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/c_probe_node_finder/1/Log ADDED
@@ -0,0 +1,756 @@
1
+ Thu Jun 5 13:50:40 2014
2
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-663-1rx3qul /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
3
+ Version 1.2.08
4
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
5
+ This is free software; see the source for copying conditions. There is NO
6
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
7
+ Compilation settings:
8
+ CATEGORIES = 2
9
+ MAXKMERLENGTH = 255
10
+
11
+ Thu Jun 5 13:50:41 2014
12
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
13
+ Version 1.2.08
14
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
15
+ This is free software; see the source for copying conditions. There is NO
16
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
17
+ Compilation settings:
18
+ CATEGORIES = 2
19
+ MAXKMERLENGTH = 255
20
+
21
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
22
+ Thu Jun 5 13:51:50 2014
23
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-707-cg0vdm /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
24
+ Version 1.2.08
25
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
26
+ This is free software; see the source for copying conditions. There is NO
27
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
28
+ Compilation settings:
29
+ CATEGORIES = 2
30
+ MAXKMERLENGTH = 255
31
+
32
+ Thu Jun 5 13:51:51 2014
33
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
34
+ Version 1.2.08
35
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
36
+ This is free software; see the source for copying conditions. There is NO
37
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
38
+ Compilation settings:
39
+ CATEGORIES = 2
40
+ MAXKMERLENGTH = 255
41
+
42
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
43
+ Thu Jun 5 15:14:07 2014
44
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3214-bxv4rw /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
45
+ Version 1.2.08
46
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
47
+ This is free software; see the source for copying conditions. There is NO
48
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
49
+ Compilation settings:
50
+ CATEGORIES = 2
51
+ MAXKMERLENGTH = 255
52
+
53
+ Thu Jun 5 15:14:07 2014
54
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
55
+ Version 1.2.08
56
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
57
+ This is free software; see the source for copying conditions. There is NO
58
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
59
+ Compilation settings:
60
+ CATEGORIES = 2
61
+ MAXKMERLENGTH = 255
62
+
63
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
64
+ Thu Jun 5 15:14:31 2014
65
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3226-msza0n /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
66
+ Version 1.2.08
67
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
68
+ This is free software; see the source for copying conditions. There is NO
69
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
70
+ Compilation settings:
71
+ CATEGORIES = 2
72
+ MAXKMERLENGTH = 255
73
+
74
+ Thu Jun 5 15:14:31 2014
75
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
76
+ Version 1.2.08
77
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
78
+ This is free software; see the source for copying conditions. There is NO
79
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
80
+ Compilation settings:
81
+ CATEGORIES = 2
82
+ MAXKMERLENGTH = 255
83
+
84
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
85
+ Thu Jun 5 15:15:11 2014
86
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3251-i2i91i /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
87
+ Version 1.2.08
88
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
89
+ This is free software; see the source for copying conditions. There is NO
90
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
91
+ Compilation settings:
92
+ CATEGORIES = 2
93
+ MAXKMERLENGTH = 255
94
+
95
+ Thu Jun 5 15:15:12 2014
96
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
97
+ Version 1.2.08
98
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
99
+ This is free software; see the source for copying conditions. There is NO
100
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
101
+ Compilation settings:
102
+ CATEGORIES = 2
103
+ MAXKMERLENGTH = 255
104
+
105
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
106
+ Thu Jun 5 15:15:26 2014
107
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3263-1jayngw /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
108
+ Version 1.2.08
109
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
110
+ This is free software; see the source for copying conditions. There is NO
111
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
112
+ Compilation settings:
113
+ CATEGORIES = 2
114
+ MAXKMERLENGTH = 255
115
+
116
+ Thu Jun 5 15:15:26 2014
117
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
118
+ Version 1.2.08
119
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
120
+ This is free software; see the source for copying conditions. There is NO
121
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
122
+ Compilation settings:
123
+ CATEGORIES = 2
124
+ MAXKMERLENGTH = 255
125
+
126
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
127
+ Thu Jun 5 15:15:41 2014
128
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3277-1x8qri /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
129
+ Version 1.2.08
130
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
131
+ This is free software; see the source for copying conditions. There is NO
132
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
133
+ Compilation settings:
134
+ CATEGORIES = 2
135
+ MAXKMERLENGTH = 255
136
+
137
+ Thu Jun 5 15:15:41 2014
138
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
139
+ Version 1.2.08
140
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
141
+ This is free software; see the source for copying conditions. There is NO
142
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
143
+ Compilation settings:
144
+ CATEGORIES = 2
145
+ MAXKMERLENGTH = 255
146
+
147
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
148
+ Thu Jun 5 15:15:54 2014
149
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3296-fcppi /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
150
+ Version 1.2.08
151
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
152
+ This is free software; see the source for copying conditions. There is NO
153
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
154
+ Compilation settings:
155
+ CATEGORIES = 2
156
+ MAXKMERLENGTH = 255
157
+
158
+ Thu Jun 5 15:15:54 2014
159
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
160
+ Version 1.2.08
161
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
162
+ This is free software; see the source for copying conditions. There is NO
163
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
164
+ Compilation settings:
165
+ CATEGORIES = 2
166
+ MAXKMERLENGTH = 255
167
+
168
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
169
+ Thu Jun 5 15:16:05 2014
170
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3322-pnzd4t /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
171
+ Version 1.2.08
172
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
173
+ This is free software; see the source for copying conditions. There is NO
174
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
175
+ Compilation settings:
176
+ CATEGORIES = 2
177
+ MAXKMERLENGTH = 255
178
+
179
+ Thu Jun 5 15:16:06 2014
180
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
181
+ Version 1.2.08
182
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
183
+ This is free software; see the source for copying conditions. There is NO
184
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
185
+ Compilation settings:
186
+ CATEGORIES = 2
187
+ MAXKMERLENGTH = 255
188
+
189
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
190
+ Thu Jun 5 15:16:14 2014
191
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3335-k2lwnk /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
192
+ Version 1.2.08
193
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
194
+ This is free software; see the source for copying conditions. There is NO
195
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
196
+ Compilation settings:
197
+ CATEGORIES = 2
198
+ MAXKMERLENGTH = 255
199
+
200
+ Thu Jun 5 15:16:14 2014
201
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
202
+ Version 1.2.08
203
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
204
+ This is free software; see the source for copying conditions. There is NO
205
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
206
+ Compilation settings:
207
+ CATEGORIES = 2
208
+ MAXKMERLENGTH = 255
209
+
210
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
211
+ Thu Jun 5 15:16:34 2014
212
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3351-1u544hg /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
213
+ Version 1.2.08
214
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
215
+ This is free software; see the source for copying conditions. There is NO
216
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
217
+ Compilation settings:
218
+ CATEGORIES = 2
219
+ MAXKMERLENGTH = 255
220
+
221
+ Thu Jun 5 15:16:34 2014
222
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
223
+ Version 1.2.08
224
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
225
+ This is free software; see the source for copying conditions. There is NO
226
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
227
+ Compilation settings:
228
+ CATEGORIES = 2
229
+ MAXKMERLENGTH = 255
230
+
231
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
232
+ Thu Jun 5 15:17:36 2014
233
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3412-1mhx2xm /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
234
+ Version 1.2.08
235
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
236
+ This is free software; see the source for copying conditions. There is NO
237
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
238
+ Compilation settings:
239
+ CATEGORIES = 2
240
+ MAXKMERLENGTH = 255
241
+
242
+ Thu Jun 5 15:17:36 2014
243
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
244
+ Version 1.2.08
245
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
246
+ This is free software; see the source for copying conditions. There is NO
247
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
248
+ Compilation settings:
249
+ CATEGORIES = 2
250
+ MAXKMERLENGTH = 255
251
+
252
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
253
+ Thu Jun 5 15:21:42 2014
254
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3454-1aoxw62 /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
255
+ Version 1.2.08
256
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
257
+ This is free software; see the source for copying conditions. There is NO
258
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
259
+ Compilation settings:
260
+ CATEGORIES = 2
261
+ MAXKMERLENGTH = 255
262
+
263
+ Thu Jun 5 15:21:42 2014
264
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
265
+ Version 1.2.08
266
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
267
+ This is free software; see the source for copying conditions. There is NO
268
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
269
+ Compilation settings:
270
+ CATEGORIES = 2
271
+ MAXKMERLENGTH = 255
272
+
273
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
274
+ Thu Jun 5 15:27:21 2014
275
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3619-q9lrkn /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
276
+ Version 1.2.08
277
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
278
+ This is free software; see the source for copying conditions. There is NO
279
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
280
+ Compilation settings:
281
+ CATEGORIES = 2
282
+ MAXKMERLENGTH = 255
283
+
284
+ Thu Jun 5 15:27:21 2014
285
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
286
+ Version 1.2.08
287
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
288
+ This is free software; see the source for copying conditions. There is NO
289
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
290
+ Compilation settings:
291
+ CATEGORIES = 2
292
+ MAXKMERLENGTH = 255
293
+
294
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
295
+ Thu Jun 5 15:27:58 2014
296
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3638-1vdyaa8 /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
297
+ Version 1.2.08
298
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
299
+ This is free software; see the source for copying conditions. There is NO
300
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
301
+ Compilation settings:
302
+ CATEGORIES = 2
303
+ MAXKMERLENGTH = 255
304
+
305
+ Thu Jun 5 15:27:58 2014
306
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
307
+ Version 1.2.08
308
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
309
+ This is free software; see the source for copying conditions. There is NO
310
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
311
+ Compilation settings:
312
+ CATEGORIES = 2
313
+ MAXKMERLENGTH = 255
314
+
315
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
316
+ Thu Jun 5 15:29:59 2014
317
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3663-10cb0fe /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
318
+ Version 1.2.08
319
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
320
+ This is free software; see the source for copying conditions. There is NO
321
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
322
+ Compilation settings:
323
+ CATEGORIES = 2
324
+ MAXKMERLENGTH = 255
325
+
326
+ Thu Jun 5 15:30:00 2014
327
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
328
+ Version 1.2.08
329
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
330
+ This is free software; see the source for copying conditions. There is NO
331
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
332
+ Compilation settings:
333
+ CATEGORIES = 2
334
+ MAXKMERLENGTH = 255
335
+
336
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
337
+ Thu Jun 5 15:30:38 2014
338
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3675-eoq68g /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
339
+ Version 1.2.08
340
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
341
+ This is free software; see the source for copying conditions. There is NO
342
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
343
+ Compilation settings:
344
+ CATEGORIES = 2
345
+ MAXKMERLENGTH = 255
346
+
347
+ Thu Jun 5 15:30:38 2014
348
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
349
+ Version 1.2.08
350
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
351
+ This is free software; see the source for copying conditions. There is NO
352
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
353
+ Compilation settings:
354
+ CATEGORIES = 2
355
+ MAXKMERLENGTH = 255
356
+
357
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
358
+ Thu Jun 5 15:31:24 2014
359
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3701-ycedf2 /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
360
+ Version 1.2.08
361
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
362
+ This is free software; see the source for copying conditions. There is NO
363
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
364
+ Compilation settings:
365
+ CATEGORIES = 2
366
+ MAXKMERLENGTH = 255
367
+
368
+ Thu Jun 5 15:31:24 2014
369
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
370
+ Version 1.2.08
371
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
372
+ This is free software; see the source for copying conditions. There is NO
373
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
374
+ Compilation settings:
375
+ CATEGORIES = 2
376
+ MAXKMERLENGTH = 255
377
+
378
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
379
+ Thu Jun 5 15:35:28 2014
380
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3780-u1fa8x /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
381
+ Version 1.2.08
382
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
383
+ This is free software; see the source for copying conditions. There is NO
384
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
385
+ Compilation settings:
386
+ CATEGORIES = 2
387
+ MAXKMERLENGTH = 255
388
+
389
+ Thu Jun 5 15:35:28 2014
390
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
391
+ Version 1.2.08
392
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
393
+ This is free software; see the source for copying conditions. There is NO
394
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
395
+ Compilation settings:
396
+ CATEGORIES = 2
397
+ MAXKMERLENGTH = 255
398
+
399
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
400
+ Thu Jun 5 15:36:21 2014
401
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3796-yug6gq /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
402
+ Version 1.2.08
403
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
404
+ This is free software; see the source for copying conditions. There is NO
405
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
406
+ Compilation settings:
407
+ CATEGORIES = 2
408
+ MAXKMERLENGTH = 255
409
+
410
+ Thu Jun 5 15:36:21 2014
411
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
412
+ Version 1.2.08
413
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
414
+ This is free software; see the source for copying conditions. There is NO
415
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
416
+ Compilation settings:
417
+ CATEGORIES = 2
418
+ MAXKMERLENGTH = 255
419
+
420
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
421
+ Thu Jun 5 15:36:41 2014
422
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3814-2a357n /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
423
+ Version 1.2.08
424
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
425
+ This is free software; see the source for copying conditions. There is NO
426
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
427
+ Compilation settings:
428
+ CATEGORIES = 2
429
+ MAXKMERLENGTH = 255
430
+
431
+ Thu Jun 5 15:36:41 2014
432
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
433
+ Version 1.2.08
434
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
435
+ This is free software; see the source for copying conditions. There is NO
436
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
437
+ Compilation settings:
438
+ CATEGORIES = 2
439
+ MAXKMERLENGTH = 255
440
+
441
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
442
+ Thu Jun 5 15:37:20 2014
443
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140605-3867-1kzxbp7 /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
444
+ Version 1.2.08
445
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
446
+ This is free software; see the source for copying conditions. There is NO
447
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
448
+ Compilation settings:
449
+ CATEGORIES = 2
450
+ MAXKMERLENGTH = 255
451
+
452
+ Thu Jun 5 15:37:20 2014
453
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
454
+ Version 1.2.08
455
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
456
+ This is free software; see the source for copying conditions. There is NO
457
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
458
+ Compilation settings:
459
+ CATEGORIES = 2
460
+ MAXKMERLENGTH = 255
461
+
462
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
463
+ Fri Jun 6 15:36:41 2014
464
+ velveth /tmp/v 51 -fasta -short /tmp/probes.fa20140606-27704-frqv2s /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/wander/1/random1.sammy.fa -create_binary
465
+ Version 1.2.08
466
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
467
+ This is free software; see the source for copying conditions. There is NO
468
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
469
+ Compilation settings:
470
+ CATEGORIES = 2
471
+ MAXKMERLENGTH = 255
472
+
473
+ Fri Jun 6 15:36:42 2014
474
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 3.5 -tour_bus no
475
+ Version 1.2.08
476
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
477
+ This is free software; see the source for copying conditions. There is NO
478
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
479
+ Compilation settings:
480
+ CATEGORIES = 2
481
+ MAXKMERLENGTH = 255
482
+
483
+ Final graph has 1 nodes and n50 of 950, max 950, total 950, using 602/602 reads
484
+ Tue Jun 10 17:15:39 2014
485
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-14931-9854y1 -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
486
+ Version 1.2.08
487
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
488
+ This is free software; see the source for copying conditions. There is NO
489
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
490
+ Compilation settings:
491
+ CATEGORIES = 2
492
+ MAXKMERLENGTH = 255
493
+
494
+ Tue Jun 10 17:15:39 2014
495
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
496
+ Version 1.2.08
497
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
498
+ This is free software; see the source for copying conditions. There is NO
499
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
500
+ Compilation settings:
501
+ CATEGORIES = 2
502
+ MAXKMERLENGTH = 255
503
+
504
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
505
+ Tue Jun 10 17:17:13 2014
506
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15035-8xsomd -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
507
+ Version 1.2.08
508
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
509
+ This is free software; see the source for copying conditions. There is NO
510
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
511
+ Compilation settings:
512
+ CATEGORIES = 2
513
+ MAXKMERLENGTH = 255
514
+
515
+ Tue Jun 10 17:17:14 2014
516
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
517
+ Version 1.2.08
518
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
519
+ This is free software; see the source for copying conditions. There is NO
520
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
521
+ Compilation settings:
522
+ CATEGORIES = 2
523
+ MAXKMERLENGTH = 255
524
+
525
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
526
+ Tue Jun 10 17:17:52 2014
527
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15057-1na7rjw -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
528
+ Version 1.2.08
529
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
530
+ This is free software; see the source for copying conditions. There is NO
531
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
532
+ Compilation settings:
533
+ CATEGORIES = 2
534
+ MAXKMERLENGTH = 255
535
+
536
+ Tue Jun 10 17:17:53 2014
537
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
538
+ Version 1.2.08
539
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
540
+ This is free software; see the source for copying conditions. There is NO
541
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
542
+ Compilation settings:
543
+ CATEGORIES = 2
544
+ MAXKMERLENGTH = 255
545
+
546
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
547
+ Tue Jun 10 17:19:12 2014
548
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15112-1chdrye -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
549
+ Version 1.2.08
550
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
551
+ This is free software; see the source for copying conditions. There is NO
552
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
553
+ Compilation settings:
554
+ CATEGORIES = 2
555
+ MAXKMERLENGTH = 255
556
+
557
+ Tue Jun 10 17:19:12 2014
558
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
559
+ Version 1.2.08
560
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
561
+ This is free software; see the source for copying conditions. There is NO
562
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
563
+ Compilation settings:
564
+ CATEGORIES = 2
565
+ MAXKMERLENGTH = 255
566
+
567
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
568
+ Tue Jun 10 17:21:05 2014
569
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15136-1phgs7o -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
570
+ Version 1.2.08
571
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
572
+ This is free software; see the source for copying conditions. There is NO
573
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
574
+ Compilation settings:
575
+ CATEGORIES = 2
576
+ MAXKMERLENGTH = 255
577
+
578
+ Tue Jun 10 17:21:06 2014
579
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
580
+ Version 1.2.08
581
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
582
+ This is free software; see the source for copying conditions. There is NO
583
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
584
+ Compilation settings:
585
+ CATEGORIES = 2
586
+ MAXKMERLENGTH = 255
587
+
588
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
589
+ Tue Jun 10 17:21:26 2014
590
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15152-mq1qoz -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
591
+ Version 1.2.08
592
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
593
+ This is free software; see the source for copying conditions. There is NO
594
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
595
+ Compilation settings:
596
+ CATEGORIES = 2
597
+ MAXKMERLENGTH = 255
598
+
599
+ Tue Jun 10 17:21:26 2014
600
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
601
+ Version 1.2.08
602
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
603
+ This is free software; see the source for copying conditions. There is NO
604
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
605
+ Compilation settings:
606
+ CATEGORIES = 2
607
+ MAXKMERLENGTH = 255
608
+
609
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
610
+ Tue Jun 10 17:21:50 2014
611
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15173-1ylne8g -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
612
+ Version 1.2.08
613
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
614
+ This is free software; see the source for copying conditions. There is NO
615
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
616
+ Compilation settings:
617
+ CATEGORIES = 2
618
+ MAXKMERLENGTH = 255
619
+
620
+ Tue Jun 10 17:21:51 2014
621
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
622
+ Version 1.2.08
623
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
624
+ This is free software; see the source for copying conditions. There is NO
625
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
626
+ Compilation settings:
627
+ CATEGORIES = 2
628
+ MAXKMERLENGTH = 255
629
+
630
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
631
+ Tue Jun 10 17:26:02 2014
632
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15284-e1feij -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
633
+ Version 1.2.08
634
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
635
+ This is free software; see the source for copying conditions. There is NO
636
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
637
+ Compilation settings:
638
+ CATEGORIES = 2
639
+ MAXKMERLENGTH = 255
640
+
641
+ Tue Jun 10 17:26:02 2014
642
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
643
+ Version 1.2.08
644
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
645
+ This is free software; see the source for copying conditions. There is NO
646
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
647
+ Compilation settings:
648
+ CATEGORIES = 2
649
+ MAXKMERLENGTH = 255
650
+
651
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
652
+ Tue Jun 10 17:26:11 2014
653
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15300-1ke7k7g -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
654
+ Version 1.2.08
655
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
656
+ This is free software; see the source for copying conditions. There is NO
657
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
658
+ Compilation settings:
659
+ CATEGORIES = 2
660
+ MAXKMERLENGTH = 255
661
+
662
+ Tue Jun 10 17:26:11 2014
663
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
664
+ Version 1.2.08
665
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
666
+ This is free software; see the source for copying conditions. There is NO
667
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
668
+ Compilation settings:
669
+ CATEGORIES = 2
670
+ MAXKMERLENGTH = 255
671
+
672
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
673
+ Tue Jun 10 17:27:13 2014
674
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15363-1mvayyf -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
675
+ Version 1.2.08
676
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
677
+ This is free software; see the source for copying conditions. There is NO
678
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
679
+ Compilation settings:
680
+ CATEGORIES = 2
681
+ MAXKMERLENGTH = 255
682
+
683
+ Tue Jun 10 17:27:13 2014
684
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
685
+ Version 1.2.08
686
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
687
+ This is free software; see the source for copying conditions. There is NO
688
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
689
+ Compilation settings:
690
+ CATEGORIES = 2
691
+ MAXKMERLENGTH = 255
692
+
693
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
694
+ Tue Jun 10 17:27:40 2014
695
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15382-1uxfxdc -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
696
+ Version 1.2.08
697
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
698
+ This is free software; see the source for copying conditions. There is NO
699
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
700
+ Compilation settings:
701
+ CATEGORIES = 2
702
+ MAXKMERLENGTH = 255
703
+
704
+ Tue Jun 10 17:27:40 2014
705
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
706
+ Version 1.2.08
707
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
708
+ This is free software; see the source for copying conditions. There is NO
709
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
710
+ Compilation settings:
711
+ CATEGORIES = 2
712
+ MAXKMERLENGTH = 255
713
+
714
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
715
+ Tue Jun 10 17:28:09 2014
716
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140610-15403-kg169u -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
717
+ Version 1.2.08
718
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
719
+ This is free software; see the source for copying conditions. There is NO
720
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
721
+ Compilation settings:
722
+ CATEGORIES = 2
723
+ MAXKMERLENGTH = 255
724
+
725
+ Tue Jun 10 17:28:09 2014
726
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
727
+ Version 1.2.08
728
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
729
+ This is free software; see the source for copying conditions. There is NO
730
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
731
+ Compilation settings:
732
+ CATEGORIES = 2
733
+ MAXKMERLENGTH = 255
734
+
735
+ Final graph has 4 nodes and n50 of 435, max 437, total 1092, using 444/444 reads
736
+ Wed Jun 11 11:50:05 2014
737
+ velveth /tmp/v 31 -fasta -short /tmp/probes.fa20140611-32519-c4h475 -fasta.gz -short /mnt/rudd_gut/srv/home/uqbwoodc/git/priner/spec/data/gapfilling/3/reads.fa.gz -create_binary
738
+ Version 1.2.08
739
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
740
+ This is free software; see the source for copying conditions. There is NO
741
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
742
+ Compilation settings:
743
+ CATEGORIES = 2
744
+ MAXKMERLENGTH = 255
745
+
746
+ Wed Jun 11 11:50:05 2014
747
+ velvetg /tmp/v -read_trkg yes -cov_cutoff 0 -tour_bus no
748
+ Version 1.2.08
749
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
750
+ This is free software; see the source for copying conditions. There is NO
751
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
752
+ Compilation settings:
753
+ CATEGORIES = 2
754
+ MAXKMERLENGTH = 255
755
+
756
+ Final graph has 5 nodes and n50 of 435, max 437, total 1206, using 544/544 reads