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asterix-gerrit.ics.uci.edu / hyracks / 0f33ecee5bfad24d4a6407a40e131e73f9b1bfe7 / genomix / genomix-data / src
  1. 0f33ece use new genomix-data by Nan Zhang · 12 years ago
  2. fe8cb0f Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  3. 9e00650 p2 pass all the tests except 9 by Anbang Xu · 12 years ago
  4. 1307443 P2 pass test1,2,3,4 by Anbang Xu · 12 years ago
  5. d253d8f fix mergeWithRFKmer by Anbang Xu · 12 years ago
  6. 67c5eef Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  7. 4d50d8a Merge branch 'genomix/fullstack_genomix' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  8. a5e97c7 p4 pass test by Anbang Xu · 12 years ago
  9. 4416d3c debugging p4 by Anbang Xu · 12 years ago
  10. 311001a start to change graph clean part to 'contrail-graph' structure by Anbang Xu · 12 years ago
  11. dfa14d3 Fix NodeWritable and Finish contrail-graph Mapper/Reducer by Anbang Xu · 12 years ago genomix/velvet-graph-pregel
  12. 95138a4 hyracks contrail graph building partial completing by Nan Zhang · 12 years ago
  13. 84e385f Try to add globe kmerSize but fail in testing by Anbang Xu · 12 years ago
  14. bcf5a70 add hadoop test and keep both bin and txt by Anbang Xu · 12 years ago
  15. f7a23e4 add Reducer and change PositionWritable to PositionListWritable in NodeWritable by Anbang Xu · 12 years ago
  16. 0c644f4 Mapper passes test by Anbang Xu · 12 years ago
  17. 32bc798 finish Mapper and start Reducer by Anbang Xu · 12 years ago
  18. 08c7d2d change KmerListWritable and NodeWritable to new construction for new graph-'Kmer-Base system as key' by Anbang Xu · 12 years ago
  19. b14e7e6 Update for changing graph by Anbang Xu · 12 years ago
  20. 8dbe728 refactor 'size' to 'kmerByteSize' in KmerBytesWritable by Anbang Xu · 12 years ago
  21. f7fc945 refactor 'UniqueKey' to 'NodeId' by Anbang Xu · 12 years ago
  22. 1a02870 add ReadsKeyValueParserFactory for new graph using for read HDFS by Anbang Xu · 12 years ago
  23. 871743c add IntermediateNodeWritable and KmerListWritable by Anbang Xu · 12 years ago
  24. c642eeb new graph driver by Anbang Xu · 12 years ago
  25. 0a8e068 add makeUUID to PositionWritable; use for test cases by Jake Biesinger · 12 years ago
  26. aef7aaa meatier test case and tweaks for PositionWritable by Jake Biesinger · 12 years ago
  27. a9eafe7 Make PositionListWritable test code by Anbang Xu · 12 years ago
  28. 67254bc Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  29. 6010f35 Make the PositionWritable and Pass the test by Anbang Xu · 12 years ago
  30. 6b45971 Fix H4, test templates by Jake Biesinger · 12 years ago
  31. de2424c begin new graph building by Anbang Xu · 12 years ago
  32. de2a44b small adjustments to new node and position classes by Jake Biesinger · 12 years ago
  33. 970c74f move old key/value class to oldtype folder by Anbang Xu · 12 years ago
  34. 814540a remake new graph class - PositionWritable and NodeWritable by Anbang Xu · 12 years ago
  35. 9378de1 change directionFlag back by Anbang Xu · 12 years ago
  36. 3054c15 clear the code and fix messageFlag by Anbang Xu · 12 years ago
  37. b5c8428 test cases by AnbangX · 12 years ago
  38. da3b802 Apply undirected graph algorithm in p2 by AnbangX · 12 years ago
  39. 8e4fbc3 test cases and fixes for H4 by Jake Biesinger · 12 years ago
  40. b5e81d6 Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by AnbangX · 12 years ago
  41. e6d7e7a code review with Jake by AnbangX · 12 years ago
  42. 64ae953 Add mergeInDir for kmers by Jake Biesinger · 12 years ago
  43. e1dbea7 add subclass BasicVertex and fixing p2 by AnbangX · 12 years ago
  44. 46fc86e add test cases for removeBridge, removeTip and mergeBubble by AnbangX · 12 years ago
  45. db5d564 WIP H4 1 mapper + 2 reducers by Jake Biesinger · 12 years ago
  46. 5adaeec add merge and update utility functions by Jake Biesinger · 12 years ago
  47. 71ea5d2 Fix RFMerge and add tests by Jake Biesinger · 12 years ago
  48. 01ad7c2 Merge and fix FRMerge. RF still doesn't work. by Jake Biesinger · 12 years ago
  49. ab171ba refactor kmer mergeNext and mergePre -> mergeFF etc. untested :) by Jake Biesinger · 12 years ago
  50. a7216ac Add helper functions for mutating PositionListWritable's by Jake Biesinger · 12 years ago
  51. 24e076f PathNodeInitial identifies nodes needing updates by Jake Biesinger · 12 years ago
  52. cc77cf7 add test cases for path merge and other data clean patterns by AnbangX · 12 years ago
  53. 2c41eb3 add remove in PositionListWritable and test by AnbangX · 12 years ago
  54. 1e43ac4 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into jianfeng/genomix by Jianfeng Jia · 12 years ago
  55. 09cf1d1 facilitate better testing via more constructors and proper hashing/equals by Jake Biesinger · 12 years ago
  56. bc7e15f Merge branch 'genomix/fullstack_genomix' into jianfeng/genomix by Jianfeng Jia · 12 years ago
  57. bf8f525 Fix spelling by Jake Biesinger · 12 years ago
  58. 37cc20b hadoop graph building completion by Nan Zhang · 12 years ago
  59. eb8d72a Merge commit '951870ef4642f2003c4240eeef702fc90600fe77' into nanzhang/genomix by Nan Zhang · 12 years ago
  60. 3a26a3a merge with jianfeng-reverse by Nan Zhang · 12 years ago
  61. a591f26 clean up code and add copyright header by JavierJia · 12 years ago
  62. 12b4280 Merge branch 'jianfeng/genomix' into jianfeng/genomix-reverse by Jianfeng Jia · 12 years ago
  63. 5ba19e2 add more information for larger data debug by Jianfeng Jia · 12 years ago genomix/unidirection
  64. 562116a finished framework. not test yet by Jianfeng Jia · 12 years ago
  65. 8528899 finish framework by Jianfeng Jia · 12 years ago
  66. 5033f6f Update comment. by Jianfeng Jia · 12 years ago
  67. 587ddb7 finished merge pre and merge next test by Jianfeng Jia · 12 years ago
  68. 7f506a1 modify the DeepGraphBuildingMapper by Nan Zhang · 12 years ago
  69. 8663daa Merge branch 'nanzhang/genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  70. 0669e98 add isPathNode to NodeWritable by Jake Biesinger · 12 years ago
  71. 7c14c8f Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into jianfeng/genomix by Jianfeng Jia · 12 years ago
  72. 369fccb update the velvetGrapubuilding package by Nan Zhang · 12 years ago
  73. f14c403 add mergeNext function to kmerWritable by Jianfeng Jia · 12 years ago
  74. 7636684 refine the logic of generate Node by Jianfeng Jia · 12 years ago
  75. 103df19 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by AnbangX · 12 years ago
  76. f5d6db9 change all input and output format to new version by AnbangX · 12 years ago
  77. c49ce70 add package to build old package success by Nan Zhang · 12 years ago
  78. 529a089 finished EndToEnd test by Jianfeng Jia · 12 years ago
  79. 80b312a passed map kmer to readid operator by Jianfeng Jia · 12 years ago
  80. ee2e038 finished test framework by JavierJia · 12 years ago
  81. 1d11e0a finish position test by JavierJia · 12 years ago
  82. 5d192ad finished genomix-hyracks end to end by JavierJia · 12 years ago
  83. e85c8a7 merge with hadoop code by JavierJia · 12 years ago
  84. ee1fa17 Merge branch 'genomix/velvet_graphbuilding' of https://code.google.com/p/hyracks into genomix/velvet_graphbuilding by JavierJia · 12 years ago
  85. fe1391a passed genomix-data test by JavierJia · 12 years ago
  86. e34200e create some writable based on Jianfeng's hyracks by Nan Zhang · 12 years ago
  87. ba0d0d8 clean up kmerWritable by JavierJia · 12 years ago
  88. 4c33a7a finished framework by JavierJia · 12 years ago
  89. 136c411 finish mapKmerToReadID by JavierJia · 12 years ago
  90. 4803aea compatible with invalid read by Jianfeng Jia · 12 years ago
  91. 0495424 supprt zero-length kmer setting by JavierJia · 12 years ago
  92. e83982b add clearLeadBit into KmerOperation by JavierJia · 12 years ago
  93. 3c3f2b7 Change return value of shiftKmer from bitmap to genecode by JavierJia · 12 years ago
  94. bc974c4 change comparitor by JavierJia · 12 years ago
  95. 25e22f1 add protect to array index overflow by JavierJia · 12 years ago
  96. 483934a add getSubKmer function by JavierJia · 12 years ago
  97. 0076326 add default empty constructor for hadoop version by JavierJia · 12 years ago
  98. 0a7f115 make genomix-hyracks pass the test by JavierJia · 12 years ago
  99. 2bfbe83 add back old version of Kmer to support genomix-pregelix by JavierJia · 12 years ago
  100. 0c37dd0 make genomix-hadoop genomix-hyracks compilable by JavierJia · 12 years ago