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asterix-gerrit.ics.uci.edu / hyracks / 42036c17b395284d8a8c079290ae5c46ecaa16b4 / genomix / genomix-data / src
  1. 42036c1 add methods for node coverage merge/add; serialize coverage by Jake Biesinger · 12 years ago
  2. 50e9f86 add conversions for Kmer <-> VKmer by Jake Biesinger · 12 years ago
  3. ff02e22 Use VKmers in lists by Jake Biesinger · 12 years ago
  4. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  5. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  6. ceab4c1 Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  7. 94e075b update for merge by Anbang Xu · 12 years ago
  8. 6ee7bdf fix HashSet in SplitRepeat by Anbang Xu · 12 years ago
  9. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  10. d57d7e5 add CreatedVertex and ConnectedTable by Anbang Xu · 12 years ago
  11. 5a69e16 refactor graph building in hyracks using new genomix-data code by Nan Zhang · 12 years ago
  12. f2507bf debugging for hyracks by Nan Zhang · 12 years ago
  13. 844d774 update the genomix-data by Nan Zhang · 12 years ago
  14. d94f5f9 refactor 'BasicPathMergeVertex' to 'BasicGraphCleanVertex', make it more general by Anbang Xu · 12 years ago
  15. 29ebdc8 Map/Reduce version in pregel is completed by Anbang Xu · 12 years ago
  16. b89e7dc allow references in all variable-length elements by keeping track of originally allowed space by Jake Biesinger · 12 years ago
  17. 1e68c8f PositionListWritable passes tests by Jake Biesinger · 12 years ago
  18. b92f4e5 add copy-based byte array serialization for NodeWritable by Jake Biesinger · 12 years ago
  19. d907eb4 remove reference code for variable-length lists. We don't keep track of onwership of our data block by Jake Biesinger · 12 years ago
  20. d6276e7 p2 pass test by Anbang Xu · 12 years ago
  21. 11b2760 Kmer factory uses VKmers by Jake Biesinger · 12 years ago
  22. bd58f1a .hashcode and .equals need to use storage with offsets; no more super methods. by Jake Biesinger · 12 years ago
  23. a9e482e update KmerListWritable to use fixed-length kmers by Jake Biesinger · 12 years ago
  24. 9ba730c no more inherited Kmers by Jake Biesinger · 12 years ago
  25. 5fb6805 use global, static length for fixed-length kmers by Jake Biesinger · 12 years ago
  26. 0f33ece use new genomix-data by Nan Zhang · 12 years ago
  27. f472a8b add the union list function on PostionListWritable by Nan Zhang · 12 years ago
  28. fe8cb0f Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  29. 7903077 Code review: refactor offset name by Anbang Xu · 12 years ago
  30. 9e00650 p2 pass all the tests except 9 by Anbang Xu · 12 years ago
  31. 4693b43 Use Hashset for unionUpdate-ing with another KmerListWritable by Jake Biesinger · 12 years ago
  32. 71d06c2 test cases for merging across multiple edge types and kmer vs vkmer by Jake Biesinger · 12 years ago
  33. 4f80fd9 BUGFIX: mergeWithRF uses inefficient, MUCH simpler merge by Jake Biesinger · 12 years ago
  34. 78aaae4 switch VKmer to use a saner offset by Jake Biesinger · 12 years ago
  35. 9ce648a refactor KmerBytesWritable into Kmer and variable-length VKmer by Jake Biesinger · 12 years ago
  36. 9691538 starting refactor of KmerList by Jake Biesinger · 12 years ago
  37. b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
  38. 1307443 P2 pass test1,2,3,4 by Anbang Xu · 12 years ago
  39. d253d8f fix mergeWithRFKmer by Anbang Xu · 12 years ago
  40. 67c5eef Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  41. 4d50d8a Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  42. a5e97c7 p4 pass test by Anbang Xu · 12 years ago
  43. 4416d3c debugging p4 by Anbang Xu · 12 years ago
  44. 311001a start to change graph clean part to 'contrail-graph' structure by Anbang Xu · 12 years ago
  45. dfa14d3 Fix NodeWritable and Finish contrail-graph Mapper/Reducer by Anbang Xu · 12 years ago genomix/velvet-graph-pregel
  46. 95138a4 hyracks contrail graph building partial completing by Nan Zhang · 12 years ago
  47. 84e385f Try to add globe kmerSize but fail in testing by Anbang Xu · 12 years ago
  48. bcf5a70 add hadoop test and keep both bin and txt by Anbang Xu · 12 years ago
  49. f7a23e4 add Reducer and change PositionWritable to PositionListWritable in NodeWritable by Anbang Xu · 12 years ago
  50. 0c644f4 Mapper passes test by Anbang Xu · 12 years ago
  51. 32bc798 finish Mapper and start Reducer by Anbang Xu · 12 years ago
  52. 08c7d2d change KmerListWritable and NodeWritable to new construction for new graph-'Kmer-Base system as key' by Anbang Xu · 12 years ago
  53. b14e7e6 Update for changing graph by Anbang Xu · 12 years ago
  54. 8dbe728 refactor 'size' to 'kmerByteSize' in KmerBytesWritable by Anbang Xu · 12 years ago
  55. f7fc945 refactor 'UniqueKey' to 'NodeId' by Anbang Xu · 12 years ago
  56. 1a02870 add ReadsKeyValueParserFactory for new graph using for read HDFS by Anbang Xu · 12 years ago
  57. 871743c add IntermediateNodeWritable and KmerListWritable by Anbang Xu · 12 years ago
  58. c642eeb new graph driver by Anbang Xu · 12 years ago
  59. 0a8e068 add makeUUID to PositionWritable; use for test cases by Jake Biesinger · 12 years ago
  60. aef7aaa meatier test case and tweaks for PositionWritable by Jake Biesinger · 12 years ago
  61. a9eafe7 Make PositionListWritable test code by Anbang Xu · 12 years ago
  62. 67254bc Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  63. 6010f35 Make the PositionWritable and Pass the test by Anbang Xu · 12 years ago
  64. 6b45971 Fix H4, test templates by Jake Biesinger · 12 years ago
  65. de2424c begin new graph building by Anbang Xu · 12 years ago
  66. de2a44b small adjustments to new node and position classes by Jake Biesinger · 12 years ago
  67. 970c74f move old key/value class to oldtype folder by Anbang Xu · 12 years ago
  68. 814540a remake new graph class - PositionWritable and NodeWritable by Anbang Xu · 12 years ago
  69. 9378de1 change directionFlag back by Anbang Xu · 12 years ago
  70. 3054c15 clear the code and fix messageFlag by Anbang Xu · 12 years ago
  71. b5c8428 test cases by AnbangX · 12 years ago
  72. da3b802 Apply undirected graph algorithm in p2 by AnbangX · 12 years ago
  73. 8e4fbc3 test cases and fixes for H4 by Jake Biesinger · 12 years ago
  74. b5e81d6 Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by AnbangX · 12 years ago
  75. e6d7e7a code review with Jake by AnbangX · 12 years ago
  76. 64ae953 Add mergeInDir for kmers by Jake Biesinger · 12 years ago
  77. e1dbea7 add subclass BasicVertex and fixing p2 by AnbangX · 12 years ago
  78. 46fc86e add test cases for removeBridge, removeTip and mergeBubble by AnbangX · 12 years ago
  79. db5d564 WIP H4 1 mapper + 2 reducers by Jake Biesinger · 12 years ago
  80. 5adaeec add merge and update utility functions by Jake Biesinger · 12 years ago
  81. 71ea5d2 Fix RFMerge and add tests by Jake Biesinger · 12 years ago
  82. 01ad7c2 Merge and fix FRMerge. RF still doesn't work. by Jake Biesinger · 12 years ago
  83. ab171ba refactor kmer mergeNext and mergePre -> mergeFF etc. untested :) by Jake Biesinger · 12 years ago
  84. a7216ac Add helper functions for mutating PositionListWritable's by Jake Biesinger · 12 years ago
  85. 24e076f PathNodeInitial identifies nodes needing updates by Jake Biesinger · 12 years ago
  86. cc77cf7 add test cases for path merge and other data clean patterns by AnbangX · 12 years ago
  87. 2c41eb3 add remove in PositionListWritable and test by AnbangX · 12 years ago
  88. 1e43ac4 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into jianfeng/genomix by Jianfeng Jia · 12 years ago
  89. 09cf1d1 facilitate better testing via more constructors and proper hashing/equals by Jake Biesinger · 12 years ago
  90. bc7e15f Merge branch 'genomix/fullstack_genomix' into jianfeng/genomix by Jianfeng Jia · 12 years ago
  91. bf8f525 Fix spelling by Jake Biesinger · 12 years ago
  92. 37cc20b hadoop graph building completion by Nan Zhang · 12 years ago
  93. eb8d72a Merge commit '951870ef4642f2003c4240eeef702fc90600fe77' into nanzhang/genomix by Nan Zhang · 12 years ago
  94. 3a26a3a merge with jianfeng-reverse by Nan Zhang · 12 years ago
  95. a591f26 clean up code and add copyright header by JavierJia · 12 years ago
  96. 12b4280 Merge branch 'jianfeng/genomix' into jianfeng/genomix-reverse by Jianfeng Jia · 12 years ago
  97. 5ba19e2 add more information for larger data debug by Jianfeng Jia · 12 years ago genomix/unidirection
  98. 562116a finished framework. not test yet by Jianfeng Jia · 12 years ago
  99. 8528899 finish framework by Jianfeng Jia · 12 years ago
  100. 5033f6f Update comment. by Jianfeng Jia · 12 years ago