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asterix-gerrit.ics.uci.edu / hyracks / 7812d08bce6f6160cef01419da68ea86d3f9113d / genomix / genomix-hadoop / src
  1. 7812d08 Augment graph construction(hadoop) -- add ThreadList and 5PReaedId by Anbang Xu · 12 years ago
  2. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  3. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  4. 1afcd2b add graph package by Anbang Xu · 12 years ago
  5. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  6. ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
  7. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  8. 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
  9. 19b758e ervoer testUtils by Nan Zhang · 12 years ago
  10. 931fcc8 clean genomixMiniCluster by Nan Zhang · 12 years ago
  11. 3e3144b cleanning continue by Nan Zhang · 12 years ago
  12. 7dc9400 clean the useless code for project by Nan Zhang · 12 years ago
  13. 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
  14. 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  15. 95c432c BridgeAddVertex pass test by Anbang Xu · 12 years ago
  16. aac7732 SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element by Anbang Xu · 12 years ago
  17. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  18. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  19. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  20. 0f06660 start dependency refactor by Jake Biesinger · 12 years ago
  21. b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
  22. a5e97c7 p4 pass test by Anbang Xu · 12 years ago
  23. 4416d3c debugging p4 by Anbang Xu · 12 years ago
  24. dfa14d3 Fix NodeWritable and Finish contrail-graph Mapper/Reducer by Anbang Xu · 12 years ago genomix/velvet-graph-pregel
  25. 84e385f Try to add globe kmerSize but fail in testing by Anbang Xu · 12 years ago
  26. bcf5a70 add hadoop test and keep both bin and txt by Anbang Xu · 12 years ago
  27. f7a23e4 add Reducer and change PositionWritable to PositionListWritable in NodeWritable by Anbang Xu · 12 years ago
  28. 0c644f4 Mapper passes test by Anbang Xu · 12 years ago
  29. 32bc798 finish Mapper and start Reducer by Anbang Xu · 12 years ago
  30. 4e9262f add GenomixMapper for new graph - 'contrail' by Anbang Xu · 12 years ago
  31. 3335bb6 hadoop for contrail graph by Anbang Xu · 12 years ago
  32. 8dbe728 refactor 'size' to 'kmerByteSize' in KmerBytesWritable by Anbang Xu · 12 years ago
  33. 6b45971 Fix H4, test templates by Jake Biesinger · 12 years ago
  34. 970c74f move old key/value class to oldtype folder by Anbang Xu · 12 years ago
  35. 76b3277 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  36. f947fb8 add test suite case for removetip/removebridge/pathmerge by Anbang Xu · 12 years ago
  37. 54f79fb add expected output for pathmerge (singleread) by Jake Biesinger · 12 years ago
  38. fb347c0 Add test cases as input graphs by Jake Biesinger · 12 years ago
  39. 8f719e0 Use BuildAllGraphs by Jake Biesinger · 12 years ago
  40. d8f5c89 Formulate test code by Anbang Xu · 12 years ago
  41. 48c0cec q by Jake Biesinger · 12 years ago
  42. b679646 Add more test cases for path merge by Jake Biesinger · 12 years ago
  43. ac4a3fb add script for simple random read generation by Jake Biesinger · 12 years ago
  44. 4bb565e use argparse for python plotting by Jake Biesinger · 12 years ago
  45. 67e67aa more test cases by Jake Biesinger · 12 years ago
  46. c408358 Add python script for visualizing graphs by Jacob Biesinger · 12 years ago
  47. 2049ae8 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jacob Biesinger · 12 years ago
  48. 5c0184f Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  49. 8eac65c Add data for few test cases by Jake Biesinger · 12 years ago
  50. 6a6f6bc Fix old merge leftovers by Jacob Biesinger · 12 years ago
  51. b5c8428 test cases by AnbangX · 12 years ago
  52. 0fd527e Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  53. 8c8f194 test cases by Jake Biesinger · 12 years ago
  54. 5c31812 Add expected outputs for a few simple tests by Jake Biesinger · 12 years ago
  55. 15d0a8f Add sequences for simple test cases by Jake Biesinger · 12 years ago
  56. 8e4fbc3 test cases and fixes for H4 by Jake Biesinger · 12 years ago
  57. 1dea1ea PathNodeInitial uses 2 output bins instead of 3 by Jake Biesinger · 12 years ago
  58. d31a1b4 use local maximum (not min) for h4 by Jake Biesinger · 12 years ago
  59. 93e9c22 debugging p4 and fix random seed issue by AnbangX · 12 years ago
  60. 98dae20 H4 complete; fix probBeingHead by Jake Biesinger · 12 years ago
  61. 21ad290 Code review with Jake on H4 by AnbangX · 12 years ago
  62. 26d9f46 Fix nodewritable merge logic by Jake Biesinger · 12 years ago
  63. af826b9 gc optimize h4 reduce by Jake Biesinger · 12 years ago
  64. 64ae953 Add mergeInDir for kmers by Jake Biesinger · 12 years ago
  65. db5d564 WIP H4 1 mapper + 2 reducers by Jake Biesinger · 12 years ago
  66. 974c47f refactor h4 update mapper to use update messages by Jake Biesinger · 12 years ago
  67. 5adaeec add merge and update utility functions by Jake Biesinger · 12 years ago
  68. 3cda435 Remove tests using MRUnit (whose old API doesn't work with MultipleOutputs) by Jake Biesinger · 12 years ago
  69. 1f0b7d5 refactor MergePaths message types to use directions and message types by Jake Biesinger · 12 years ago
  70. 3e70ffe PathNodeInitial updateable optimization by Jake Biesinger · 12 years ago
  71. 24e076f PathNodeInitial identifies nodes needing updates by Jake Biesinger · 12 years ago
  72. 1920264 refactor: MessageFlag is now MergeMessageFlag by Jake Biesinger · 12 years ago
  73. 7c1d870 H4 driver works with multipleOutputs by Jake Biesinger · 12 years ago
  74. f20a7e7 Fix path separators in test cases by Jake Biesinger · 12 years ago
  75. 76cc619 simplify graphbuilding driver by Jake Biesinger · 12 years ago
  76. 86e8c3a simplify driver and test case for h4 graph building by Jake Biesinger · 12 years ago
  77. 87a1029 mergepaths uses multipleoutputs properly (prep for update code) by Jake Biesinger · 12 years ago
  78. c0e90ce simplify hadoop graphbuilding test case by Jake Biesinger · 12 years ago
  79. ec499a1 remove tips initial by Jake Biesinger · 12 years ago
  80. 82b237b Better testing for initial path merge by Jake Biesinger · 12 years ago
  81. 09cf1d1 facilitate better testing via more constructors and proper hashing/equals by Jake Biesinger · 12 years ago
  82. 90752e7 non-path nodes are pushed to "complete" output by Jake Biesinger · 12 years ago
  83. 57971b6 path node works for complex starts by Jake Biesinger · 12 years ago
  84. e0fa424 Update H4 to new graph style by Jake Biesinger · 12 years ago
  85. 5932b3b fix test case paths by Jake Biesinger · 12 years ago
  86. bf8f525 Fix spelling by Jake Biesinger · 12 years ago
  87. 9ac3f6c reformat by Jake Biesinger · 12 years ago
  88. 03364d3 restore strangely deleted MergePaths code by Jake Biesinger · 12 years ago
  89. d91b4fb Fix H3 test case by Jake Biesinger · 12 years ago
  90. 5215ff5 Updated base class for tests allows mutliple Test cases by Jake Biesinger · 12 years ago
  91. 79da38a clean code by Nan Zhang · 12 years ago
  92. 5d3d527 delete he pcommon by Nan Zhang · 12 years ago
  93. 37cc20b hadoop graph building completion by Nan Zhang · 12 years ago
  94. e66c773 build graph by Nan Zhang · 12 years ago
  95. eb8d72a Merge commit '951870ef4642f2003c4240eeef702fc90600fe77' into nanzhang/genomix by Nan Zhang · 12 years ago
  96. 3a26a3a merge with jianfeng-reverse by Nan Zhang · 12 years ago
  97. 3931ef7 Broke test cases into base class plus small tests by Jake Biesinger · 12 years ago
  98. e7b1730 Merge branch 'genomix/fullstack_bidirection' into jianfeng/genomix-reverse by Jianfeng Jia · 12 years ago
  99. f8261bc Add a unit test for H3 which builds the graph by Jake Biesinger · 12 years ago
  100. 9bc1c38 modify building by Nan Zhang · 12 years ago