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asterix-gerrit.ics.uci.edu / hyracks / 62127801b14c543e4a0a22b8ecdc90557ffa492c / genomix / genomix-pregelix
  1. 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
  2. 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
  3. 37a8489 Adapt MergeBubbleVertex to new graph structure. TODO: check if bubble flip and merge all metadata except kmer by Anbang Xu · 12 years ago
  4. c69d141 Add node to BubbleMessage by Anbang Xu · 12 years ago
  5. 14de2c6 save current state by Anbang Xu · 12 years ago
  6. 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  7. 4370b2b adapt TipAddVertex and TipRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  8. 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago
  9. e7885ee Pregel TestSuite is completed by Anbang Xu · 12 years ago
  10. 0e037c1 Prepare to clean up pregel testSuite by Anbang Xu · 12 years ago
  11. 6f88379 save current state and prepare to clean up hadoop test result by Anbang Xu · 12 years ago
  12. 5d431a1 temporary save modified state by Anbang Xu · 12 years ago
  13. b02033e BasicPathMergeVertex is completed by Anbang Xu · 12 years ago
  14. 0d72095 Make generic message class for all patterns by Anbang Xu · 12 years ago
  15. a5a1e63 Make basic msg class: MessageWritable and subclasses: PathMergeMessage, BubbleMergeMessage, BFSMessage by Anbang Xu · 12 years ago
  16. 6bdf197 add EdgeList[dir].getKeys() by Anbang Xu · 12 years ago
  17. 58875bf delete SelfPath.txt~ by Anbang Xu · 12 years ago
  18. c448987 refactoring edgelists; still some to do by Jake Biesinger · 12 years ago
  19. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  20. b1c9c7d P1ForPathMergeVertex is completed, but one issue about even length and message from both size can't be solve by Anbang Xu · 12 years ago
  21. 67c7e22 debuging SplitRepeatVertex by Anbang Xu · 12 years ago
  22. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  23. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  24. 1de8032 Half done BFSTraverseVertex Framework by Anbang Xu · 12 years ago
  25. f010494 adapt new NodeWritable and extends it in VertexValue by Anbang Xu · 12 years ago
  26. 361916b save current state by Anbang Xu · 12 years ago
  27. 52bda5c add new graph result to PathMergeTestSet by Anbang Xu · 12 years ago
  28. 813f143 adapt pregel package to new graph by Anbang Xu · 12 years ago
  29. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  30. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  31. 2065960 NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  32. 580f6cd add vertex.activate() to notice update and change DirectionFlag to 2 bits by Anbang Xu · 12 years ago
  33. 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  34. 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  35. 47fc29c NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  36. 8ded1a3 Clean genomix package and complete mergeing with Master by Anbang Xu · 12 years ago
  37. c5e5abc remove dependency on hyracks-hdfs-core test-jar by Jake Biesinger · 12 years ago
  38. 05fc10d clean pregel package for latest master by Anbang Xu · 12 years ago
  39. dfd2e50 fix genomix pom.xml's to use 0.2.10-SNAPSHOT by Jake Biesinger · 12 years ago
  40. e0b35ce Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  41. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  42. ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
  43. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  44. 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
  45. 61bfb93 add computeSimilarity and mergeAverageCoverage to MergeBubbleVertex by Anbang Xu · 12 years ago
  46. 4ac4a5b Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  47. 3744b98 fix the pom.xml for genomix-hadoop by Nan Zhang · 12 years ago
  48. cb4391e clean pregel package for build by Anbang Xu · 12 years ago
  49. c4961c9 complete MergeBubbleVertex & wait for compute fracSimilarity by Anbang Xu · 12 years ago
  50. 3986b17 debugging BubbleMergeVertex by Anbang Xu · 12 years ago
  51. 3e3144b cleanning continue by Nan Zhang · 12 years ago
  52. 8e8e99f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  53. 6ad60bf fix bug in readFields of KmerListWritable by Anbang Xu · 12 years ago
  54. 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
  55. ad800e8 more cleanup of setByRead interface by Jake Biesinger · 12 years ago genomix/before-nodeid-graph-cleanup-Aug2013
  56. b8626fd make GraphViz for test by Anbang Xu · 12 years ago
  57. 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  58. 9f949c4 MergeBubbleVertex half done by Anbang Xu · 12 years ago
  59. 39f1cf1 Merge commit '07acebba2c4470834919a82092faec0c982411e5' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  60. 07acebb Merge MergeBubbleMessageWritable to MessageWritable by Anbang Xu · 12 years ago
  61. ac6a090 Fix BubbleAddVertex and pass test by Anbang Xu · 12 years ago
  62. 6d8afff fix RemoveBridgeVertex and update for merge by Anbang Xu · 12 years ago
  63. ec095b2 RemoveTipVertex pass test by Anbang Xu · 12 years ago
  64. 95c432c BridgeAddVertex pass test by Anbang Xu · 12 years ago
  65. 6f81b59 small update by Anbang Xu · 12 years ago
  66. 714d906 adapt BridgeAddVertex to new graph construction by Anbang Xu · 12 years ago
  67. d1075a0 adapt TipAddVertex to new graph construction by Anbang Xu · 12 years ago
  68. aac7732 SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element by Anbang Xu · 12 years ago
  69. 0b9da1e Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  70. c68e510 finish the debugging by Nan Zhang · 12 years ago
  71. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  72. 34d3d73 there is an issue in KmerListWritable and try to fix it by Anbang Xu · 12 years ago
  73. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  74. ceab4c1 Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  75. 94e075b update for merge by Anbang Xu · 12 years ago
  76. 6ee7bdf fix HashSet in SplitRepeat by Anbang Xu · 12 years ago
  77. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  78. d57d7e5 add CreatedVertex and ConnectedTable by Anbang Xu · 12 years ago
  79. 37c6933 start coding SplitRepeat by Anbang Xu · 12 years ago
  80. 5412086 refactor LogAlgorithm to P2 by Anbang Xu · 12 years ago
  81. 9db1ea8 merge MapReduceVertex to p2 and p2 is completed by Anbang Xu · 12 years ago
  82. d94f5f9 refactor 'BasicPathMergeVertex' to 'BasicGraphCleanVertex', make it more general by Anbang Xu · 12 years ago
  83. 29ebdc8 Map/Reduce version in pregel is completed by Anbang Xu · 12 years ago
  84. 0f06660 start dependency refactor by Jake Biesinger · 12 years ago
  85. 5dfa7b6 add MapReduceVertex for mapper/reducer in pregel by Anbang Xu · 12 years ago
  86. d6276e7 p2 pass test by Anbang Xu · 12 years ago
  87. a9e482e update KmerListWritable to use fixed-length kmers by Jake Biesinger · 12 years ago
  88. b8e0097 p2 pass test9 by Anbang Xu · 12 years ago
  89. 9e00650 p2 pass all the tests except 9 by Anbang Xu · 12 years ago
  90. 2990977 debugging p2 by Anbang Xu · 12 years ago
  91. b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
  92. 1307443 P2 pass test1,2,3,4 by Anbang Xu · 12 years ago
  93. d253d8f fix mergeWithRFKmer by Anbang Xu · 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. 311001a start to change graph clean part to 'contrail-graph' structure by Anbang Xu · 12 years ago
  97. 4e9262f add GenomixMapper for new graph - 'contrail' by Anbang Xu · 12 years ago
  98. 8dbe728 refactor 'size' to 'kmerByteSize' in KmerBytesWritable by Anbang Xu · 12 years ago
  99. 970c74f move old key/value class to oldtype folder by Anbang Xu · 12 years ago
  100. c71a2d3 removeBridge pass tests by Anbang Xu · 12 years ago Alpha Alpha-Graph-v2.0