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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@@ -0,0 +1,72 @@
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+ /*
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+ Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
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+
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+ This file is part of Velvet.
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+
6
+ Velvet is free software; you can redistribute it and/or modify
7
+ it under the terms of the GNU General Public License as published by
8
+ the Free Software Foundation; either version 2 of the License, or
9
+ (at your option) any later version.
10
+
11
+ Velvet is distributed in the hope that it will be useful,
12
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
13
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14
+ GNU General Public License for more details.
15
+
16
+ You should have received a copy of the GNU General Public License
17
+ along with Velvet; if not, write to the Free Software
18
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
19
+
20
+ */
21
+ #ifndef _GRAPHSTATS_H_
22
+ #define _GRAPHSTATS_H_
23
+
24
+
25
+ void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads);
26
+
27
+ void exportLongNodeSequences(char *filename, Graph * graph,
28
+ Coordinate minLength, ReadSet * reads, ShortLength * readLengths, IDnum minCov);
29
+
30
+ Coordinate readCoverage(Node * node);
31
+
32
+ Coordinate n50(Graph * graph);
33
+
34
+ double estimated_cov(Graph * graph, char * directory);
35
+
36
+ Coordinate maxLength(Graph * graph);
37
+
38
+ boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
39
+ double minCov,
40
+ ReadSet * reads,
41
+ boolean export,
42
+ Coordinate minLength,
43
+ char *filename);
44
+
45
+ void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
46
+ double minCov,
47
+ ReadSet * reads,
48
+ boolean * dubious,
49
+ boolean export,
50
+ Coordinate minLength,
51
+ char *filename);
52
+
53
+ void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLongCov, ReadSet * reads);
54
+
55
+ void exportAMOSContigs(char *filename, Graph * graph,
56
+ Coordinate cutoff_length, ReadSet * reads);
57
+
58
+ IDnum usedReads(Graph * graph, Coordinate minContigLength);
59
+
60
+ Coordinate totalAssemblyLength(Graph * graph);
61
+
62
+ void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *directory);
63
+
64
+ void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLength, char* filename);
65
+
66
+ void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,
67
+ Coordinate minLength, SequencesReader *seqReadInfo);
68
+
69
+ void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, char * filename);
70
+
71
+ void removeLowArcs(Graph * graph, double cutoff);
72
+ #endif
@@ -0,0 +1,52 @@
1
+ struct arc_st {
2
+ Arc *twinArc; // 64
3
+ Arc *next; // 64
4
+ Arc *previous; // 64
5
+ Arc *nextInLookupTable; // 64
6
+ Node *destination; // 64
7
+ IDnum multiplicity; // 32
8
+ } ATTRIBUTE_PACKED; // 352 Total
9
+
10
+ struct node_st {
11
+ Node *twinNode; // 64
12
+ Arc *arc; // 64
13
+ Descriptor *descriptor; // 64
14
+ PassageMarkerI marker; // 32
15
+ IDnum length; // 32
16
+ #ifndef SINGLE_COV_CAT
17
+ IDnum virtualCoverage[CATEGORIES]; // 32 * 2
18
+ IDnum originalVirtualCoverage[CATEGORIES]; // 32 * 2
19
+ #else
20
+ IDnum virtualCoverage; // 32 * 2
21
+ #endif
22
+ IDnum ID; // 32
23
+ IDnum arcCount; // 32
24
+ boolean status; // 1
25
+ boolean uniqueness; // 1
26
+ } ATTRIBUTE_PACKED; // 418 Total
27
+
28
+ struct shortReadMarker_st {
29
+ IDnum position;
30
+ IDnum readID;
31
+ ShortLength offset;
32
+ } ATTRIBUTE_PACKED;
33
+
34
+ struct gapMarker_st {
35
+ GapMarker *next;
36
+ IDnum position;
37
+ IDnum length;
38
+ } ATTRIBUTE_PACKED;
39
+
40
+ struct graph_st {
41
+ Node **nodes;
42
+ Arc **arcLookupTable;
43
+ ShortReadMarker **nodeReads;
44
+ IDnum *nodeReadCounts;
45
+ GapMarker **gapMarkers;
46
+ Coordinate insertLengths[CATEGORIES + 1];
47
+ double insertLengths_var[CATEGORIES + 1];
48
+ IDnum sequenceCount;
49
+ IDnum nodeCount;
50
+ int wordLength;
51
+ boolean double_stranded;
52
+ };
@@ -0,0 +1,652 @@
1
+ /*
2
+ Copyright 2007, 2008, 2009 Daniel Zerbino (zerbino@ebi.ac.uk)
3
+
4
+ This file is part of Velvet.
5
+
6
+ Velvet is free software; you can redistribute it and/or modify
7
+ it under the terms of the GNU General Public License as published by
8
+ the Free Software Foundation; either version 2 of the License, or
9
+ (at your option) any later version.
10
+
11
+ Velvet is distributed in the hope that it will be useful,
12
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
13
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14
+ GNU General Public License for more details.
15
+
16
+ You should have received a copy of the GNU General Public License
17
+ along with Velvet; if not, write to the Free Software
18
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
19
+
20
+ */
21
+ #include <stdlib.h>
22
+ #include <stdio.h>
23
+
24
+ #include "globals.h"
25
+ #include "kmer.h"
26
+ #include "utility.h"
27
+
28
+ static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62;
29
+ static const uint32_t longLeftFilter = (uint32_t) 3 << 30;
30
+ static const uint16_t intLeftFilter = (uint16_t) 3 << 14;
31
+ static const uint8_t charLeftFilter = (uint8_t) 3 << 6;
32
+
33
+ #if KMER_LONGLONGS
34
+ static uint64_t longLongWordFilter = (uint64_t) ((int64_t) -1);
35
+ #endif
36
+ static uint32_t longWordFilter = (uint32_t) ((int32_t) -1);
37
+ static uint16_t intWordFilter = (uint16_t) ((int16_t) -1);
38
+ static uint8_t charWordFilter = (uint8_t) ((int8_t) -1);
39
+
40
+ #define UNDEFINED 0
41
+ #define CHARS 1
42
+ #define INTS 2
43
+ #define LONGS 3
44
+ #define LONGLONGS 4
45
+ static int kmerFilterIndex = UNDEFINED;
46
+ static int kmerFilterOffset = 0;
47
+ static int kmerFilterLength = 0;
48
+ #if KMER_LONGLONGS
49
+ static int longLongKmerFilterIndex = KMER_LONGLONGS - 1;
50
+ static uint64_t longLongKmerFilter = (uint64_t) ((int64_t) -1);
51
+ #endif
52
+
53
+ static uint64_t keyFilter = 0;
54
+ static int keyFilterIndex = UNDEFINED;
55
+ static int keyFilterOffset = 0;
56
+ static int keyFilterLength = 0;
57
+ #if KMER_LONGLONGS
58
+ static int longLongKeyFilterIndex = KMER_LONGLONGS - 1;
59
+ #endif
60
+
61
+ void resetWordFilter(int wordLength) {
62
+ int kmer_bit_size = wordLength * 2;
63
+
64
+ if (wordLength > MAXKMERLENGTH)
65
+ exitErrorf(EXIT_FAILURE, true, "Word length %i greater than max allowed value (%i).\nRecompile Velvet to deal with this word length.", wordLength, MAXKMERLENGTH);
66
+
67
+ #if KMER_LONGLONGS
68
+ int i;
69
+ for (i = 0; i < KMER_LONGLONGS; i++) {
70
+ if (kmer_bit_size > 64) {
71
+ kmer_bit_size -= 64;
72
+ continue;
73
+ } else if (kmer_bit_size == 64) {
74
+ longLongKmerFilterIndex = i;
75
+ longLongKmerFilter = longLongWordFilter;
76
+ kmerFilterIndex = LONGLONGS;
77
+ kmerFilterOffset = kmer_bit_size - 2;
78
+ kmerFilterLength = kmer_bit_size;
79
+ longWordFilter = 0;
80
+ intWordFilter = 0;
81
+ charWordFilter = 0;
82
+ return;
83
+ } else {
84
+ longLongKmerFilterIndex = i;
85
+ longLongKmerFilter = (((uint64_t) 1) << kmer_bit_size) - 1;
86
+ kmerFilterIndex = LONGLONGS;
87
+ kmerFilterOffset = kmer_bit_size - 2;
88
+ kmerFilterLength = kmer_bit_size;
89
+ longWordFilter = 0;
90
+ intWordFilter = 0;
91
+ charWordFilter = 0;
92
+ return;
93
+ }
94
+ }
95
+ #endif
96
+ #if KMER_LONGS
97
+ if (kmer_bit_size > 32)
98
+ kmer_bit_size -= 32;
99
+ else if (kmer_bit_size == 32) {
100
+ kmerFilterIndex = LONGS;
101
+ kmerFilterOffset = kmer_bit_size - 2;
102
+ kmerFilterLength = kmer_bit_size;
103
+ intWordFilter = 0;
104
+ charWordFilter = 0;
105
+ return;
106
+ } else {
107
+ longWordFilter = (((uint32_t) 1) << kmer_bit_size) - 1;
108
+ kmerFilterIndex = LONGS;
109
+ kmerFilterOffset = kmer_bit_size - 2;
110
+ kmerFilterLength = kmer_bit_size;
111
+ intWordFilter = 0;
112
+ charWordFilter = 0;
113
+ return;
114
+ }
115
+ #endif
116
+ #if KMER_INTS
117
+ if (kmer_bit_size > 16)
118
+ kmer_bit_size -= 16;
119
+ else if (kmer_bit_size == 16) {
120
+ kmerFilterIndex = INTS;
121
+ kmerFilterOffset = kmer_bit_size - 2;
122
+ kmerFilterLength = kmer_bit_size;
123
+ charWordFilter = 0;
124
+ return;
125
+ } else {
126
+ intWordFilter = (((uint16_t) 1) << kmer_bit_size) - 1;
127
+ kmerFilterIndex = INTS;
128
+ kmerFilterOffset = kmer_bit_size - 2;
129
+ kmerFilterLength = kmer_bit_size;
130
+ charWordFilter = 0;
131
+ return;
132
+ }
133
+
134
+ #endif
135
+ #if KMER_CHARS
136
+ if (kmer_bit_size < 8)
137
+ charWordFilter = (((uint8_t) 1) << kmer_bit_size) - 1;
138
+
139
+ kmerFilterIndex = CHARS;
140
+ kmerFilterOffset = kmer_bit_size - 2;
141
+ kmerFilterLength = kmer_bit_size;
142
+ #endif
143
+
144
+ }
145
+
146
+ void resetKeyFilter(int keyLength) {
147
+ int kmer_bit_size = keyLength;
148
+
149
+ if (keyLength > MAXKMERLENGTH)
150
+ exitErrorf(EXIT_FAILURE, true, "Key length %i greater than max allowed value (%i).\nRecompile Velvet to deal with this word length.", keyLength, MAXKMERLENGTH);
151
+
152
+ #if KMER_CHARS
153
+ if (kmerFilterIndex == CHARS) {
154
+ if (kmer_bit_size > kmerFilterLength) {
155
+ kmer_bit_size -= kmerFilterLength;
156
+ } else {
157
+ keyFilterIndex = CHARS;
158
+ keyFilterLength = kmer_bit_size;
159
+ keyFilterOffset = kmerFilterLength - keyFilterLength;
160
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
161
+ return;
162
+ }
163
+ }
164
+ #endif
165
+ #if KMER_INTS
166
+ if (kmerFilterIndex == INTS) {
167
+ if (kmer_bit_size > kmerFilterLength) {
168
+ kmer_bit_size -= kmerFilterLength;
169
+ } else {
170
+ keyFilterIndex = INTS;
171
+ keyFilterLength = kmer_bit_size;
172
+ keyFilterOffset = kmerFilterLength - keyFilterLength;
173
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
174
+ return;
175
+ }
176
+ } else if (intWordFilter) {
177
+ if (kmer_bit_size > 16)
178
+ kmer_bit_size -= 16;
179
+ else {
180
+ keyFilterIndex = INTS;
181
+ keyFilterLength = kmer_bit_size;
182
+ keyFilterOffset = 16 - keyFilterLength;
183
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
184
+ return;
185
+ }
186
+ }
187
+ #endif
188
+ #if KMER_LONGS
189
+ if (kmerFilterIndex == LONGS) {
190
+ if (kmer_bit_size > kmerFilterLength) {
191
+ kmer_bit_size -= kmerFilterLength;
192
+ } else {
193
+ keyFilterIndex = LONGS;
194
+ keyFilterLength = kmer_bit_size;
195
+ keyFilterOffset = kmerFilterLength - keyFilterLength;
196
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
197
+ return;
198
+ }
199
+ } else if (longWordFilter) {
200
+ if (kmer_bit_size > 32)
201
+ kmer_bit_size -= 32;
202
+ else {
203
+ keyFilterIndex = LONGS;
204
+ keyFilterLength = kmer_bit_size;
205
+ keyFilterOffset = 32 - keyFilterLength;
206
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
207
+ return;
208
+ }
209
+ }
210
+ #endif
211
+ #if KMER_LONGLONGS
212
+ if (kmerFilterIndex == LONGLONGS) {
213
+ if (kmer_bit_size > kmerFilterLength) {
214
+ kmer_bit_size -= kmerFilterLength;
215
+ } else {
216
+ keyFilterIndex = LONGLONGS;
217
+ longLongKeyFilterIndex = longLongKmerFilterIndex;
218
+ keyFilterLength = kmer_bit_size;
219
+ keyFilterOffset = kmerFilterLength - keyFilterLength;
220
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
221
+ return;
222
+ }
223
+ } else {
224
+ if (kmer_bit_size > 64)
225
+ abort();
226
+ else {
227
+ keyFilterIndex = LONGLONGS;
228
+ longLongKeyFilterIndex = longLongKmerFilterIndex;
229
+ keyFilterLength = kmer_bit_size;
230
+ keyFilterOffset = 64 - keyFilterLength;
231
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
232
+ return;
233
+ }
234
+ }
235
+
236
+ if (kmer_bit_size > 64)
237
+ abort();
238
+ else {
239
+ keyFilterIndex = LONGLONGS;
240
+ longLongKeyFilterIndex = longLongKmerFilterIndex - 1;
241
+ keyFilterLength = kmer_bit_size;
242
+ keyFilterOffset = 64 - keyFilterLength;
243
+ keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;
244
+ return;
245
+ }
246
+ #endif
247
+
248
+ }
249
+
250
+ static void shiftRight(Kmer * kmer) {
251
+ uint64_t leftBits = 0;
252
+ uint64_t rightBits;
253
+
254
+ #if KMER_CHARS
255
+
256
+ #if KMER_INTS | KMER_LONGS | KMER_LONGLONGS
257
+ rightBits = kmer->chars & 3;
258
+ #endif
259
+
260
+ kmer->chars >>= 2;
261
+ kmer->chars += (uint8_t) leftBits;
262
+
263
+ #if KMER_INTS | KMER_LONGS | KMER_LONGLONGS
264
+ leftBits = rightBits;
265
+ #endif
266
+ #endif
267
+
268
+ #if KMER_INTS
269
+
270
+ #if KMER_LONGS | KMER_LONGLONGS
271
+ rightBits = kmer->ints & 3;
272
+ #endif
273
+
274
+ leftBits <<= 14;
275
+ kmer->ints >>= 2;
276
+ kmer->ints += (uint16_t) leftBits;
277
+
278
+ #if KMER_LONGS | KMER_LONGLONGS
279
+ leftBits = rightBits;
280
+ #endif
281
+ #endif
282
+
283
+ #if KMER_LONGS
284
+
285
+ #if KMER_LONGLONGS
286
+ rightBits = kmer->longs & 3;
287
+ #endif
288
+
289
+ leftBits <<= 30;
290
+ kmer->longs >>= 2;
291
+ kmer->longs += (uint32_t) leftBits;
292
+
293
+ #if KMER_LONGLONGS
294
+ leftBits = rightBits;
295
+ #endif
296
+ #endif
297
+
298
+ #if KMER_LONGLONGS
299
+ int i;
300
+ for (i = KMER_LONGLONGS - 1; i >= 0; i--) {
301
+ rightBits = kmer->longlongs[i] & 3;
302
+ leftBits <<= 62;
303
+ kmer->longlongs[i] >>= 2;
304
+ kmer->longlongs[i] += leftBits;
305
+ leftBits = rightBits;
306
+ }
307
+ #endif
308
+ }
309
+
310
+ void copyKmers(Kmer* k1, Kmer* k2) {
311
+
312
+ #if KMER_LONGLONGS
313
+ int i;
314
+ for (i = 0; i < KMER_LONGLONGS; i++)
315
+ k1->longlongs[i] = k2->longlongs[i];
316
+ #endif
317
+ #if KMER_LONGS
318
+ k1->longs = k2->longs;
319
+ #endif
320
+ #if KMER_INTS
321
+ k1->ints = k2->ints;
322
+ #endif
323
+ #if KMER_CHARS
324
+ k1->chars = k2->chars;
325
+ #endif
326
+ }
327
+
328
+ int compareKmers(Kmer* k1, Kmer* k2) {
329
+ #if KMER_LONGLONGS
330
+ int i;
331
+ #endif
332
+
333
+ #if KMER_CHARS
334
+ if (k1->chars == k2->chars)
335
+ ;
336
+ else if (k1->chars > k2->chars)
337
+ return 1;
338
+ else
339
+ return -1;
340
+ #endif
341
+ #if KMER_INTS
342
+ if (k1->ints == k2->ints)
343
+ ;
344
+ else if (k1->ints > k2->ints)
345
+ return 1;
346
+ else
347
+ return -1;
348
+ #endif
349
+ #if KMER_LONGS
350
+ if (k1->longs == k2->longs)
351
+ ;
352
+ else if (k1->longs > k2->longs)
353
+ return 1;
354
+ else
355
+ return -1;
356
+ #endif
357
+ #if KMER_LONGLONGS
358
+ for (i = KMER_LONGLONGS - 1; i >= 0; i--) {
359
+ if (k1->longlongs[i] == k2->longlongs[i])
360
+ continue;
361
+ else if (k1->longlongs[i] > k2->longlongs[i])
362
+ return 1;
363
+ else
364
+ return -1;
365
+ }
366
+ #endif
367
+
368
+ return 0;
369
+ }
370
+
371
+ void clearKmer(Kmer * kmer) {
372
+ #if KMER_LONGLONGS
373
+ int i;
374
+ for (i = 0; i < KMER_LONGLONGS; i++)
375
+ kmer->longlongs[i] = 0;
376
+ #endif
377
+ #if KMER_LONGS
378
+ kmer->longs = 0;
379
+ #endif
380
+ #if KMER_INTS
381
+ kmer->ints = 0;
382
+ #endif
383
+ #if KMER_CHARS
384
+ kmer->chars = 0;
385
+ #endif
386
+ }
387
+
388
+ void printKmer(Kmer * kmer) {
389
+
390
+ #if KMER_CHARS
391
+ velvetLog("%hx\t", kmer->chars);
392
+ #endif
393
+ #if KMER_INTS
394
+ velvetLog("%x\t", kmer->ints);
395
+ #endif
396
+ #if KMER_LONGS
397
+ velvetLog("%x\t", kmer->longs);
398
+ #endif
399
+ #if KMER_LONGLONGS
400
+ int i;
401
+ for (i = KMER_LONGLONGS - 1; i >= 0; i--)
402
+ velvetLog("%llx\t", (long long) kmer->longlongs[i]);
403
+ #endif
404
+ velvetLog("\n");
405
+ }
406
+
407
+ void pushNucleotide(Kmer * kmer, Nucleotide nucleotide) {
408
+
409
+ #if KMER_LONGLONGS
410
+ uint64_t * ptr;
411
+ int i;
412
+ #endif
413
+ #if KMER_LONGLONGS > 1 | KMER_LONGS | KMER_INTS | KMER_CHARS
414
+ uint64_t leftBits;
415
+ #endif
416
+ uint64_t rightBits = 0;
417
+
418
+ #if KMER_LONGLONGS
419
+ ptr = kmer->longlongs;
420
+
421
+ #if KMER_LONGLONGS > 1
422
+ for (i = 0; i < longLongKmerFilterIndex; i++) {
423
+ leftBits = (*ptr & longLongLeftFilter);
424
+ leftBits >>= 62;
425
+ *ptr <<= 2;
426
+ *ptr += rightBits;
427
+ *ptr &= longLongWordFilter;
428
+ rightBits = leftBits;
429
+ ptr++;
430
+ }
431
+ #endif
432
+
433
+ #if KMER_LONGS | KMER_INTS | KMER_CHARS
434
+ leftBits = (*ptr & longLongLeftFilter);
435
+ leftBits >>= 62;
436
+ #endif
437
+
438
+ *ptr <<= 2;
439
+ *ptr += rightBits;
440
+ *ptr &= longLongKmerFilter;
441
+
442
+ #if KMER_LONGS | KMER_INTS | KMER_CHARS
443
+ rightBits = leftBits;
444
+ #endif
445
+ #endif
446
+
447
+ #if KMER_LONGS
448
+
449
+ #if KMER_INTS | KMER_CHARS
450
+ leftBits = kmer->longs & longLeftFilter;
451
+ leftBits >>= 30;
452
+ #endif
453
+ kmer->longs <<= 2;
454
+ kmer->longs += rightBits;
455
+ kmer->longs &= longWordFilter;
456
+
457
+ #if KMER_INTS | KMER_CHARS
458
+ rightBits = leftBits;
459
+ #endif
460
+
461
+ #endif
462
+
463
+ #if KMER_INTS
464
+
465
+ #if KMER_CHARS
466
+ leftBits = kmer->ints & intLeftFilter;
467
+ leftBits >>= 14;
468
+ #endif
469
+ kmer->ints <<= 2;
470
+ kmer->ints += rightBits;
471
+ kmer->ints &= intWordFilter;
472
+
473
+ #if KMER_CHARS
474
+ rightBits = leftBits;
475
+ #endif
476
+
477
+ #endif
478
+
479
+ #if KMER_CHARS
480
+ kmer->chars <<= 2;
481
+ kmer->chars += rightBits;
482
+ kmer->chars &= charWordFilter;
483
+ #endif
484
+
485
+ #if KMER_LONGLONGS
486
+ kmer->longlongs[0] += nucleotide;
487
+ if (kmer->longlongs[0] >= nucleotide)
488
+ return;
489
+
490
+ for (i = 1; i < KMER_LONGLONGS; i++)
491
+ if (++kmer->longlongs[i])
492
+ return;
493
+ #if KMER_LONGS
494
+ if (++kmer->longs)
495
+ return;
496
+ #endif
497
+ #if KMER_INTS
498
+ if (++kmer->ints)
499
+ return;
500
+ #endif
501
+ #if KMER_CHARS
502
+ ++kmer->chars;
503
+ #endif
504
+
505
+ #else
506
+
507
+ #if KMER_LONGS
508
+ kmer->longs += nucleotide;
509
+ if (kmer->longs >= nucleotide)
510
+ return;
511
+ #if KMER_INTS
512
+ if (++kmer->ints)
513
+ return;
514
+ #endif
515
+ #if KMER_CHARS
516
+ ++kmer->chars;
517
+ #endif
518
+
519
+ #else
520
+
521
+ #if KMER_INTS
522
+ kmer->ints += nucleotide;
523
+ if (kmer->ints >= nucleotide)
524
+ return;
525
+ #if KMER_CHARS
526
+ ++kmer->chars;
527
+ #endif
528
+
529
+ #else
530
+
531
+ #if KMER_CHARS
532
+ kmer->chars += nucleotide;
533
+ #endif
534
+
535
+ #endif
536
+ #endif
537
+ #endif
538
+ }
539
+
540
+ Nucleotide popNucleotide(Kmer * kmer) {
541
+ Nucleotide nucl;
542
+
543
+ #if KMER_LONGLONGS
544
+ nucl = kmer->longlongs[0] & 3;
545
+ #elif KMER_LONGS
546
+ nucl = kmer->longs & 3;
547
+ #elif KMER_INTS
548
+ nucl = kmer->ints & 3;
549
+ #elif KMER_CHARS
550
+ nucl = kmer->chars & 3;
551
+ #endif
552
+
553
+ shiftRight(kmer);
554
+ return nucl;
555
+ }
556
+
557
+ void reversePushNucleotide(Kmer * kmer, Nucleotide nucleotide) {
558
+ uint64_t templongLong = nucleotide;
559
+
560
+ shiftRight(kmer);
561
+
562
+ switch(kmerFilterIndex) {
563
+ case UNDEFINED:
564
+ abort();
565
+ #if KMER_LONGLONGS
566
+ case LONGLONGS:
567
+ kmer->longlongs[longLongKmerFilterIndex] += templongLong << kmerFilterOffset;
568
+ return;
569
+ #endif
570
+ #if KMER_LONGS
571
+ case LONGS:
572
+ kmer->longs += templongLong << kmerFilterOffset;
573
+ return;
574
+ #endif
575
+ #if KMER_INTS
576
+ case INTS:
577
+ kmer->ints += templongLong << kmerFilterOffset;
578
+ return;
579
+ #endif
580
+ #if KMER_CHARS
581
+ case CHARS:
582
+ kmer->chars += templongLong << kmerFilterOffset;
583
+ return;
584
+ #endif
585
+ }
586
+
587
+ exitErrorf(EXIT_FAILURE, true, "Anomaly in k-mer filering");
588
+ }
589
+
590
+ KmerKey getKmerKey(Kmer * kmer) {
591
+ KmerKey key = 0;
592
+
593
+ #if KMER_CHARS
594
+ if (keyFilterIndex == CHARS) {
595
+ key = kmer->chars & keyFilter;
596
+ key >>= keyFilterOffset;
597
+ return key;
598
+ }
599
+ #endif
600
+
601
+ #if KMER_INTS
602
+ if (keyFilterIndex == INTS) {
603
+ #if KMER_CHARS
604
+ key += kmer->chars;
605
+ #endif
606
+ key <<= keyFilterLength;
607
+ key += (kmer->ints & keyFilter) >> keyFilterOffset;
608
+ return key;
609
+ }
610
+ #endif
611
+
612
+ #if KMER_LONGS
613
+ if (keyFilterIndex == LONGS) {
614
+ #if KMER_CHARS
615
+ key += kmer->chars;
616
+ #endif
617
+ #if KMER_INTS
618
+ key <<= 16;
619
+ key += kmer->ints;
620
+ #endif
621
+ key <<= keyFilterLength;
622
+ key += (kmer->longs & keyFilter) >> keyFilterOffset;
623
+ return key;
624
+ }
625
+ #endif
626
+
627
+ #if KMER_LONGLONGS
628
+ if (keyFilterIndex == LONGLONGS) {
629
+ #if KMER_CHARS
630
+ key += kmer->chars;
631
+ #endif
632
+ #if KMER_INTS
633
+ key <<= 16;
634
+ key += kmer->ints;
635
+ #endif
636
+ #if KMER_LONGS
637
+ key <<= 32;
638
+ key += kmer->longs;
639
+ #endif
640
+ if (longLongKeyFilterIndex != longLongKmerFilterIndex) {
641
+ key <<= kmerFilterLength;
642
+ key += kmer->longlongs[longLongKmerFilterIndex];
643
+ }
644
+ key <<= keyFilterLength;
645
+ key += (kmer->longlongs[longLongKeyFilterIndex] & keyFilter) >> keyFilterOffset;
646
+
647
+ return key;
648
+ }
649
+ #endif
650
+ abort();
651
+ return 0;
652
+ }