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asterix-gerrit.ics.uci.edu / hyracks / d5f760c40c6d5c52ac067ae8766ef401e0075271 / genomix / genomix-pregelix
  1. d5f760c add p2 graph input format, initiate prependMergeNode and appendMergeNode by Anbang Xu · 12 years ago
  2. 188c182 add processP2Merge to P2, P2 need a specific merge method by Anbang Xu · 12 years ago
  3. dd52a40 add getMessageType and getMergeNode to P2Message by Anbang Xu · 12 years ago
  4. d94f456 using prependNode and appendNode instead of LinkedList of mergeNodes by Anbang Xu · 12 years ago
  5. 1f85b15 add parameter(mergeDest) to configureMergeMsgToNeighber by Anbang Xu · 12 years ago
  6. 5983e8b add P2ValueWritable and P2MessageWritable to P2 by Anbang Xu · 12 years ago
  7. 065eec8 Clean up io folder by Anbang Xu · 12 years ago
  8. 362358f seperate io folder to io.common and io.message by Anbang Xu · 12 years ago
  9. 183807a add GraphCleanVertexInputFormat and GraphCleanVertexOutputFormat by Anbang Xu · 12 years ago
  10. eb09388 Adapt all clean patterns to use subclass V by Anbang Xu · 12 years ago
  11. e0dff62 add MessageType class to store msg type from head by Anbang Xu · 12 years ago
  12. 01c5e31 add subclass V to extend VertexValueWritable by Anbang Xu · 12 years ago
  13. d4b0267 refactor newState to state, there is no new state by Anbang Xu · 12 years ago
  14. d488e98 refactor MessageTypeFromHead to MessageType(P2) by Anbang Xu · 12 years ago
  15. 7616083 add only old head update edges by Anbang Xu · 12 years ago
  16. 9bbef65 make name more readable, refactor setPredecessorMsg to setPredecessorToMeDir by Anbang Xu · 12 years ago
  17. f5e5816 override sendUpdateMsg without parameter by Anbang Xu · 12 years ago
  18. 38db5c3 add linkedListWritable for P2 by Anbang Xu · 12 years ago
  19. 36fb2e2 Merge with main brnach by Anbang Xu · 12 years ago
  20. 8f6b461 refactor pregelix job creation by Anbang Xu · 12 years ago
  21. 5cda522 format test case by Anbang Xu · 12 years ago
  22. 2246913 Small change by Anbang Xu · 12 years ago
  23. a90fdd9 update pregelix vertexes to initialize static values by Jake Biesinger · 12 years ago
  24. a1b1e45 add simple command to each pattern by Anbang Xu · 12 years ago
  25. 86edb32 change command for scaffolding by Anbang Xu · 12 years ago
  26. 423fd16 Fix all synchronization issues by Anbang Xu · 12 years ago
  27. 81833a0 add scaffoldingAggregator by Anbang Xu · 12 years ago
  28. ee7dac3 Add synchronization to static variable by Anbang Xu · 12 years ago
  29. 7a47e8b Begin to debug P2 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. a9c60b3 The aggregator for all the patterns are completed by Anbang Xu · 12 years ago
  32. 1aed014 add statistics counters to removeTip, pathMerge, removeBridge by Anbang Xu · 12 years ago
  33. 7f2208f PathMerge aggregator is completed by Anbang Xu · 12 years ago
  34. 52a279f Aggregator passes test by Anbang Xu · 12 years ago
  35. b1c7809 testing by Anbang Xu · 12 years ago
  36. f3a548c move aggregator output to test by Anbang Xu · 12 years ago
  37. ca28b1b add StatisticsCounterAggregator by Anbang Xu · 12 years ago
  38. 8c187a6 add RandonWalk test case by Anbang Xu · 12 years ago
  39. 88e9442 RemoveTip pass test by Anbang Xu · 12 years ago
  40. e71a964 Unroll Repeat pass test by Anbang Xu · 12 years ago
  41. 17b99f2 add stop haltNode in pathmerge and fix the bug Jake mentioned by Anbang Xu · 12 years ago
  42. 39cfc58 add synthetic test case by Jake Biesinger · 12 years ago
  43. 9dec13e remove generated genomix-pregel test case xml files by Jake Biesinger · 12 years ago
  44. c2aa582 Merge branch 'anbangx/backupMergingWithMaster' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  45. 1e03787 Merge branch 'anbangx/backupMergingWithMaster_errorcase' into wbiesing/merge_fs_backup by Jake Biesinger · 12 years ago
  46. b19ba95 BubbleMerge pass complicated test cases by Anbang Xu · 12 years ago
  47. fc4fe25 add failing pathmerge testcase by Jake Biesinger · 12 years ago
  48. 32a956b fix one bug in path merge by Anbang Xu · 12 years ago
  49. 630586c add test case for synthetic data by Jake Biesinger · 12 years ago
  50. 5747845 Pregelix JobGenerator uses proper GenomixJobConf by Jake Biesinger · 12 years ago
  51. 96eab83 Merge branch 'anbangx/backupMergingWithMaster' into wbiesing/driver_backup_merge by Jake Biesinger · 12 years ago
  52. 26e7332 BubbleMerge test is almost finished except grid test case by Anbang Xu · 12 years ago
  53. ab0b235 test Rectangle by Anbang Xu · 12 years ago
  54. 85dfedf Add broadcaseKillselfAndNoticeToUpdateEdges and responseToDeadVertexAndUpdateEdges by Anbang Xu · 12 years ago
  55. c0b37b1 change bubble's pre-condition -- pathNode to anyNode by Anbang Xu · 12 years ago
  56. 97d97cd add bubble's addReadIDs by Jake Biesinger · 12 years ago
  57. e763a06 add complicated test case for BubbleMerge by Anbang Xu · 12 years ago
  58. 25a66b3 stop removing `expected` dir during clean (used for testing) by Jake Biesinger · 12 years ago
  59. 6ddc6cc testing BubbleMerge by Anbang Xu · 12 years ago
  60. 3aba0f0 SplitRepeat test is completed by Anbang Xu · 12 years ago
  61. 0ea5c92 Remove pregel dependence on hadoop and hyracks by Anbang Xu · 12 years ago
  62. 41ffd05 Merge with main branch by Anbang Xu · 12 years ago
  63. 4a9e45c Add testcases for SplitRepeat by Anbang Xu · 12 years ago
  64. 8270c5a Merge cycle to a single node in path merge. P4 test is completed by Anbang Xu · 12 years ago
  65. d688b5a Add skip tandem repeat to pathmerge. TODO: detect cycle in pathmerge by Anbang Xu · 12 years ago
  66. 74dd489 fix appassembler for pregelix by Jake Biesinger · 12 years ago
  67. adac3ef modify path for static test in driver by Jake Biesinger · 12 years ago
  68. 87b679f Merge branch 'anbangx/fullstack_genomix' into wbiesing/driver by Jake Biesinger · 12 years ago
  69. 2f3e3bb PathMerge pass test except TandemRepeat. TODO: skip TandemRepeat in pathmerge by Anbang Xu · 12 years ago
  70. 03434ff add hyracks-built graph as a pregelix test case by Jake Biesinger · 12 years ago
  71. 569945a add RF/FR with/without head test for pathmerge by Anbang Xu · 12 years ago
  72. 7a75b07 add updateEdges for pathmerge. Issue: mergeWithStartreads by Anbang Xu · 12 years ago
  73. 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
  74. 6fc84f1 Add additional merge info to pathmerge by Anbang Xu · 12 years ago
  75. d06c50f add testcase for pathmerge by Anbang Xu · 12 years ago
  76. fea8393 add unrollTandem to driver by Jake Biesinger · 12 years ago
  77. bb9901e re-remove nodes cleared out of Anbang's branch by Jake Biesinger · 12 years ago
  78. b7d6d4f add convenience functions for new Jobs in genomix-pregelix operators by Jake Biesinger · 12 years ago
  79. 2accbdf remove constants from new pregelix code by Jake Biesinger · 12 years ago
  80. 58a483d remove old config files by Jake Biesinger · 12 years ago
  81. 6eade1d use local test cluster by Jake Biesinger · 12 years ago
  82. 639c806 separate config from driver and pipeline setup by Jake Biesinger · 12 years ago
  83. 4f05864 Refactor configuration for all jobs into global GenomixJobConf by Jake Biesinger · 12 years ago
  84. ced394a Make pathmerge robost by Anbang Xu · 12 years ago
  85. ca15771 UnrollTandemRepeat is completed by Anbang Xu · 12 years ago
  86. b37b705 Add UnRollTandemRepeat. TODO: add the corresponding MSG and update edges by Anbang Xu · 12 years ago
  87. 6efa434 Completed P2 debugging by Anbang Xu · 12 years ago
  88. a3c0538 Clean up P2 code and prepare to deep debug it by Anbang Xu · 12 years ago
  89. feec5be Fix BubbleMerge by Anbang Xu · 12 years ago
  90. 5e01f76 Adapt RemoveLowCoverageVertex to new graph structure. Finally, all the patterns are adapted to new graph by Anbang Xu · 12 years ago
  91. e7856d5 Adapt ScaffoldingVertex to new graph structure by Anbang Xu · 12 years ago
  92. c970d65 Adapt BTSTraverseVertex to new graph structure by Anbang Xu · 12 years ago
  93. 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
  94. 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
  95. 37a8489 Adapt MergeBubbleVertex to new graph structure. TODO: check if bubble flip and merge all metadata except kmer by Anbang Xu · 12 years ago
  96. c69d141 Add node to BubbleMessage by Anbang Xu · 12 years ago
  97. 14de2c6 save current state by Anbang Xu · 12 years ago
  98. 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  99. 4370b2b adapt TipAddVertex and TipRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  100. 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago