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/gapfilling/1/velvetAssembly/Log ADDED
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+ Mon Sep 16 18:24:55 2013
2
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-5665-10b1dyo -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:24:55 2013
12
+ velvetg velvetAssembly -read_trkg yes
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 27, max 27, total 27, using 0/6 reads
22
+ Mon Sep 16 18:26:26 2013
23
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-5684-x1dxgz -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:26:26 2013
33
+ velvetg velvetAssembly -read_trkg yes
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 27, max 27, total 27, using 0/7 reads
43
+ Mon Sep 16 18:31:38 2013
44
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-5907-12xqs92 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:31:38 2013
54
+ velvetg velvetAssembly -read_trkg yes
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 6 nodes and n50 of 289, max 289, total 335, using 4/14 reads
64
+ Mon Sep 16 18:33:53 2013
65
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-5937-rg1dkm -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:33:53 2013
75
+ velvetg velvetAssembly -read_trkg yes
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 6 nodes and n50 of 289, max 289, total 335, using 4/14 reads
85
+ Mon Sep 16 18:35:37 2013
86
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-5980-49ybv5 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:35:37 2013
96
+ velvetg velvetAssembly -read_trkg yes
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 6 nodes and n50 of 289, max 289, total 335, using 14/49 reads
106
+ Mon Sep 16 18:36:21 2013
107
+ velveth velvetAssembly 73 -short /tmp/anchors.fa20130916-6001-1vt3ga1 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:36:21 2013
117
+ velvetg velvetAssembly -read_trkg yes
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 6 nodes and n50 of 289, max 289, total 335, using 22/77 reads
127
+ Mon Sep 16 18:36:46 2013
128
+ velveth velvetAssembly 33 -short /tmp/anchors.fa20130916-6016-vupn28 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 18:36:46 2013
138
+ velvetg velvetAssembly -read_trkg yes
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 4 nodes and n50 of 323, max 323, total 472, using 77/77 reads
148
+ Mon Sep 16 19:08:03 2013
149
+ velveth velvetAssembly 33 -short /tmp/anchors.fa20130916-6393-zzzm25 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 19:08:04 2013
159
+ velvetg velvetAssembly -read_trkg yes
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 3 nodes and n50 of 323, max 323, total 503, using 79/79 reads
169
+ Mon Sep 16 19:15:44 2013
170
+ velveth velvetAssembly 33 -short /tmp/anchors.fa20130916-6447-1scyu58 -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 19:16:21 2013
180
+ velveth velvetAssembly 33 -short /tmp/anchors.fa20130916-6460-20wrnh -short2 -fasta.gz reads.fa.gz
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
+ Mon Sep 16 19:16:21 2013
190
+ velvetg velvetAssembly -read_trkg yes -max_divergence 1.0
191
+ Version 1.2.08
192
+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
193
+ This is free software; see the source for copying conditions. There is NO
194
+ warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
195
+ Compilation settings:
196
+ CATEGORIES = 2
197
+ MAXKMERLENGTH = 255
198
+
199
+ Final graph has 3 nodes and n50 of 323, max 323, total 503, using 79/79 reads
data/spec/data/gapfilling/1/velvetAssembly/PreGraph ADDED
@@ -0,0 +1,7 @@
1
+ 3 79 33 1
2
+ NODE 1 156
3
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGAT
4
+ NODE 2 323
5
+ ATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTATAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTATAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTAATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTATTTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
6
+ NODE 3 24
7
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGAT
data/spec/data/gapfilling/1/velvetAssembly/Roadmaps ADDED
@@ -0,0 +1,239 @@
1
+ 79 0 33 1
2
+ ROADMAP 1
3
+ ROADMAP 2
4
+ ROADMAP 3
5
+ ROADMAP 4
6
+ 3 0 32 48
7
+ 1 3 0 22
8
+ ROADMAP 5
9
+ 1 0 53 67
10
+ ROADMAP 6
11
+ 5 0 14 27
12
+ 2 11 0 34
13
+ ROADMAP 7
14
+ 2 24 0 34
15
+ ROADMAP 8
16
+ 6 0 5 11
17
+ 2 0 0 61
18
+ ROADMAP 9
19
+ 2 0 6 69
20
+ ROADMAP 10
21
+ 3 0 0 48
22
+ ROADMAP 11
23
+ 3 0 32 48
24
+ 4 0 0 3
25
+ 1 0 0 22
26
+ ROADMAP 12
27
+ 1 0 53 67
28
+ 5 0 0 27
29
+ ROADMAP 13
30
+ 5 0 14 27
31
+ 6 0 0 11
32
+ 2 0 0 34
33
+ ROADMAP 14
34
+ 7 0 0 24
35
+ 2 0 0 34
36
+ ROADMAP 15
37
+ 6 0 5 11
38
+ 2 0 0 61
39
+ ROADMAP 16
40
+ 2 0 6 69
41
+ 9 0 0 254
42
+ ROADMAP 17
43
+ 3 0 0 48
44
+ ROADMAP 18
45
+ 3 0 32 48
46
+ 4 0 0 3
47
+ 1 0 0 22
48
+ ROADMAP 19
49
+ 1 0 53 67
50
+ 5 0 0 27
51
+ ROADMAP 20
52
+ 5 0 14 27
53
+ 6 0 0 11
54
+ 2 0 0 34
55
+ ROADMAP 21
56
+ 7 0 0 24
57
+ 2 0 0 34
58
+ ROADMAP 22
59
+ 6 0 5 11
60
+ 2 0 0 61
61
+ ROADMAP 23
62
+ 2 0 6 69
63
+ 9 0 0 254
64
+ ROADMAP 24
65
+ 3 0 0 48
66
+ ROADMAP 25
67
+ 3 0 32 48
68
+ 4 0 0 3
69
+ 1 0 0 22
70
+ ROADMAP 26
71
+ 1 0 53 67
72
+ 5 0 0 27
73
+ ROADMAP 27
74
+ 5 0 14 27
75
+ 6 0 0 11
76
+ 2 0 0 34
77
+ ROADMAP 28
78
+ 7 0 0 24
79
+ 2 0 0 34
80
+ ROADMAP 29
81
+ 6 0 5 11
82
+ 2 0 0 61
83
+ ROADMAP 30
84
+ 2 0 6 69
85
+ 9 0 0 254
86
+ ROADMAP 31
87
+ 3 0 0 48
88
+ ROADMAP 32
89
+ 3 0 32 48
90
+ 4 0 0 3
91
+ 1 0 0 22
92
+ ROADMAP 33
93
+ 1 0 53 67
94
+ 5 0 0 27
95
+ ROADMAP 34
96
+ 5 0 14 27
97
+ 6 0 0 11
98
+ 2 0 0 34
99
+ ROADMAP 35
100
+ 7 0 0 24
101
+ 2 0 0 34
102
+ ROADMAP 36
103
+ 6 0 5 11
104
+ 2 0 0 61
105
+ ROADMAP 37
106
+ 2 0 6 69
107
+ 9 0 0 254
108
+ ROADMAP 38
109
+ 3 0 0 48
110
+ ROADMAP 39
111
+ 3 0 32 48
112
+ 4 0 0 3
113
+ 1 0 0 22
114
+ ROADMAP 40
115
+ 1 0 53 67
116
+ 5 0 0 27
117
+ ROADMAP 41
118
+ 5 0 14 27
119
+ 6 0 0 11
120
+ 2 0 0 34
121
+ ROADMAP 42
122
+ 7 0 0 24
123
+ 2 0 0 34
124
+ ROADMAP 43
125
+ 6 0 5 11
126
+ 2 0 0 61
127
+ ROADMAP 44
128
+ 2 0 6 69
129
+ 9 0 0 254
130
+ ROADMAP 45
131
+ 3 0 0 48
132
+ ROADMAP 46
133
+ 3 0 32 48
134
+ 4 0 0 3
135
+ 1 0 0 22
136
+ ROADMAP 47
137
+ 1 0 53 67
138
+ 5 0 0 27
139
+ ROADMAP 48
140
+ 5 0 14 27
141
+ 6 0 0 11
142
+ 2 0 0 34
143
+ ROADMAP 49
144
+ 7 0 0 24
145
+ 2 0 0 34
146
+ ROADMAP 50
147
+ 6 0 5 11
148
+ 2 0 0 61
149
+ ROADMAP 51
150
+ 2 0 6 69
151
+ 9 0 0 254
152
+ ROADMAP 52
153
+ -3 0 47 -1
154
+ ROADMAP 53
155
+ -1 0 21 -1
156
+ -4 0 2 -1
157
+ -3 0 47 31
158
+ ROADMAP 54
159
+ -5 0 26 -1
160
+ -1 0 66 52
161
+ ROADMAP 55
162
+ -2 0 33 -1
163
+ -6 0 10 -1
164
+ -5 0 26 13
165
+ ROADMAP 56
166
+ -2 0 33 -1
167
+ -7 0 23 -1
168
+ ROADMAP 57
169
+ -2 0 60 -1
170
+ -6 0 10 4
171
+ ROADMAP 58
172
+ -9 0 253 -1
173
+ -2 0 68 5
174
+ ROADMAP 59
175
+ -3 0 47 -1
176
+ ROADMAP 60
177
+ -1 0 21 -1
178
+ -4 0 2 -1
179
+ -3 0 47 31
180
+ ROADMAP 61
181
+ -5 0 26 -1
182
+ -1 0 66 52
183
+ ROADMAP 62
184
+ -2 0 33 -1
185
+ -6 0 10 -1
186
+ -5 0 26 13
187
+ ROADMAP 63
188
+ -2 0 33 -1
189
+ -7 0 23 -1
190
+ ROADMAP 64
191
+ -2 0 60 -1
192
+ -6 0 10 4
193
+ ROADMAP 65
194
+ -9 0 253 -1
195
+ -2 0 68 5
196
+ ROADMAP 66
197
+ -3 0 47 -1
198
+ ROADMAP 67
199
+ -1 0 21 -1
200
+ -4 0 2 -1
201
+ -3 0 47 31
202
+ ROADMAP 68
203
+ -5 0 26 -1
204
+ -1 0 66 52
205
+ ROADMAP 69
206
+ -2 0 33 -1
207
+ -6 0 10 -1
208
+ -5 0 26 13
209
+ ROADMAP 70
210
+ -2 0 33 -1
211
+ -7 0 23 -1
212
+ ROADMAP 71
213
+ -2 0 60 -1
214
+ -6 0 10 4
215
+ ROADMAP 72
216
+ -9 0 253 -1
217
+ -2 0 68 5
218
+ ROADMAP 73
219
+ -3 0 47 -1
220
+ ROADMAP 74
221
+ -1 0 21 -1
222
+ -4 0 2 -1
223
+ -3 0 47 31
224
+ ROADMAP 75
225
+ -5 0 26 -1
226
+ -1 0 66 52
227
+ ROADMAP 76
228
+ -2 0 33 -1
229
+ -6 0 10 -1
230
+ -5 0 26 13
231
+ ROADMAP 77
232
+ -2 0 33 -1
233
+ -7 0 23 -1
234
+ ROADMAP 78
235
+ -2 0 60 -1
236
+ -6 0 10 4
237
+ ROADMAP 79
238
+ -9 0 253 -1
239
+ -2 0 68 5
data/spec/data/gapfilling/1/velvetAssembly/Sequences ADDED
@@ -0,0 +1,281 @@
1
+ >anchor1 1 0
2
+ AAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAAAAAGTAGATTCAGAAAATA
3
+ TTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGG
4
+ >anchor2 2 0
5
+ ATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAG
6
+ GAAAGGGTGTAACTGATAAAAATGGACGAGTTATATTTACT
7
+ >r1 3 2
8
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
9
+ TAACAACTTATACATGGGGA
10
+ >r2 4 2
11
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
12
+ AAAGTAGATTCAG
13
+ >r3 5 2
14
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
15
+ GTAATTGGTAAAT
16
+ >r4 6 2
17
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
18
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
19
+ >r4.slightly_different 7 2
20
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
21
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
22
+ >r5 8 2
23
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
24
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
25
+ >r6 9 2
26
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
27
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
28
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
29
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
30
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
31
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
32
+ >r_again1 10 2
33
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
34
+ TAACAACTTATACATGGGGA
35
+ >r_again2 11 2
36
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
37
+ AAAGTAGATTCAG
38
+ >r_again3 12 2
39
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
40
+ GTAATTGGTAAAT
41
+ >r_again4 13 2
42
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
43
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
44
+ >r_again4.slightly_different 14 2
45
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
46
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
47
+ >r_again5 15 2
48
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
49
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
50
+ >r_again6 16 2
51
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
52
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
53
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
54
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
55
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
56
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
57
+ >r_again1 17 2
58
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
59
+ TAACAACTTATACATGGGGA
60
+ >r_again2 18 2
61
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
62
+ AAAGTAGATTCAG
63
+ >r_again3 19 2
64
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
65
+ GTAATTGGTAAAT
66
+ >r_again4 20 2
67
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
68
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
69
+ >r_again4.slightly_different 21 2
70
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
71
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
72
+ >r_again5 22 2
73
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
74
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
75
+ >r_again6 23 2
76
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
77
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
78
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
79
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
80
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
81
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
82
+ >r_again1 24 2
83
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
84
+ TAACAACTTATACATGGGGA
85
+ >r_again2 25 2
86
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
87
+ AAAGTAGATTCAG
88
+ >r_again3 26 2
89
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
90
+ GTAATTGGTAAAT
91
+ >r_again4 27 2
92
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
93
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
94
+ >r_again4.slightly_different 28 2
95
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
96
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
97
+ >r_again5 29 2
98
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
99
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
100
+ >r_again6 30 2
101
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
102
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
103
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
104
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
105
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
106
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
107
+ >r_again1 31 2
108
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
109
+ TAACAACTTATACATGGGGA
110
+ >r_again2 32 2
111
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
112
+ AAAGTAGATTCAG
113
+ >r_again3 33 2
114
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
115
+ GTAATTGGTAAAT
116
+ >r_again4 34 2
117
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
118
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
119
+ >r_again4.slightly_different 35 2
120
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
121
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
122
+ >r_again5 36 2
123
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
124
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
125
+ >r_again6 37 2
126
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
127
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
128
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
129
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
130
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
131
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
132
+ >r_again1 38 2
133
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
134
+ TAACAACTTATACATGGGGA
135
+ >r_again2 39 2
136
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
137
+ AAAGTAGATTCAG
138
+ >r_again3 40 2
139
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
140
+ GTAATTGGTAAAT
141
+ >r_again4 41 2
142
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
143
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
144
+ >r_again4.slightly_different 42 2
145
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
146
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
147
+ >r_again5 43 2
148
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
149
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
150
+ >r_again6 44 2
151
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
152
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
153
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
154
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
155
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
156
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
157
+ >r_again1 45 2
158
+ CACTTATCTCTACCAAAGATCACGATTTAGAATCAAACTATAAAGTTTTAGAAGATAAAG
159
+ TAACAACTTATACATGGGGA
160
+ >r_again2 46 2
161
+ TCAAACTATAAAGTTTTAGAAGATAAAGTAACAACTTATACATGGGGATTCGGAGTTAAA
162
+ AAAGTAGATTCAG
163
+ >r_again3 47 2
164
+ GAAAATATTTCAATAGATCTTGCAGGCGCAGCTTTTTCTGTTAGGGATAAAAATGGTAAT
165
+ GTAATTGGTAAAT
166
+ >r_again4 48 2
167
+ CAGCTTTTTCTGTTAGGGATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTA
168
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
169
+ >r_again4.slightly_different 49 2
170
+ CAGCTTTTTCTGTTAGGGATGGGGATGGTAATGTAATTGGTAAATATACGTATGATTCTA
171
+ CTGGAAATGTGGTTTTATTAAAAGGAAAGG
172
+ >r_again5 50 2
173
+ ATAAAAATGGTAATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTAT
174
+ TAAAAGGAAAGGGTGTAACTGATAAAAATGGACGAGTTA
175
+ >r_again6 51 2
176
+ ATGTAATTGGTAAATATACGTATGATTCTACTGGAAATGTGGTTTTATTAAAAGGAAAGG
177
+ GTGTAACTGATAAAAATGGACGAGTTATATTTACTGGTTTAAAAGAAGGAGATTACTTTA
178
+ TAAAAGAAGAAAAAGCTCCTAAAGGGTATAGCCTTTTAAAAGAACCAGTAAAAGTTACTA
179
+ TAACAGCTCAAAAAGATGATAATGGAGAGTATACTGGTCAAGCAACTATATCTGTAACTA
180
+ ATGGCAATGAAGCTGGAAGTATAATAAATAATATTACTATGAATGATGGCAATGTATTAT
181
+ TTAATGTACAAATTAAAAACTATGCTGGTATTTCACTTCCAGGTACAGG
182
+ >r_again1_revcom 52 2
183
+ TCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTG
184
+ ATCTTTGGTAGAGATAAGTG
185
+ >r_again2_revcom 53 2
186
+ CTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAA
187
+ CTTTATAGTTTGA
188
+ >r_again3_revcom 54 2
189
+ ATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTA
190
+ TTGAAATATTTTC
191
+ >r_again4_revcom 55 2
192
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
193
+ TACCATTTTTATCCCTAACAGAAAAAGCTG
194
+ >r_again4.slightly_different_revcom 56 2
195
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
196
+ TACCATCCCCATCCCTAACAGAAAAAGCTG
197
+ >r_again5_revcom 57 2
198
+ TAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAG
199
+ AATCATACGTATATTTACCAATTACATTACCATTTTTAT
200
+ >r_again6_revcom 58 2
201
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
202
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
203
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
204
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
205
+ CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
206
+ AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
207
+ >r_again1_revcom 59 2
208
+ TCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTG
209
+ ATCTTTGGTAGAGATAAGTG
210
+ >r_again2_revcom 60 2
211
+ CTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAA
212
+ CTTTATAGTTTGA
213
+ >r_again3_revcom 61 2
214
+ ATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTA
215
+ TTGAAATATTTTC
216
+ >r_again4_revcom 62 2
217
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
218
+ TACCATTTTTATCCCTAACAGAAAAAGCTG
219
+ >r_again4.slightly_different_revcom 63 2
220
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
221
+ TACCATCCCCATCCCTAACAGAAAAAGCTG
222
+ >r_again5_revcom 64 2
223
+ TAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAG
224
+ AATCATACGTATATTTACCAATTACATTACCATTTTTAT
225
+ >r_again6_revcom 65 2
226
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
227
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
228
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
229
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
230
+ CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
231
+ AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
232
+ >r_again1_revcom 66 2
233
+ TCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTG
234
+ ATCTTTGGTAGAGATAAGTG
235
+ >r_again2_revcom 67 2
236
+ CTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAA
237
+ CTTTATAGTTTGA
238
+ >r_again3_revcom 68 2
239
+ ATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTA
240
+ TTGAAATATTTTC
241
+ >r_again4_revcom 69 2
242
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
243
+ TACCATTTTTATCCCTAACAGAAAAAGCTG
244
+ >r_again4.slightly_different_revcom 70 2
245
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
246
+ TACCATCCCCATCCCTAACAGAAAAAGCTG
247
+ >r_again5_revcom 71 2
248
+ TAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAG
249
+ AATCATACGTATATTTACCAATTACATTACCATTTTTAT
250
+ >r_again6_revcom 72 2
251
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
252
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
253
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
254
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
255
+ CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
256
+ AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
257
+ >r_again1_revcom 73 2
258
+ TCCCCATGTATAAGTTGTTACTTTATCTTCTAAAACTTTATAGTTTGATTCTAAATCGTG
259
+ ATCTTTGGTAGAGATAAGTG
260
+ >r_again2_revcom 74 2
261
+ CTGAATCTACTTTTTTAACTCCGAATCCCCATGTATAAGTTGTTACTTTATCTTCTAAAA
262
+ CTTTATAGTTTGA
263
+ >r_again3_revcom 75 2
264
+ ATTTACCAATTACATTACCATTTTTATCCCTAACAGAAAAAGCTGCGCCTGCAAGATCTA
265
+ TTGAAATATTTTC
266
+ >r_again4_revcom 76 2
267
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
268
+ TACCATTTTTATCCCTAACAGAAAAAGCTG
269
+ >r_again4.slightly_different_revcom 77 2
270
+ CCTTTCCTTTTAATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT
271
+ TACCATCCCCATCCCTAACAGAAAAAGCTG
272
+ >r_again5_revcom 78 2
273
+ TAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTTAATAAAACCACATTTCCAGTAG
274
+ AATCATACGTATATTTACCAATTACATTACCATTTTTAT
275
+ >r_again6_revcom 79 2
276
+ CCTGTACCTGGAAGTGAAATACCAGCATAGTTTTTAATTTGTACATTAAATAATACATTG
277
+ CCATCATTCATAGTAATATTATTTATTATACTTCCAGCTTCATTGCCATTAGTTACAGAT
278
+ ATAGTTGCTTGACCAGTATACTCTCCATTATCATCTTTTTGAGCTGTTATAGTAACTTTT
279
+ ACTGGTTCTTTTAAAAGGCTATACCCTTTAGGAGCTTTTTCTTCTTTTATAAAGTAATCT
280
+ CCTTCTTTTAAACCAGTAAATATAACTCGTCCATTTTTATCAGTTACACCCTTTCCTTTT
281
+ AATAAAACCACATTTCCAGTAGAATCATACGTATATTTACCAATTACAT