACGTTCAG
170
+ TAGAGATACTTGACCATCCGCCCTGGTGTGA
171
+ GTGTGATCCCCTACGCTAACTTGGCTAATAA
172
+ TGGTGTGATCCCCTACGCTAACTTGGCTAAT
173
+ ACTTGGCTAATAAATTTCAAGAAGCCCCGGG
174
+ TGGACTTTTCGGATAGGCTCTAAGAATGAAG
175
+ TAGATTAGCATTAGAGATACTTGACCATCCG
176
+ AACCCTCGACCTCGTCCTGATTGTCCTGCAT
177
+ CCCCGGGAGGGATTTGAACCCTCGACCTCGT
178
+ AAATTTCAAGAAGCCCCGGGAGGGATTTGAA
179
+ TGTGATCCCCTACGCTAACTTGGCTAATAAA
180
+ TCGCATGTGCATGGATAACGTTCAGAGCTTC
181
+ GAGCTTCTGGACTTTTCGGATAGGCTCTAAG
182
+ AGGGATTTGAACCCTCGACCTCGTCCTGATT
183
+ ATGCCTAGATTAGCATTAGAGATACTTGACC
184
+ AGAATGAAGATAATAAAATCTGATTCAGGCG
185
+ CGTTCAGAGCTTCTGGACTTTTCGGATAGGC
186
+ TAACGTTCAGAGCTTCTGGACTTTTCGGATA
187
+ TGGCTAATAAATTTCAAGAAGCCCCGGGAGG
188
+ GATAATAAAATCTGATTCAGGCGACGGATGC
189
+ TGTGCATGGATAACGTTCAGAGCTTCTGGAC
190
+ CAGGCGACGGATGCCTAGATTAGCATTAGAG
191
+ TTGGCTAATAAATTTCAAGAAGCCCCGGGAG
192
+ GGGATTTGAACCCTCGACCTCGTCCTGATTG
193
+ CGCATGTGCATGGATAACGTTCAGAGCTTCT
194
+ TGATCCCCTACGCTAACTTGGCTAATAAATT
195
+ CTTCTGGACTTTTCGGATAGGCTCTAAGAAT
196
+ TGCATGGATAACGTTCAGAGCTTCTGGACTT
197
+ CTAAGAATGAAGATAATAAAATCTGATTCAG
198
+ AGATACTTGACCATCCGCCCTGGTGTGATCC
199
+ ATGGATAACGTTCAGAGCTTCTGGACTTTTC
200
+ TCGGATAGGCTCTAAGAATGAAGATAATAAA
201
+ CCGCCCTGGTGTGATCCCCTACGCTAACTTG
202
+ CCTGATTGTCCTGCATTCAGTGCCGGTTACC
203
+ ATTTGAACCCTCGACCTCGTCCTGATTGTCC
204
+ TTGTCCTGCATTCAGTGCCGGTTACCAAGGA
205
+ ATAAATTTCAAGAAGCCCCGGGAGGGATTTG
206
+ AATGAAGATAATAAAATCTGATTCAGGCGAC
207
+ TTCAGAGCTTCTGGACTTTTCGGATAGGCTC
208
+ GGATTTGAACCCTCGACCTCGTCCTGATTGT
209
+ CTAGATTAGCATTAGAGATACTTGACCATCC
210
+ ATACTTGACCATCCGCCCTGGTGTGATCCCC
211
+ GAAGCCCCGGGAGGGATTTGAACCCTCGACC
212
+ TCAGAGCTTCTGGACTTTTCGGATAGGCTCT
213
+ AATAAATTTCAAGAAGCCCCGGGAGGGATTT
214
+ ATAATAAAATCTGATTCAGGCGACGGATGCC
215
+ CCTAGATTAGCATTAGAGATACTTGACCATC
216
+ TTCGCATGTGCATGGATAACGTTCAGAGCTT
217
+ GGCGACGGATGCCTAGATTAGCATTAGAGAT
218
+ CATGGATAACGTTCAGAGCTTCTGGACTTTT
219
+ TCCTGCATTCAGTGCCGGTTACCAAGGACGC
220
+ TTCAAGAAGCCCCGGGAGGGATTTGAACCCT
data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 ADDED
@@ -0,0 +1,220 @@
1
+ CTCTTCTGGATTCCAATATATTCCCCAGAAA
2
+ TATTCCCCAGAAATTCTTTATGTGGTTCAAA
3
+ TTTATGTGGTTCAAAGAGCTCTTCTATACTG
4
+ ATTCTTTATGTGGTTCAAAGAGCTCTTCTAT
5
+ TTCTATACTGCTCTCTATTATCTGGGTATCA
6
+ TGAGTTCGTTGATTGGTATAACAATCGACCT
7
+ AAACTGGATGAACTATAGGGGATATGCCCAT
8
+ AACTGGATGAACTATAGGGGATATGCCCATT
9
+ TATGTGGTTCAAAGAGCTCTTCTATACTGCT
10
+ GAACTATAGGGGATATGCCCATTACTCTTCT
11
+ TCTATTATCTGGGTATCACCAAGCTCACTAA
12
+ AACAAAAGAAATCTGGATAAACTGGATGAAC
13
+ TTGAAACAAAAGAAATCTGGATAAACTGGAT
14
+ CTATACTGCTCTCTATTATCTGGGTATCACC
15
+ ACCTCATGGAAGCCTTAATTTTAAGGAACTT
16
+ CTGGATAAACTGGATGAACTATAGGGGATAT
17
+ TCTCTATTATCTGGGTATCACCAAGCTCACT
18
+ AGCCTTAATTTTAAGGAACTTGAAACAAAAG
19
+ CCGCAGATTCAGGAAATCCTTCTCCAGCTTT
20
+ AATATATTCCCCAGAAATTCTTTATGTGGTT
21
+ TCATGGAAGCCTTAATTTTAAGGAACTTGAA
22
+ AAATCCTTCTCCAGCTTTGATGAGTTCGTTG
23
+ CGACCTCATGGAAGCCTTAATTTTAAGGAAC
24
+ AATTCTTTATGTGGTTCAAAGAGCTCTTCTA
25
+ TAAGGAACTTGAAACAAAAGAAATCTGGATA
26
+ CTTAATTTTAAGGAACTTGAAACAAAAGAAA
27
+ AAATTCTTTATGTGGTTCAAAGAGCTCTTCT
28
+ TCCAGCTTTGATGAGTTCGTTGATTGGTATA
29
+ CAGGAAATCCTTCTCCAGCTTTGATGAGTTC
30
+ GGATGAACTATAGGGGATATGCCCATTACTC
31
+ TTTGATGAGTTCGTTGATTGGTATAACAATC
32
+ ATAAACTGGATGAACTATAGGGGATATGCCC
33
+ TTGATGAGTTCGTTGATTGGTATAACAATCG
34
+ CAATCGACCTCATGGAAGCCTTAATTTTAAG
35
+ CAGAAATTCTTTATGTGGTTCAAAGAGCTCT
36
+ CTTTGATGAGTTCGTTGATTGGTATAACAAT
37
+ TTCAGGAAATCCTTCTCCAGCTTTGATGAGT
38
+ TAAACTGGATGAACTATAGGGGATATGCCCA
39
+ ATGAGTTCGTTGATTGGTATAACAATCGACC
40
+ CCTTAATTTTAAGGAACTTGAAACAAAAGAA
41
+ TGATGAGTTCGTTGATTGGTATAACAATCGA
42
+ AATCCTTCTCCAGCTTTGATGAGTTCGTTGA
43
+ TCGTTGATTGGTATAACAATCGACCTCATGG
44
+ TAGGGGATATGCCCATTACTCTTCTGGATTC
45
+ AAGGAACTTGAAACAAAAGAAATCTGGATAA
46
+ GTTCGTTGATTGGTATAACAATCGACCTCAT
47
+ CGTTGATTGGTATAACAATCGACCTCATGGA
48
+ GGAAGCCTTAATTTTAAGGAACTTGAAACAA
49
+ AGGGGATATGCCCATTACTCTTCTGGATTCC
50
+ ATACTGCTCTCTATTATCTGGGTATCACCAA
51
+ CTGGATTCCAATATATTCCCCAGAAATTCTT
52
+ GGGATATGCCCATTACTCTTCTGGATTCCAA
53
+ TTGATTGGTATAACAATCGACCTCATGGAAG
54
+ AAATCTGGATAAACTGGATGAACTATAGGGG
55
+ TAATTTTAAGGAACTTGAAACAAAAGAAATC
56
+ ATGAACTATAGGGGATATGCCCATTACTCTT
57
+ TAACAATCGACCTCATGGAAGCCTTAATTTT
58
+ TTCTCCAGCTTTGATGAGTTCGTTGATTGGT
59
+ TCTTTATGTGGTTCAAAGAGCTCTTCTATAC
60
+ TACTGCTCTCTATTATCTGGGTATCACCAAG
61
+ ACAAAAGAAATCTGGATAAACTGGATGAACT
62
+ ACTATAGGGGATATGCCCATTACTCTTCTGG
63
+ GTTCAAAGAGCTCTTCTATACTGCTCTCTAT
64
+ ATATGCCCATTACTCTTCTGGATTCCAATAT
65
+ ATCTGGGTATCACCAAGCTCACTAATCTTCA
66
+ TTCGTTGATTGGTATAACAATCGACCTCATG
67
+ CTGGATGAACTATAGGGGATATGCCCATTAC
68
+ CAAAAGAAATCTGGATAAACTGGATGAACTA
69
+ TCTCCAGCTTTGATGAGTTCGTTGATTGGTA
70
+ GAGTTCGTTGATTGGTATAACAATCGACCTC
71
+ GATTCCAATATATTCCCCAGAAATTCTTTAT
72
+ TACTCTTCTGGATTCCAATATATTCCCCAGA
73
+ ATATATTCCCCAGAAATTCTTTATGTGGTTC
74
+ ATTTTAAGGAACTTGAAACAAAAGAAATCTG
75
+ TATAGGGGATATGCCCATTACTCTTCTGGAT
76
+ GGATTCCAATATATTCCCCAGAAATTCTTTA
77
+ CGCAGATTCAGGAAATCCTTCTCCAGCTTTG
78
+ ATGTGGTTCAAAGAGCTCTTCTATACTGCTC
79
+ AAGAAATCTGGATAAACTGGATGAACTATAG
80
+ TTGGTATAACAATCGACCTCATGGAAGCCTT
81
+ CAAAGAGCTCTTCTATACTGCTCTCTATTAT
82
+ TTCAAAGAGCTCTTCTATACTGCTCTCTATT
83
+ GAAGCCTTAATTTTAAGGAACTTGAAACAAA
84
+ GCCTTAATTTTAAGGAACTTGAAACAAAAGA
85
+ GCAGATTCAGGAAATCCTTCTCCAGCTTTGA
86
+ TTAATTTTAAGGAACTTGAAACAAAAGAAAT
87
+ GGAAATCCTTCTCCAGCTTTGATGAGTTCGT
88
+ TGGATGAACTATAGGGGATATGCCCATTACT
89
+ TTACTCTTCTGGATTCCAATATATTCCCCAG
90
+ AATCGACCTCATGGAAGCCTTAATTTTAAGG
91
+ GATATGCCCATTACTCTTCTGGATTCCAATA
92
+ TCCAATATATTCCCCAGAAATTCTTTATGTG
93
+ ATTATCTGGGTATCACCAAGCTCACTAATCT
94
+ GAGCTCTTCTATACTGCTCTCTATTATCTGG
95
+ CTATTATCTGGGTATCACCAAGCTCACTAAT
96
+ CCCCAGAAATTCTTTATGTGGTTCAAAGAGC
97
+ TGCCCATTACTCTTCTGGATTCCAATATATT
98
+ TTCCAATATATTCCCCAGAAATTCTTTATGT
99
+ AAAGAGCTCTTCTATACTGCTCTCTATTATC
100
+ CTGCTCTCTATTATCTGGGTATCACCAAGCT
101
+ TCTGGGTATCACCAAGCTCACTAATCTTCAT
102
+ CTTTATGTGGTTCAAAGAGCTCTTCTATACT
103
+ TGATTGGTATAACAATCGACCTCATGGAAGC
104
+ TGGATTCCAATATATTCCCCAGAAATTCTTT
105
+ GGTTCAAAGAGCTCTTCTATACTGCTCTCTA
106
+ GGAACTTGAAACAAAAGAAATCTGGATAAAC
107
+ GATTGGTATAACAATCGACCTCATGGAAGCC
108
+ GCTCTTCTATACTGCTCTCTATTATCTGGGT
109
+ ACTGCTCTCTATTATCTGGGTATCACCAAGC
110
+ AAGCCTTAATTTTAAGGAACTTGAAACAAAA
111
+ GCCCATTACTCTTCTGGATTCCAATATATTC
112
+ CCTTCTCCAGCTTTGATGAGTTCGTTGATTG
113
+ TATTATCTGGGTATCACCAAGCTCACTAATC
114
+ CATTACTCTTCTGGATTCCAATATATTCCCC
115
+ AAACAAAAGAAATCTGGATAAACTGGATGAA
116
+ GAAATCTGGATAAACTGGATGAACTATAGGG
117
+ ACTCTTCTGGATTCCAATATATTCCCCAGAA
118
+ GAAATCCTTCTCCAGCTTTGATGAGTTCGTT
119
+ TCTATACTGCTCTCTATTATCTGGGTATCAC
120
+ TGTGGTTCAAAGAGCTCTTCTATACTGCTCT
121
+ CAGCTTTGATGAGTTCGTTGATTGGTATAAC
122
+ TCGACCTCATGGAAGCCTTAATTTTAAGGAA
123
+ CCAATATATTCCCCAGAAATTCTTTATGTGG
124
+ AAGAGCTCTTCTATACTGCTCTCTATTATCT
125
+ AAAAGAAATCTGGATAAACTGGATGAACTAT
126
+ ATAGGGGATATGCCCATTACTCTTCTGGATT
127
+ TCTTCTGGATTCCAATATATTCCCCAGAAAT
128
+ AAAGAAATCTGGATAAACTGGATGAACTATA
129
+ GAACTTGAAACAAAAGAAATCTGGATAAACT
130
+ TTCCCCAGAAATTCTTTATGTGGTTCAAAGA
131
+ TTTTAAGGAACTTGAAACAAAAGAAATCTGG
132
+ ATAACAATCGACCTCATGGAAGCCTTAATTT
133
+ ACTGGATGAACTATAGGGGATATGCCCATTA
134
+ TTATGTGGTTCAAAGAGCTCTTCTATACTGC
135
+ ATATTCCCCAGAAATTCTTTATGTGGTTCAA
136
+ TTATCTGGGTATCACCAAGCTCACTAATCTT
137
+ TATGCCCATTACTCTTCTGGATTCCAATATA
138
+ GACCTCATGGAAGCCTTAATTTTAAGGAACT
139
+ TATAACAATCGACCTCATGGAAGCCTTAATT
140
+ CTTGAAACAAAAGAAATCTGGATAAACTGGA
141
+ AGCTCTTCTATACTGCTCTCTATTATCTGGG
142
+ TATATTCCCCAGAAATTCTTTATGTGGTTCA
143
+ GGATATGCCCATTACTCTTCTGGATTCCAAT
144
+ CTCTTCTATACTGCTCTCTATTATCTGGGTA
145
+ AACAATCGACCTCATGGAAGCCTTAATTTTA
146
+ ATCCTTCTCCAGCTTTGATGAGTTCGTTGAT
147
+ TCTGGATTCCAATATATTCCCCAGAAATTCT
148
+ AGGAACTTGAAACAAAAGAAATCTGGATAAA
149
+ ATCTGGATAAACTGGATGAACTATAGGGGAT
150
+ ATTCCCCAGAAATTCTTTATGTGGTTCAAAG
151
+ TCCTTCTCCAGCTTTGATGAGTTCGTTGATT
152
+ CCCAGAAATTCTTTATGTGGTTCAAAGAGCT
153
+ TGCTCTCTATTATCTGGGTATCACCAAGCTC
154
+ GCTCTCTATTATCTGGGTATCACCAAGCTCA
155
+ AACTTGAAACAAAAGAAATCTGGATAAACTG
156
+ ACTTGAAACAAAAGAAATCTGGATAAACTGG
157
+ ATTGGTATAACAATCGACCTCATGGAAGCCT
158
+ TATCTGGGTATCACCAAGCTCACTAATCTTC
159
+ AGCTTTGATGAGTTCGTTGATTGGTATAACA
160
+ ACAATCGACCTCATGGAAGCCTTAATTTTAA
161
+ CTTCTCCAGCTTTGATGAGTTCGTTGATTGG
162
+ TTTAAGGAACTTGAAACAAAAGAAATCTGGA
163
+ CTCTCTATTATCTGGGTATCACCAAGCTCAC
164
+ TGAACTATAGGGGATATGCCCATTACTCTTC
165
+ GATGAGTTCGTTGATTGGTATAACAATCGAC
166
+ CCATTACTCTTCTGGATTCCAATATATTCCC
167
+ TTCTGGATTCCAATATATTCCCCAGAAATTC
168
+ TCCCCAGAAATTCTTTATGTGGTTCAAAGAG
169
+ ATTCAGGAAATCCTTCTCCAGCTTTGATGAG
170
+ ATGCCCATTACTCTTCTGGATTCCAATATAT
171
+ ATTCCAATATATTCCCCAGAAATTCTTTATG
172
+ GATTCAGGAAATCCTTCTCCAGCTTTGATGA
173
+ AATTTTAAGGAACTTGAAACAAAAGAAATCT
174
+ CTCCAGCTTTGATGAGTTCGTTGATTGGTAT
175
+ ATCGACCTCATGGAAGCCTTAATTTTAAGGA
176
+ GTTGATTGGTATAACAATCGACCTCATGGAA
177
+ AGGAAATCCTTCTCCAGCTTTGATGAGTTCG
178
+ GATGAACTATAGGGGATATGCCCATTACTCT
179
+ GGGGATATGCCCATTACTCTTCTGGATTCCA
180
+ GTGGTTCAAAGAGCTCTTCTATACTGCTCTC
181
+ CCCATTACTCTTCTGGATTCCAATATATTCC
182
+ CCAGAAATTCTTTATGTGGTTCAAAGAGCTC
183
+ AGAAATCTGGATAAACTGGATGAACTATAGG
184
+ AATCTGGATAAACTGGATGAACTATAGGGGA
185
+ TGGTATAACAATCGACCTCATGGAAGCCTTA
186
+ TATACTGCTCTCTATTATCTGGGTATCACCA
187
+ CCTCATGGAAGCCTTAATTTTAAGGAACTTG
188
+ TGGTTCAAAGAGCTCTTCTATACTGCTCTCT
189
+ AGAAATTCTTTATGTGGTTCAAAGAGCTCTT
190
+ CTTCTATACTGCTCTCTATTATCTGGGTATC
191
+ TCAGGAAATCCTTCTCCAGCTTTGATGAGTT
192
+ TCTTCTATACTGCTCTCTATTATCTGGGTAT
193
+ TGGAAGCCTTAATTTTAAGGAACTTGAAACA
194
+ ATGGAAGCCTTAATTTTAAGGAACTTGAAAC
195
+ CAGATTCAGGAAATCCTTCTCCAGCTTTGAT
196
+ TTAAGGAACTTGAAACAAAAGAAATCTGGAT
197
+ ATTACTCTTCTGGATTCCAATATATTCCCCA
198
+ CATGGAAGCCTTAATTTTAAGGAACTTGAAA
199
+ GAAATTCTTTATGTGGTTCAAAGAGCTCTTC
200
+ GATAAACTGGATGAACTATAGGGGATATGCC
201
+ GGATAAACTGGATGAACTATAGGGGATATGC
202
+ GTATAACAATCGACCTCATGGAAGCCTTAAT
203
+ GAAACAAAAGAAATCTGGATAAACTGGATGA
204
+ AACTATAGGGGATATGCCCATTACTCTTCTG
205
+ CCAGCTTTGATGAGTTCGTTGATTGGTATAA
206
+ CAATATATTCCCCAGAAATTCTTTATGTGGT
207
+ TTCTTTATGTGGTTCAAAGAGCTCTTCTATA
208
+ AGATTCAGGAAATCCTTCTCCAGCTTTGATG
209
+ GCTTTGATGAGTTCGTTGATTGGTATAACAA
210
+ CTATAGGGGATATGCCCATTACTCTTCTGGA
211
+ TCAAAGAGCTCTTCTATACTGCTCTCTATTA
212
+ AGTTCGTTGATTGGTATAACAATCGACCTCA
213
+ GGTATAACAATCGACCTCATGGAAGCCTTAA
214
+ CTCATGGAAGCCTTAATTTTAAGGAACTTGA
215
+ CTTCTGGATTCCAATATATTCCCCAGAAATT
216
+ TCTGGATAAACTGGATGAACTATAGGGGATA
217
+ TGGATAAACTGGATGAACTATAGGGGATATG
218
+ CTCTATTATCTGGGTATCACCAAGCTCACTA
219
+ TGAAACAAAAGAAATCTGGATAAACTGGATG
220
+ AGAGCTCTTCTATACTGCTCTCTATTATCTG