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asterix-gerrit.ics.uci.edu / hyracks / 68bf4b8eb5ce399aa4947595cea4ba1790c66964 / genomix / genomix-hadoop / src
  1. 83af358 static is redundant on enums by Jake Biesinger · 12 years ago
  2. 2279e99 remove kmerSize from GenomixReducer by Jake Biesinger · 12 years ago
  3. ac60f5b plot histograms of all statistics (in bubble gum red...) by Jake Biesinger · 12 years ago
  4. 97dd3be sort stats output by Jake Biesinger · 12 years ago
  5. 6bb2077 add STATS step, saving counters to txt file by Jake Biesinger · 12 years ago
  6. 89a4708 standardize kmer name in hadoop graphbuild by Jake Biesinger · 12 years ago
  7. 28162e5 add hadoop job for graph statistics (uses counters) by Jake Biesinger · 12 years ago
  8. a3ec17d Merge branch 'genomix/fullstack_genomix' into wbiesing/refactor_p4 by Jake Biesinger · 12 years ago
  9. 3e02877 refactor names in getKmerNeighbors.py by Jake Biesinger · 12 years ago
  10. f7d0baf Add enum EDGETYPE by Anbang Xu · 12 years ago
  11. fde129e update kmerNeighbors script by Jake Biesinger · 12 years ago
  12. 4273653 add ThreeNodesCycle, and it succeeds to pass test by Anbang Xu · 12 years ago
  13. 03ba0f7 Add simple RF FR RF test case by Jake Biesinger · 12 years ago
  14. 7b57ae6 add RandomSeed by Anbang Xu · 12 years ago
  15. 395ce71 Merge branch 'wbiesing/debug_hyracks_build' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  16. ebeba41 use ps in linux by Anbang Xu · 12 years ago
  17. 4a0d101 add neighbor-finding python script by Jake Biesinger · 12 years ago
  18. df811e5 add SymmetryChecker by Anbang Xu · 12 years ago
  19. 6c79239 add AAA testcase by Anbang Xu · 12 years ago
  20. 5de7afd remove incompatible words for results checking tool by Nan Zhang · 12 years ago
  21. d17a2a2 remove NLineInputFormat for hadoop graph building by Nan Zhang · 12 years ago
  22. b204a4a remove the io.sort factor in hadoop by Nan Zhang · 12 years ago
  23. 4b21369 Fix TandemRepeatAndCycle bug by Anbang Xu · 12 years ago
  24. 3e91447 add test case for tandem repeats with multiple self-edges by Jake Biesinger · 12 years ago
  25. 5ecb66f seperate MessageFlag and State by Anbang Xu · 12 years ago
  26. 55a9adc add test case for P2 by Anbang Xu · 12 years ago
  27. 558ea60 Merge aggregator with main branch by Anbang Xu · 12 years ago
  28. 50b28b6 Adpat hadoop testsuite to have linespermap arg by Anbang Xu · 12 years ago
  29. 806ff79 add linesPerMap parameter to hadoop graph building driver by Anbang Xu · 12 years ago
  30. 4da15b2 add many similar bubbles in one pattern test case and BubbleMerge pass test by Anbang Xu · 12 years ago
  31. 6ec5f66 don't use NLineInputFormat for now by Jake Biesinger · 12 years ago
  32. 270d47a add NlineInputFormat by Nan Zhang · 12 years ago
  33. 014dafc add graph building checking job by Nan Zhang · 12 years ago
  34. 7ac727c Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  35. 9fdf74d larger chunks for hadoop graphbuilding by Jake Biesinger · 12 years ago
  36. 8c187a6 add RandonWalk test case by Anbang Xu · 12 years ago
  37. f9e6e5f add hadoop building to the driver by Jake Biesinger · 12 years ago
  38. 39cfc58 add synthetic test case by Jake Biesinger · 12 years ago
  39. b19ba95 BubbleMerge pass complicated test cases by Anbang Xu · 12 years ago
  40. 32a956b fix one bug in path merge by Anbang Xu · 12 years ago
  41. 26e7332 BubbleMerge test is almost finished except grid test case by Anbang Xu · 12 years ago
  42. c0b37b1 change bubble's pre-condition -- pathNode to anyNode by Anbang Xu · 12 years ago
  43. e763a06 add complicated test case for BubbleMerge by Anbang Xu · 12 years ago
  44. 6ddc6cc testing BubbleMerge by Anbang Xu · 12 years ago
  45. 3aba0f0 SplitRepeat test is completed by Anbang Xu · 12 years ago
  46. 4a9e45c Add testcases for SplitRepeat by Anbang Xu · 12 years ago
  47. d688b5a Add skip tandem repeat to pathmerge. TODO: detect cycle in pathmerge by Anbang Xu · 12 years ago
  48. 569945a add RF/FR with/without head test for pathmerge by Anbang Xu · 12 years ago
  49. 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
  50. d06c50f add testcase for pathmerge by Anbang Xu · 12 years ago
  51. de3a280 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  52. df21153 complete hyracks graph building Junit4 Testing normalization by Nan Zhang · 12 years ago
  53. e7856d5 Adapt ScaffoldingVertex to new graph structure by Anbang Xu · 12 years ago
  54. 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
  55. 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
  56. 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  57. 128eb0e Revert "update hyracks_genomix branch" by Nan Zhang · 12 years ago
  58. 9a664b7 update hyracks_genomix branch by Nan Zhang · 12 years ago
  59. 7401944 test cases again :) by Jake Biesinger · 12 years ago
  60. 585dbb5 fastq parser for hadoop graphbuild by Jake Biesinger · 12 years ago
  61. 202f2ab Hadoop graphbuild uses filename for mateid; tests by Jake Biesinger · 12 years ago
  62. 6266614 Simplify edgewritable interface by Jake Biesinger · 12 years ago
  63. 2d17c5b Complete the Graph construction(Hadoop) by Anbang Xu · 12 years ago
  64. e73873e merge with new argmented graph by Anbang Xu · 12 years ago
  65. 034979c Partial refactor following edge type changes in NodeWritable by Jake Biesinger · 12 years ago
  66. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  67. 13348bf Graph construcion is completed by Anbang Xu · 12 years ago
  68. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  69. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  70. 52bda5c add new graph result to PathMergeTestSet by Anbang Xu · 12 years ago
  71. 7812d08 Augment graph construction(hadoop) -- add ThreadList and 5PReaedId by Anbang Xu · 12 years ago
  72. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  73. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  74. 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  75. 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  76. 1afcd2b add graph package by Anbang Xu · 12 years ago
  77. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  78. ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
  79. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  80. 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
  81. 19b758e ervoer testUtils by Nan Zhang · 12 years ago
  82. 931fcc8 clean genomixMiniCluster by Nan Zhang · 12 years ago
  83. 3e3144b cleanning continue by Nan Zhang · 12 years ago
  84. 7dc9400 clean the useless code for project by Nan Zhang · 12 years ago
  85. 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
  86. 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  87. 95c432c BridgeAddVertex pass test by Anbang Xu · 12 years ago
  88. aac7732 SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element by Anbang Xu · 12 years ago
  89. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  90. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  91. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  92. 0f06660 start dependency refactor by Jake Biesinger · 12 years ago
  93. b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
  94. a5e97c7 p4 pass test by Anbang Xu · 12 years ago
  95. 4416d3c debugging p4 by Anbang Xu · 12 years ago
  96. dfa14d3 Fix NodeWritable and Finish contrail-graph Mapper/Reducer by Anbang Xu · 12 years ago genomix/velvet-graph-pregel
  97. 84e385f Try to add globe kmerSize but fail in testing by Anbang Xu · 12 years ago
  98. bcf5a70 add hadoop test and keep both bin and txt by Anbang Xu · 12 years ago
  99. f7a23e4 add Reducer and change PositionWritable to PositionListWritable in NodeWritable by Anbang Xu · 12 years ago
  100. 0c644f4 Mapper passes test by Anbang Xu · 12 years ago