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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data/spec/data/t/details.txt ADDED
@@ -0,0 +1,5 @@
1
+ IDaa,MrC,US,25
2
+ IDdd,MrsQ,,78
3
+ IDkk,MrN,IN,67
4
+ IDtt,MrsD,,35
5
+ IDxx,MrA,GB,43
data/spec/data/t/details.txt.srt ADDED
@@ -0,0 +1,5 @@
1
+ IDaa,MrC,US,25
2
+ IDdd,MrsQ,,78
3
+ IDkk,MrN,IN,67
4
+ IDtt,MrsD,,35
5
+ IDxx,MrA,GB,43
data/spec/data/t/location.txt ADDED
@@ -0,0 +1,3 @@
1
+ IDkk,IN
2
+ IDxx,GB
3
+ IDaa,US
data/spec/data/t/location.txt.srt ADDED
@@ -0,0 +1,3 @@
1
+ IDaa,US
2
+ IDkk,IN
3
+ IDxx,GB
data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_5000
2
+ TTCCGGGTGTTATGGTGTCGCCGTGTTAACTAATAACTTTGTCCGTGTCAATTGATAACGTAAACTGCCTATCTCACGTACGATCCACTACGCGCACCCGAACTTCGGAGAATTAGCAAAGGAAAGTGTATCAAGCATTTGGTAAAACAGATGGTATTCCTCAATACTGGGCTGACGCGGAAATAGCGCGAACTTATTTATCGGTACGTTAGGTGTATCTACTAAGTAAGATTTCTGATAGTTATCAGGGCGTTCTAAATTTAGTCTCACAGACCCCTGCGTATGCAGCCGCACAGCCAATGCCGATCCTTTCTAAGATAACTCCCGCAGGAAACGTGTAGATCCAAGCTTGTTCCTCGGAGTAGCAAGCTAACTTCAAGCTTACTCAAAGCAGACAAGTTTTAATAGTGCACGCCGTAACGTTCCCCGCAACGAGTATGTGATCCGGATGCGATAAACAAGCTGAGTCACCGTGACGGGGTACTAAGTAATGACATATTGCGAGCATATGCTCCACAAGAAATGTCATACAATAGCACCAATGAGCAAGTTCATATCTGTTATTATTCAGTTACTAAAAATATACTAGTAACTCGACCTGTTAGGTTATCTGCAAATCACTAGCTACTGTATCTCATAAGATTGTCAATCGCGTCATGTCCGCAACCAGGTGCGAACGTCTTGTCCCGGTATCTTGGAATTGAAAGGGACTTGCCAGTCATTAGGACACTAAACCGGATAAACCAGAAAAAAGGAATGCGCGCCGCGGAGGTGCACGATGCCAGCGCAGACAATAACGCCGGACCTTCCAGGGTTCATGGTCAAGTTAAGCGTGCGGCTGCAGCGCAAAATCGTTATCCCACCTCTTATATGCAACACCGTCGACGAAGCGAAGGATTATGAGGGTAGCTCGATAGAATGAAAGCACGTCTTGGGCGGAGGTTCGTTATGATGAAGGCGGTCTGGAGGTACGAGCCGAAAGAGGAGCCGCGTGCGACTCCGACTCGCGTAGTTGAAATCAGGGGGTTTAAACTCTACTTGCCAATTCACCTGATGTGTAACCTGAGGCTATGAGTTGCCAGAGGTCCAATATTTGCTAGTCTGGCTGAGGTTAAGCTAGTAGTTCTAACTACAGGCGGCAGGCCAATTGTGAGCCAACGCACTAGATCACGTGCATACAACCACAACACATAAACTCGCTTTAAAGTGCGGGGTGCCCCCGGTCGAACTAAGCTCTCGTCCACGTTTTGGGGGAAAAGTCCTATGGATCCTGAGACAGCGCGCCTCCACGGAGCAAAAGTTGTTGACCAATAGTCTGACCATAACAACATGTGACTGGGTAGCCCCTGGTCATCCCCCCACATTGCCGATTTGTCAACAGTTGCACTGCCTGGAGGATCATGCGTCAGGATCAAGTCTATCGCCCACGACATATGAATTTCCACTGTCCGTGCGTCGAACCACGACAGTATGTGAGACGTGTCGAAGTCCCCCCCTTAGTGAAACGGCACTTTCTTAACCAAAGATTAAGCGGCGCCTTGGAATGGTTATCCTACGAGGAGTATGTCATACTCACTCTGTTTCTAGAACAAGTCCGTGAGAATTAGGCTGTCGGAGTAGTTTAGATAAGTGTATTTTATCTTCCGAGGCTATGGCTGGTGTGAACAATTCCCCAGACTTCCGAATTTGACTTCCTCAGTTCCGGGGCTCCCCATGACCAAACTAGATGGAATAACCTACATGACCAAACTGTCGCTTCCTGTATTGTGCTCTCAAGACTATATGAGTCGAATTCCAAGGCGCTATATCGCCTATTAAGGCAAGGCAGCCTCTAGCGCTATGCATTTCGTAACGGAATTAACGCCCACACCATCCTCAATTAACGTTAGGTACTCATATCCCCCTCATATTGGGGCCAATACCCCAAGGAGTTCGGACACGATCAACCAGCGGCGTCACCGCCCCCAGTGTGCAACGTTGTGGGGGAACACGAAATATATAGTGTAAAGTTGATCTCCATTGCCCCGCAGACGAATTCGTACGAGAACAATGAGTATGGATAGCTAGACACAAACGTTGCATAAAATTCTTTAACTTAAAGAAAAAACAATCTCAGGCTACAATCTTCGTTCACAACTAACTTACCGGTCCTCCCTCAAAACATCAGGTGGACGCTTCTTCAACTTCCTCCCCATATTATCGGGCGTATGTCTATCAAAGTGCTCCGCTAGCACTCGGGAAGGACTTATGATAACTACTGATGCCACTCGGAGTCGCGTTCACATCGTTCCCTCGGTTAAGAAGCAGAGGGCGTCATTAGCATTCAGCACGATCACCTATCCTAGTCTGATGGGACATAGGTGCTTCAAGCACTCGCACATATTAGATTTGCTGCCGCTTATAGCCAATAAATTGTCTATGATATAACGTTCATAGCCATGTGCGTTACCCTAATGTTGAAGGCGTGGTGTAAAGGCCATCCGACAACGCACTTTCTGGGTGTTTCGGCTTGCTGCAACTCCCATATTCATCCCTCGCGATGTGCCCTTAACGCTGTGTCCTATGAACCGGAAGAGCTCTTGCTTTCCCTGATTAGTTTCGAAGCAGTCGTCAGGACTACCACTCTGTATGGGGGCCTGGAGGAGCTTGGGTACAGGGTACTGTCGAGGGTAAAACTCGTAGGCAAAGGAGCAATTCGCGGACCATTCAGGGCATGCTTCTCCGGCTCCTTAGCGGAGATTAAGTAGACTAAATAGAGAGTAATGATGGGTTTCAATTTGGTTTGCCGATGTTTTGGTGTGTGCTAGCGACTTGCAATCTTCAGTTCACTAAACAGATCGGGTCGCGGACTATACTTTATCCGACGAACAGTTCTCCGCCGTATATACGGGGCGAAGCGTGGCTATCGTGAGCACCAGATACAGAGATAGCGATTGGGGACACATATAAATTCAAATACGTACGGGTAGCTCACAAATGTAGGTCCCCAGGGTGCGTCGTAACCACCAGCGCTAACCGCCCGGGAGTTAGAGAGTCCAGTGGTGTGTGATCAAAGACCCGTTTAGCCGATGCCTACCACACCCGAACGGCAAACAGCGGTGTTCAACTACCGTGGCCGCCGCGTGCTTCCAGTCTTATAGTCCCTGTACCTACGGAGTGATCTACATCGAATAGGTTGTGATTGAACCGCGGCTCTCGGCACCCTAAGGCCTCTTCATTAATACCTCAATTTGGCATGAGGAGCGCTTCGCCATTCTGCTTATACATGTACCGGCTTGGGTGAGGTTGGAGAAAAAGCGACCTGTGGCGCCACGTGATGTCCTCCTAAGAGGCAGAATCCCCTCGCTTGTGGTTTTGCCGTAATCCTGGTGTAAGGTTAGGTGTACAATATCGCTGGTACTCTGATCGCCGAGATCCAGTATCGGCCCTGTGCAAAATCACACCATATTGTATAGTCAGGCCGTACAGAAATGACACCATTCGAGAGAGCCTTTCCACAAGAAATATCGGTTCTACTGTCGAGATTCCCGCCGGACTCGATCTCACGCCCGGAGGTCGGGGAACGTTTCCTTTGTGATTAGCATATGGAGACTATTTATGACTGGCGATGCTGTGGAGTCACTTAGTGGAAAGACACCTAATCGTGAGGGTACTATCAACGTGGCTGAGCCAATACATTGGATGAGTGTCCCCCCTGTCCCCCTTTCTATGTTCGTCCCGGAGGTCCCGATGTGTTTGATAGCCGCGAGGGATGATCGATGAGTACTGCCGCTGTCTTTCTGCGAGGTGCCAGCTTCCAAAAATGTGTCGGAGTCGTATCTTTCTTACGAAGGTTAGAAGTCTGAGCGCTAGATTTCTTAAATTTGCCGAGATAAAGCGCCGTGACTTTAATATGAGGATGGGAGCAACTACCTTCGCGCTCAGCATCCGTACCTTCGTGCGTTACCACAACCCCGAAGGCGTACAGGTAACCGTTCGAATTGACTACCCAAGGGCCCGGAAGTTAAATAGTAGGTTAGTGCAATGTGCGACTACTGTGGGTGTAAGTATATAATCGCCGGGACGTACAACCCTGGCAGCTTGTAGTCCAATTTCGCACATGTCGGTATAATTCTCGCTTAATCAGCATCATGGAGATCCCTTCGAGGCCAAGGGCCTAGAGAAACTAACGCGTAAACTACGCACTCTAAGGTACAGGGGTGAATCCGTAGCGACTACATTATCGCTGAAACCTCGGATCGTCGCTTTTTTCCAATCCTCAGGCGGCGAAACTTCGTAAATTGTACCAACCTGTGGCCGTGGCTAGGGTCGGTAAGATAGCGGGGAAACATGGTAAGTTACGATCGGGATGTCTGTAAGAACCAACCACGGACGCGACCGAAACCCCTACGCCATTAAAATCGGTTCTAATCCAGATTTATTCTATAATGCGCCTGTTGATCGTCGGCGGAACGAGCACGGCTGATCGACGTAGTACTCGCTTAGGTGCCCTCGGCCGTCCCCAACTTGTTTTATAGTTGTCTAAATTCTCCGTCTAGGACGTGGCCATCCGAGAGTTTTTACAACGAGAATTAGGAAACTATCGTCGCCGATTCCTTACCCTTATTGGAATGATGGGGCCGGGCTATAGTATCAGGACAGACCTGTTGACAATTAATATCTACTAGGATTGAAGCGACAGAACTCGGGTTATGACTTAACTATGTCTTCTTTATAATGACGAGACCTCAATTTGGGCGTAATGTGAGGAGCATAAGGATGTTCGTCACAAAAACAGTATGTCCGTCACACATATTCCTTATGGGTGGGTAAGCGGCTAAAATGTCTCGATCACAAACAAAGAACTGGATATCGGGGTGTATTACGGGGGGTATGCAATGTAAGCGCTGAGTAATCGCAAGAGGCTTAAAATGACGAATCTAAGTTCATTGCCTACCCTTAACGAGTATGGCTAATCGGTAGCCCTTCGCTGATGACTAAAACCTAAGCGCCGCCACAGA
data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa ADDED
@@ -0,0 +1,6 @@
1
+ >random_sequence_length_5000_chopped_1-600_then_N_then_chopped_700-2000
2
+ TTCCGGGTGTTATGGTGTCGCCGTGTTAACTAATAACTTTGTCCGTGTCAATTGATAACGTAAACTGCCTATCTCACGTACGATCCACTACGCGCACCCGAACTTCGGAGAATTAGCAAAGGAAAGTGTATCAAGCATTTGGTAAAACAGATGGTATTCCTCAATACTGGGCTGACGCGGAAATAGCGCGAACTTATTTATCGGTACGTTAGGTGTATCTACTAAGTAAGATTTCTGATAGTTATCAGGGCGTTCTAAATTTAGTCTCACAGACCCCTGCGTATGCAGCCGCACAGCCAATGCCGATCCTTTCTAAGATAACTCCCGCAGGAAACGTGTAGATCCAAGCTTGTTCCTCGGAGTAGCAAGCTAACTTCAAGCTTACTCAAAGCAGACAAGTTTTAATAGTGCACGCCGTAACGTTCCCCGCAACGAGTATGTGATCCGGATGCGATAAACAAGCTGAGTCACCGTGACGGGGTACTAAGTAATGACATATTGCGAGCATATGCTCCACAAGAAATGTCATACAATAGCACCAATGAGCAAGTTCATATCTGTTATTATTCAGTTACTAAAAATATACTAGTAACTCGACCT
3
+ NNNNNN
4
+ ATTGAAAGGGACTTGCCAGTCATTAGGACACTAAACCGGATAAACCAGAAAAAAGGAATGCGCGCCGCGGAGGTGCACGATGCCAGCGCAGACAATAACGCCGGACCTTCCAGGGTTCATGGTCAAGTTAAGCGTGCGGCTGCAGCGCAAAATCGTTATCCCACCTCTTATATGCAACACCGTCGACGAAGCGAAGGATTATGAGGGTAGCTCGATAGAATGAAAGCACGTCTTGGGCGGAGGTTCGTTATGATGAAGGCGGTCTGGAGGTACGAGCCGAAAGAGGAGCCGCGTGCGACTCCGACTCGCGTAGTTGAAATCAGGGGGTTTAAACTCTACTTGCCAATTCACCTGATGTGTAACCTGAGGCTATGAGTTGCCAGAGGTCCAATATTTGCTAGTCTGGCTGAGGTTAAGCTAGTAGTTCTAACTACAGGCGGCAGGCCAATTGTGAGCCAACGCACTAGATCACGTGCATACAACCACAACACATAAACTCGCTTTAAAGTGCGGGGTGCCCCCGGTCGAACTAAGCTCTCGTCCACGTTTTGGGGGAAAAGTCCTATGGATCCTGAGACAGCGCGCCTCCACGGAGCAAAAGTTGTTGACCAATAGTCTGACCATAACAACATGTGACTGGGTAGCCCCTGGTCATCCCCCCACATTGCCGATTTGTCAACAGTTGCACTGCCTGGAGGATCATGCGTCAGGATCAAGTCTATCGCCCACGACATATGAATTTCCACTGTCCGTGCGTCGAACCACGACAGTATGTGAGACGTGTCGAAGTCCCCCCCTTAGTGAAACGGCACTTTCTTAACCAAAGATTAAGCGGCGCCTTGGAATGGTTATCCTACGAGGAGTATGTCATACTCACTCTGTTTCTAGAACAAGTCCGTGAGAATTAGGCTGTCGGAGTAGTTTAGATAAGTGTATTTTATCTTCCGAGGCTATGGCTGGTGTGAACAATTCCCCAGACTTCCGAATTTGACTTCCTCAGTTCCGGGGCTCCCCATGACCAAACTAGATGGAATAACCTACATGACCAAACTGTCGCTTCCTGTATTGTGCTCTCAAGACTATATGAGTCGAATTCCAAGGCGCTATATCGCCTATTAAGGCAAGGCAGCCTCTAGCGCTATGCATTTCGTAACGGAATTAACGCCCACACCATCCTCAATTAACGTTAGGTACTCATATCCCCCTCATATTGGGGCCAATACCCCAAGGAGTTCGGACACGATCAACCAGCGGCGTCACCGCCCCCAGTGTGCAACGTTGTGGGGGAACACGAAATATAT
5
+ >random_sequence_length_5000_chopped_3000-5000$
6
+ TAACCACCAGCGCTAACCGCCCGGGAGTTAGAGAGTCCAGTGGTGTGTGATCAAAGACCCGTTTAGCCGATGCCTACCACACCCGAACGGCAAACAGCGGTGTTCAACTACCGTGGCCGCCGCGTGCTTCCAGTCTTATAGTCCCTGTACCTACGGAGTGATCTACATCGAATAGGTTGTGATTGAACCGCGGCTCTCGGCACCCTAAGGCCTCTTCATTAATACCTCAATTTGGCATGAGGAGCGCTTCGCCATTCTGCTTATACATGTACCGGCTTGGGTGAGGTTGGAGAAAAAGCGACCTGTGGCGCCACGTGATGTCCTCCTAAGAGGCAGAATCCCCTCGCTTGTGGTTTTGCCGTAATCCTGGTGTAAGGTTAGGTGTACAATATCGCTGGTACTCTGATCGCCGAGATCCAGTATCGGCCCTGTGCAAAATCACACCATATTGTATAGTCAGGCCGTACAGAAATGACACCATTCGAGAGAGCCTTTCCACAAGAAATATCGGTTCTACTGTCGAGATTCCCGCCGGACTCGATCTCACGCCCGGAGGTCGGGGAACGTTTCCTTTGTGATTAGCATATGGAGACTATTTATGACTGGCGATGCTGTGGAGTCACTTAGTGGAAAGACACCTAATCGTGAGGGTACTATCAACGTGGCTGAGCCAATACATTGGATGAGTGTCCCCCCTGTCCCCCTTTCTATGTTCGTCCCGGAGGTCCCGATGTGTTTGATAGCCGCGAGGGATGATCGATGAGTACTGCCGCTGTCTTTCTGCGAGGTGCCAGCTTCCAAAAATGTGTCGGAGTCGTATCTTTCTTACGAAGGTTAGAAGTCTGAGCGCTAGATTTCTTAAATTTGCCGAGATAAAGCGCCGTGACTTTAATATGAGGATGGGAGCAACTACCTTCGCGCTCAGCATCCGTACCTTCGTGCGTTACCACAACCCCGAAGGCGTACAGGTAACCGTTCGAATTGACTACCCAAGGGCCCGGAAGTTAAATAGTAGGTTAGTGCAATGTGCGACTACTGTGGGTGTAAGTATATAATCGCCGGGACGTACAACCCTGGCAGCTTGTAGTCCAATTTCGCACATGTCGGTATAATTCTCGCTTAATCAGCATCATGGAGATCCCTTCGAGGCCAAGGGCCTAGAGAAACTAACGCGTAAACTACGCACTCTAAGGTACAGGGGTGAATCCGTAGCGACTACATTATCGCTGAAACCTCGGATCGTCGCTTTTTTCCAATCCTCAGGCGGCGAAACTTCGTAAATTGTACCAACCTGTGGCCGTGGCTAGGGTCGGTAAGATAGCGGGGAAACATGGTAAGTTACGATCGGGATGTCTGTAAGAACCAACCACGGACGCGACCGAAACCCCTACGCCATTAAAATCGGTTCTAATCCAGATTTATTCTATAATGCGCCTGTTGATCGTCGGCGGAACGAGCACGGCTGATCGACGTAGTACTCGCTTAGGTGCCCTCGGCCGTCCCCAACTTGTTTTATAGTTGTCTAAATTCTCCGTCTAGGACGTGGCCATCCGAGAGTTTTTACAACGAGAATTAGGAAACTATCGTCGCCGATTCCTTACCCTTATTGGAATGATGGGGCCGGGCTATAGTATCAGGACAGACCTGTTGACAATTAATATCTACTAGGATTGAAGCGACAGAACTCGGGTTATGACTTAACTATGTCTTCTTTATAATGACGAGACCTCAATTTGGGCGTAATGTGAGGAGCATAAGGATGTTCGTCACAAAAACAGTATGTCCGTCACACATATTCCTTATGGGTGGGTAAGCGGCTAAAATGTCTCGATCACAAACAAAGAACTGGATATCGGGGTGTATTACGGGGGGTATGCAATGTAAGCGCTGAGTAATCGCAAGAGGCTTAAAATGACGAATCTAAGTTCATTGCCTACCCTTAACGAGTATGGCTAATCGGTAGCCCTTCGCTGATGACTAAAACCTAAGCGCCGCCACAGA
data/spec/data/tweak/2_second_genome/answer2.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_3000
2
+ AACTTATCAACCCACAGGATGTGCGAAGCAGGATACGTTTGCGGAGCTGAAGCGGACTCCGCGCGGCCGGCAGATGTAGATGGCCTCGGCGCCCAAGTTTGGAATATGGTCAGTCCAACAAGAAAGTTTTTAAGCGCGAAGATTATGTCGCGAACTTCCTCCGCAGCGTCAGTGGTATAAGAAGACAGCGCGGGAGTTGAGGAGAACAGGAGATACCTACCGGGACACATCACCAGGCGCGTAGCTGGGCAGGTCAGCCGCTGGAGTGGGTTTATCATCTAAAACGAGGCTCCGGCATTTCGGTTAATCATAGCTCGGGGCTAGGTTGATTGTCGGAGGTCTTCTGTTCGGTCCGGCGTTAGTAATAAGCTGCCTCGGATATTGACTTCCTGGATTAGCCGATATATCTTACAGGCAGGACTTTATCAGCGGTTACCAACGCAAAATACTTTAAGAAATGGCTGACCCACGCCCTAACGCGTTACTTGGGTACACGTGTTGAAAAGCCGTCCAATCGCCCTCATATCGAATACTGGGTTCCTACATATGTGGGTGGCACGTGACCTCTCGAAGTCGCTATTGGTTAAGTACTACTATACTTCCAAATTGAACTCTCTCGAAGCTTAATCGCCATCTGCTATCGTGCCCCCCTGCTTGCGTGACCAAACGCCTAGGGATGAAATTAGAAATAAACGAATTCTCAGGGCCAAACTCTAACGACCAGCCGAGGCAGCACGCTGTGATCTTCGTGTGTTCACCATGACTAGGACACAAGGGCCGGAGCGGGACCGGCCATGCAATACTGGCCCGGCCTCTATCAAAGGTTTCTGGGCCATGGTGATACGGGTGTGTGTAGCCGATTCATTTGCTAGTCCTCAATGCCATGCGCGGAGCCTGAGTAAGGCCGTTCGTATCTGTCCACTAATCACGGGTGATTACCACCCGGGCACTAGCCGCGGTAATATCTACCTACAGCGAGAAGCCCCTCGAAGATTATCGCGACGACGTGCTGCCCCTGGGCATCCACTTGTCACTCCAGAACTGTGGTAGGTTATCCGGCAATATATAATTTTAGATACGACTAGACCGTACAGATCATGTTAATGTTACCGTCACGTCCTCTATTGGGAACATCGCACGACACCCAGCTGGACCCCGCCACCGTTACTGCGGAACTCCAGTCTTTTAGCTTGCCGCAGTGATGGACAGTACAAGTCGCAGGTGCGGGCCTGTCAGCCTCACCTTTTTCGCAACGGCAAGTTATGAGGGAATCTTGATCAAGAGGTTAAGATGAAATGCGAAGTGATTCGTGAATGTCTTCGCGTACAACCGCGCTGAGGATATAGATAGAATAACGCAATTCACTCGTCACCAGGATCCCTATAAGGGTTAAGACCTCTTACGGTTTAAAGTAATCTGTTGATGCTGCATTGTCATGACTGGGTGATTTTTAGATCCCTATAAGGACTCCTCGTATCTATAGACGGCGCCTATAAATACCACAGGCTACCCTTTGAGGTGTGACTCCCCGTATTTGAAGTGGTCCACTGCTGAATTATGGATTTTTCGAATCTACAGGATGACTACGGTCATCCACGGACCTGGCGAGTGGATTTATGCTTCTGTAAGCGATAAGGATTCGGTGGGTATTAGATGCGGCGCGCATGGTGTCCATCCTGGCCCGCCAAGCTAACGTGCCGGCGTTACGGAGTATGACGAGCATTTAGCGACGCTTCTGTCAAGGAGCCGGAAGTGGGAGTAGGCTGTTTGCCAGCGCGGGTCCCCATGCATCTCACCTGAGTACCCTTCGGACAACTGCCTCGTAGAGATTAATCTGGCAAACCTAGAGATATGCCAAGCTTTTTCACTGCCATTATAAATAAGGCTTGGGAGTTGAGTAACATATGAAAGCATCGTTCCTTCACCAGAGGTGAATTTACCACGCAAACTTGGTCTGCGTTACTTGCAAAACTGCAGGAACGGCTAAAAAGCACTGGGGCTGATCGAGTACGTTCTATGTCATGTGCCCCTTGTAAGTGCTGATATATATCCCTCTAATGGAAAGGCTACTAGGACTGCGCAAATCGCACGCTCCGTCGCACGGTAGATTCAGGCCTGATGAACGTTAATATAGGTTTTCACTCCATGTTGCGAATCTTCGGTCTCTAGACCGACTACCTTCATGACTCGGGGAAACGTAGGAAGCCGGAGCATGATGTTGTGCACTAACTCTCCCTAATCACCATGTCGAGATTAACAAGCAAAGTTCCCTGGGGGTTCCTAGCCGCACATCCCACACTTAGGTGTTGCCTCTACGTCTGAGGGACAAAAAACATAGGCCTGGTGCATGTACTAAGGATTACCTTTACTATGAGCTTGATAGGCACTTCGGCCGATCGAGGTTTAACCGGCGCGCTAGCAAAAGGTGGCGTAGTTGCGCAATTGGTCGACTTGGGCGTCTTACAACTGCCGGTTCCTCAGTAGTTCTTTCTCGTATAGGCATGTAATCACGCCACACCCCGCCACTAAGGGGTAGCCGGTCGCGATTGTAAGTGTACCGCATTTAGGTGTCAGGCGAATCGGACCTCTCCTTCGGCGTGTAAAACTATCGCTGACCCCAATAGTATTCCCGCCCCTAATTGGCTCCTCGCCCCGATCCAGGGGCGATTTGTTTGACTACACCGCTTCCACCAATACATGCACAAACTCGTAAGATTGTAGAAACATGCAGTATTTGTGCGACACCGAGCATTATTTAGGACACACCGGCCGGTGCATACCCCAACGGTGAGGCTCTCTATCGCGTATCCGACTTTGTAACTATGGCGTCCTATAACCACTAGTTGAAGTAATTCAGCCTATCTAAAGCCGGTTTGTGCGGTGTGTGACATGTTGCCATTAGACAGACTAACTCCGTTACTCAATGAAGAACTAGCGTCAAGCCAATGCGATAAGATGAACACTATGGAAGAGCAGGTCAAGTGGCTAGGCTGCGACGTG
data/spec/data/tweak/3_variant/answer.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_1000
2
+ AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTACACTCGTACCATGCATACTGGCGCGGGTGACGTTGGCCCGACGCGGACGACGTTTGTTCAGATACCGTGCAGTTACAATCCCATGTAAGCGATTCCCGGGGTTGAAATGCTTCCCGGCATACTCTGACGAAGATGCTCGAGTTCCAAGGTCAATCCGTAGCATTCGGGGATATGCGTCTGCTTCAGACAGGTCCTCCTCTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
data/spec/data/tweak/3_variant/lesser_answer.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_1000_4G_at_position485
2
+ AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTACACTCGTACCATGCATACTGGCGCGGGTGACGTTGGCCCGACGCGGACGACGTTTGTTCAGATACCGTGCAGTTACAATCCCGGGGGATGTAAGCGATTCCCGGGGTTGAAATGCTTCCCGGCATACTCTGACGAAGATGCTCGAGTTCCAAGGTCAATCCGTAGCATTCGGGGATATGCGTCTGCTTCAGACAGGTCCTCCTCTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
data/spec/data/tweak/3_variant/with_gaps.fa ADDED
@@ -0,0 +1,2 @@
1
+ >random_sequence_length_with_gaps
2
+ AATGCACATCGACTATATTTAGGCGTCAGGCCTCGCGTCTGAGGGGATAGCACCATTATAGATGGAAAGTGACTGCTGATACGGAGTGCTGAGTTGTAGTGCGAGAGGCAGCCAAGTGTCGAGAATGTCGGAACGTTGTGACATAGTCGATGTACGTTCATCGAAGCAAGAGCCTAAAGACCGTCCGCTATGACTATTGGGCGAGGACCGGCCGAATGTTAAACATCCGATACAGCACGTACAAGGTCGCTCACCGAAGGCGCAAGATATTTTCCGCGATTGAAAAGTAACCACTTCCACGCAATTGAGGCGAAACCAACTAGCAGCTGCTCCCACTGTCGTCCATTGCCGTCAGGGGGATAAGCTCCATGCTACGTGGAACTATTGGGACCAGGTCGGTACACTCGTACCATGCATACTGGCGCGGGTGACGTTGGCCCGACGCGGACGACGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGAAGATGCTCGAGTTCCAAGGTCAATCCGTAGCATTCGGGGATATGCGTCTGCTTCAGACAGGTCCTCCTCTCATTCACCGCTAGCGGGTCGTAAGGGGGAGTAAAGTTCGTGTCCCCAGGATGGGAGGAGCACACTCATCCCTGAGGGAAGCTAGGCCCAATCTGGACTTCCGAGCATCATACAATTTGAAAGGCCTGCAGGTCCCCAAGTCCGCCTCTGCCTGTGTTATAAAGTGGCCTACTATGCAGGACAGGGTCAAAAGGGCCCAGTCCGGGAACCAGAACCTTGAGGCCCCCGTGGCGTACGCCCCAAGCCCGCCTCCAGGGCGGCGCTGTTTTATTCTGACGGCTTTGATCGGCGAACACTGCCTGGTTAGGCACTGAATATAAAAATTCAGACACTGCCCTCCACTGAGTGACCAATCGAACATTCGTTGAGCATTGGCGCTTGTTTTCCCTTAGATTCTACC
data/spec/data/velvet_test_trails/Assem/Graph ADDED
@@ -0,0 +1,17 @@
1
+ 4 5 31 1
2
+ NODE 1 228 1140 1140 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3
+ AATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
4
+ TTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG
5
+ NODE 2 29 58 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6
+ GTTTAAAAGAAGGAGATTACTTTATAAAA
7
+ AGTAAATATAACTCGTCCATTTTTATCAG
8
+ NODE 3 38 114 114 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9
+ CGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
10
+ CCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAG
11
+ NODE 4 224 1120 1120 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12
+ TTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
13
+ GAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
14
+ ARC 1 2 2
15
+ ARC 1 3 3
16
+ ARC 2 -4 2
17
+ ARC 3 -4 3
data/spec/data/velvet_test_trails/Assem/Graph2 ADDED
@@ -0,0 +1,40 @@
1
+ 4 5 31 1
2
+ NODE 1 228 1140 1140 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3
+ AATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
4
+ TTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG
5
+ NODE 2 29 58 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6
+ GTTTAAAAGAAGGAGATTACTTTATAAAA
7
+ AGTAAATATAACTCGTCCATTTTTATCAG
8
+ NODE 3 38 114 114 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9
+ CGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
10
+ CCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAG
11
+ NODE 4 224 1120 1120 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12
+ TTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
13
+ GAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
14
+ ARC 1 2 2
15
+ ARC 1 3 3
16
+ ARC 2 -4 2
17
+ ARC 3 -4 3
18
+ NR -4 3
19
+ 1 0 257
20
+ 2 0 266
21
+ 4 0 266
22
+ NR -3 1
23
+ 5 0 224
24
+ NR -2 1
25
+ 3 0 224
26
+ NR -1 2
27
+ 3 0 253
28
+ 5 0 262
29
+ NR 1 3
30
+ 1 0 0
31
+ 2 0 0
32
+ 4 0 0
33
+ NR 2 1
34
+ 1 0 228
35
+ NR 3 2
36
+ 2 0 228
37
+ 4 0 228
38
+ NR 4 2
39
+ 3 0 0
40
+ 5 0 0
data/spec/data/velvet_test_trails/Assem/LastGraph ADDED
@@ -0,0 +1,40 @@
1
+ 4 5 31 1
2
+ NODE 1 228 1140 1140 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3
+ AATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
4
+ TTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG
5
+ NODE 2 29 58 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6
+ GTTTAAAAGAAGGAGATTACTTTATAAAA
7
+ AGTAAATATAACTCGTCCATTTTTATCAG
8
+ NODE 3 38 114 114 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9
+ CGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
10
+ CCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAG
11
+ NODE 4 224 1120 1120 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12
+ TTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
13
+ GAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
14
+ ARC 1 2 2
15
+ ARC 1 3 3
16
+ ARC 2 -4 2
17
+ ARC 3 -4 3
18
+ NR -4 3
19
+ 1 0 257
20
+ 2 0 266
21
+ 4 0 266
22
+ NR -3 1
23
+ 5 0 224
24
+ NR -2 1
25
+ 3 0 224
26
+ NR -1 2
27
+ 3 0 253
28
+ 5 0 262
29
+ NR 1 3
30
+ 1 0 0
31
+ 2 0 0
32
+ 4 0 0
33
+ NR 2 1
34
+ 1 0 228
35
+ NR 3 2
36
+ 2 0 228
37
+ 4 0 228
38
+ NR 4 2
39
+ 3 0 0
40
+ 5 0 0
data/spec/data/velvet_test_trails/Assem/Log ADDED
@@ -0,0 +1,35 @@
1
+ Tue Jun 4 10:31:32 2013
2
+ velveth Assem 31 -short reads.fa
3
+ Version 1.2.07
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 = 30
9
+ MAXKMERLENGTH = 95
10
+ OPENMP
11
+
12
+ Tue Jun 4 10:31:36 2013
13
+ velvetg Assem
14
+ Version 1.2.07
15
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
16
+ This is free software; see the source for copying conditions. There is NO
17
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
18
+ Compilation settings:
19
+ CATEGORIES = 30
20
+ MAXKMERLENGTH = 95
21
+ OPENMP
22
+
23
+ Final graph has 4 nodes and n50 of 224, max 228, total 519, using 0/5 reads
24
+ Tue Jun 4 10:33:55 2013
25
+ velvetg Assem -read_trkg yes
26
+ Version 1.2.07
27
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
28
+ This is free software; see the source for copying conditions. There is NO
29
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
30
+ Compilation settings:
31
+ CATEGORIES = 30
32
+ MAXKMERLENGTH = 95
33
+ OPENMP
34
+
35
+ Final graph has 4 nodes and n50 of 224, max 228, total 519, using 5/5 reads
data/spec/data/velvet_test_trails/Assem/PreGraph ADDED
@@ -0,0 +1,9 @@
1
+ 4 5 31 1
2
+ NODE 1 228
3
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
4
+ NODE 2 29
5
+ CTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAA
6
+ NODE 3 38
7
+ CTGATAAAAATGGACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
8
+ NODE 4 224
9
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
data/spec/data/velvet_test_trails/Assem/Roadmaps ADDED
@@ -0,0 +1,89 @@
1
+ 5 0 31 1
2
+ ROADMAP 1
3
+ 2 0 0 4
4
+ 4 0 0 17
5
+ 2 0 4 11
6
+ 4 0 17 30
7
+ 4 8 30 34
8
+ 2 8 11 19
9
+ 4 8 34 40
10
+ 2 8 19 27
11
+ 4 12 40 61
12
+ 2 14 27 56
13
+ 4 14 61 80
14
+ 2 14 56 62
15
+ 4 14 80 93
16
+ 2 14 62 92
17
+ 4 14 93 119
18
+ 2 14 92 95
19
+ -3 24 242 -1
20
+ ROADMAP 2
21
+ 4 4 0 17
22
+ 4 11 17 30
23
+ 1 11 0 8
24
+ 4 11 30 34
25
+ 4 19 34 40
26
+ 1 27 8 12
27
+ 4 27 40 61
28
+ 1 27 12 14
29
+ 4 56 61 80
30
+ 4 62 80 93
31
+ 4 92 93 119
32
+ -5 110 22 -1
33
+ -3 110 223 -1
34
+ ROADMAP 3
35
+ -1 243 23 13
36
+ -2 243 94 91
37
+ -4 243 118 92
38
+ -2 243 91 61
39
+ -4 243 92 79
40
+ -2 243 61 55
41
+ -4 243 79 60
42
+ -2 243 55 26
43
+ -1 243 13 11
44
+ -4 243 60 39
45
+ -1 243 11 7
46
+ -2 243 26 18
47
+ -4 243 39 33
48
+ -2 243 18 10
49
+ -4 243 33 29
50
+ -1 243 7 -1
51
+ -4 243 29 16
52
+ -2 243 10 3
53
+ -4 243 16 -1
54
+ -2 243 3 -1
55
+ ROADMAP 4
56
+ 2 0 0 4
57
+ 2 17 4 11
58
+ 1 30 0 8
59
+ 2 34 11 19
60
+ 2 40 19 27
61
+ 1 40 8 12
62
+ 1 61 12 14
63
+ 2 61 27 56
64
+ 2 80 56 62
65
+ 2 93 62 92
66
+ 2 119 92 110
67
+ -5 119 22 -1
68
+ -3 119 223 -1
69
+ ROADMAP 5
70
+ 3 0 0 224
71
+ -2 23 109 91
72
+ -4 23 118 92
73
+ -2 23 91 61
74
+ -4 23 92 79
75
+ -2 23 61 55
76
+ -4 23 79 60
77
+ -2 23 55 26
78
+ -1 23 13 11
79
+ -4 23 60 39
80
+ -1 23 11 7
81
+ -2 23 26 18
82
+ -4 23 39 33
83
+ -2 23 18 10
84
+ -4 23 33 29
85
+ -1 23 7 -1
86
+ -4 23 29 16
87
+ -2 23 10 3
88
+ -4 23 16 -1
89
+ -2 23 3 -1
data/spec/data/velvet_test_trails/Assem/Sequences ADDED
@@ -0,0 +1,50 @@
1
+ >1 1 0
2
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
3
+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
4
+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
5
+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
6
+ GACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTC
7
+ CTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATG
8
+ ATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAA
9
+ GTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAA
10
+ ACTATGCTGGTATTTCACTTCCAGGTACAGG
11
+ >2 2 0
12
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
13
+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
14
+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
15
+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
16
+ GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
17
+ AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
18
+ AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
19
+ AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
20
+ AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
21
+ >NODE_1_length_481_cov_1.471933_revcom 3 0
22
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
23
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
24
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
25
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
26
+ CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
27
+ AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTACCATTTTTA
28
+ TCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAATCTACTTTT
29
+ TTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGAT
30
+ TCTAAATCGTGATCTTTGGTAGAGATAAGTG
31
+ >3 4 0
32
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
33
+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
34
+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
35
+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
36
+ GACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAG
37
+ AAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTC
38
+ AAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATG
39
+ AAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTAC
40
+ AAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
41
+ >3_revcom 5 0
42
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
43
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
44
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
45
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
46
+ CCTTCTTTTAAACCCCCCCCCGCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCC
47
+ TTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACATTA
48
+ CCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTATTGAAATATTTTCTGAA
49
+ TCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTA
50
+ TAGTTTGATTCTAAATCGTGATCTTTGGTAGAGATAAGTG
data/spec/data/velvet_test_trails/Assem/a.svg ADDED
@@ -0,0 +1,53 @@
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+ <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
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+ <g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 223.09)">
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+ <polygon fill="white" stroke="white" points="-4,4 -4,-223.09 431.698,-223.09 431.698,4 -4,4"/>
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+ <g id="node1" class="node"><title>1</title>
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+ <text text-anchor="middle" x="128.039" y="-83.4418" font-family="Times,serif" font-size="14.00">n1_length228_coverage5</text>
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+ </g>
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+ <!-- 2 -->
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+ <g id="node2" class="node"><title>2</title>
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+ <ellipse fill="none" stroke="black" cx="305.509" cy="-131.142" rx="122.379" ry="18"/>
20
+ <text text-anchor="middle" x="305.509" y="-127.442" font-family="Times,serif" font-size="14.00">n2_length29_coverage2</text>
21
+ </g>
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+ <!-- 1&#45;&gt;2 -->
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+ <g id="edge1" class="edge"><title>1&#45;&gt;2</title>
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+ <path fill="none" stroke="black" d="M191.358,-102.84C204.815,-106.177 219.124,-109.724 232.897,-113.139"/>
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+ <polygon fill="black" stroke="black" points="232.262,-116.588 242.811,-115.597 233.947,-109.793 232.262,-116.588"/>
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+ </g>
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+ <!-- 3 -->
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+ <g id="node3" class="node"><title>3</title>
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+ <ellipse fill="none" stroke="black" cx="217.72" cy="-18" rx="122.379" ry="18"/>
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+ <text text-anchor="middle" x="217.72" y="-14.3" font-family="Times,serif" font-size="14.00">n3_length38_coverage3</text>
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+ </g>
32
+ <!-- 1&#45;&gt;3 -->
33
+ <g id="edge2" class="edge"><title>1&#45;&gt;3</title>
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+ <path fill="none" stroke="black" d="M151.134,-69.3361C161.909,-61.0292 174.893,-51.0183 186.524,-42.0511"/>
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+ <polygon fill="black" stroke="black" points="188.921,-44.623 194.703,-35.7454 184.647,-39.0793 188.921,-44.623"/>
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+ <g id="node4" class="node"><title>4</title>
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+ <text text-anchor="middle" x="216.385" y="-197.39" font-family="Times,serif" font-size="14.00">n4_length224_coverage5</text>
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+ </g>
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+ <!-- 2&#45;&gt;4 -->
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+ <g id="edge3" class="edge"><title>2&#45;&gt;4</title>
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+ <path fill="none" stroke="black" d="M282.557,-149.155C270.602,-158.538 255.909,-170.07 243.407,-179.882"/>
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+ <polyline fill="none" stroke="black" points="239.258,-183.138 243.192,-180.051 "/>
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+ </g>
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+ <!-- 3&#45;&gt;4 -->
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+ <g id="edge4" class="edge"><title>3&#45;&gt;4</title>
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+ <path fill="none" stroke="black" d="M217.587,-36.2248C217.343,-69.6744 216.824,-140.814 216.555,-177.747"/>
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+ <polyline fill="none" stroke="black" points="216.517,-182.939 216.554,-177.939 "/>
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+ </g>
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data/spec/data/velvet_test_trails/Assem/contigs.fa ADDED
@@ -0,0 +1,15 @@
1
+ >NODE_1_length_228_cov_5.000000
2
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
3
+ TAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAG
4
+ ATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATA
5
+ CGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATG
6
+ GACGAGTTATATTTACTG
7
+ >NODE_3_length_38_cov_3.000000
8
+ CTGATAAAAATGGACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACT
9
+ TTATAAAA
10
+ >NODE_4_length_224_cov_5.000000
11
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
12
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
13
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
14
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
15
+ CCTTCTTTTAAACC
data/spec/data/velvet_test_trails/Assem/stats.txt ADDED
@@ -0,0 +1,5 @@
1
+ ID lgth out in long_cov short1_cov short1_Ocov short2_cov short2_Ocov short3_cov short3_Ocov short4_cov short4_Ocov short5_cov short5_Ocov short6_cov short6_Ocov short7_cov short7_Ocov short8_cov short8_Ocov short9_cov short9_Ocov short10_cov short10_Ocov short11_cov short11_Ocov short12_cov short12_Ocov short13_cov short13_Ocov short14_cov short14_Ocov short15_cov short15_Ocov short16_cov short16_Ocov short17_cov short17_Ocov short18_cov short18_Ocov short19_cov short19_Ocov short20_cov short20_Ocov short21_cov short21_Ocov short22_cov short22_Ocov short23_cov short23_Ocov short24_cov short24_Ocov short25_cov short25_Ocov short26_cov short26_Ocov short27_cov short27_Ocov short28_cov short28_Ocov short29_cov short29_Ocov short30_cov short30_Ocov long_nb short1_nb short2_nb short3_nb short4_nb short5_nb short6_nb short7_nb short8_nb short9_nb short10_nb short11_nb short12_nb short13_nb short14_nb short15_nb short16_nb short17_nb short18_nb short19_nb short20_nb short21_nb short22_nb short23_nb short24_nb short25_nb short26_nb short27_nb short28_nb short29_nb short30_nb
2
+ 1 228 2 0 0.000000 5.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3
+ 2 29 1 1 0.000000 2.000000 2.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4
+ 3 38 1 1 0.000000 3.000000 3.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5
+ 4 224 2 0 0.000000 5.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
data/spec/data/velvet_test_trails/node_fwds.fa ADDED
@@ -0,0 +1,8 @@
1
+ >1
2
+ AATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
3
+ >2
4
+ GTTTAAAAGAAGGAGATTACTTTATAAAA
5
+ >3
6
+ CGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
7
+ >4
8
+ TTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
data/spec/data/velvet_test_trails/node_seqs.fa ADDED
@@ -0,0 +1,9 @@
1
+ >1
2
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTG
3
+ >2
4
+ CTGATAAAAATGGACGAGTTATATTTACTA
5
+ >3
6
+ CTGATAAAAATGGACGAGTTATATTTACTGCGGGGGGGGGTTTAAAAGAAGGAGATTACTTTATAAAA
7
+ >4
8
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTGCCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGATATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTTACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCTCCTTCTTTTAAACC
9
+