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asterix-gerrit.ics.uci.edu / hyracks / 1aad5349b08558eb1e9eb65654464f4c2a4e17af / genomix / genomix-hadoop / src
  1. de3a280 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  2. df21153 complete hyracks graph building Junit4 Testing normalization by Nan Zhang · 12 years ago
  3. e7856d5 Adapt ScaffoldingVertex to new graph structure by Anbang Xu · 12 years ago
  4. 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
  5. 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
  6. 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  7. 128eb0e Revert "update hyracks_genomix branch" by Nan Zhang · 12 years ago
  8. 9a664b7 update hyracks_genomix branch by Nan Zhang · 12 years ago
  9. 7401944 test cases again :) by Jake Biesinger · 12 years ago
  10. 585dbb5 fastq parser for hadoop graphbuild by Jake Biesinger · 12 years ago
  11. 202f2ab Hadoop graphbuild uses filename for mateid; tests by Jake Biesinger · 12 years ago
  12. 6266614 Simplify edgewritable interface by Jake Biesinger · 12 years ago
  13. 2d17c5b Complete the Graph construction(Hadoop) by Anbang Xu · 12 years ago
  14. e73873e merge with new argmented graph by Anbang Xu · 12 years ago
  15. 034979c Partial refactor following edge type changes in NodeWritable by Jake Biesinger · 12 years ago
  16. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  17. 13348bf Graph construcion is completed by Anbang Xu · 12 years ago
  18. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  19. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  20. 52bda5c add new graph result to PathMergeTestSet by Anbang Xu · 12 years ago
  21. 7812d08 Augment graph construction(hadoop) -- add ThreadList and 5PReaedId by Anbang Xu · 12 years ago
  22. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  23. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  24. 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  25. 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  26. 1afcd2b add graph package by Anbang Xu · 12 years ago
  27. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  28. ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
  29. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  30. 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
  31. 19b758e ervoer testUtils by Nan Zhang · 12 years ago
  32. 931fcc8 clean genomixMiniCluster by Nan Zhang · 12 years ago
  33. 3e3144b cleanning continue by Nan Zhang · 12 years ago
  34. 7dc9400 clean the useless code for project by Nan Zhang · 12 years ago
  35. 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
  36. 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  37. 95c432c BridgeAddVertex pass test by Anbang Xu · 12 years ago
  38. aac7732 SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element by Anbang Xu · 12 years ago
  39. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  40. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  41. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  42. 0f06660 start dependency refactor by Jake Biesinger · 12 years ago
  43. b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
  44. a5e97c7 p4 pass test by Anbang Xu · 12 years ago
  45. 4416d3c debugging p4 by Anbang Xu · 12 years ago
  46. dfa14d3 Fix NodeWritable and Finish contrail-graph Mapper/Reducer by Anbang Xu · 12 years ago genomix/velvet-graph-pregel
  47. 84e385f Try to add globe kmerSize but fail in testing by Anbang Xu · 12 years ago
  48. bcf5a70 add hadoop test and keep both bin and txt by Anbang Xu · 12 years ago
  49. f7a23e4 add Reducer and change PositionWritable to PositionListWritable in NodeWritable by Anbang Xu · 12 years ago
  50. 0c644f4 Mapper passes test by Anbang Xu · 12 years ago
  51. 32bc798 finish Mapper and start Reducer by Anbang Xu · 12 years ago
  52. 4e9262f add GenomixMapper for new graph - 'contrail' by Anbang Xu · 12 years ago
  53. 3335bb6 hadoop for contrail graph by Anbang Xu · 12 years ago
  54. 8dbe728 refactor 'size' to 'kmerByteSize' in KmerBytesWritable by Anbang Xu · 12 years ago
  55. 6b45971 Fix H4, test templates by Jake Biesinger · 12 years ago
  56. 970c74f move old key/value class to oldtype folder by Anbang Xu · 12 years ago
  57. 76b3277 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  58. f947fb8 add test suite case for removetip/removebridge/pathmerge by Anbang Xu · 12 years ago
  59. 54f79fb add expected output for pathmerge (singleread) by Jake Biesinger · 12 years ago
  60. fb347c0 Add test cases as input graphs by Jake Biesinger · 12 years ago
  61. 8f719e0 Use BuildAllGraphs by Jake Biesinger · 12 years ago
  62. d8f5c89 Formulate test code by Anbang Xu · 12 years ago
  63. 48c0cec q by Jake Biesinger · 12 years ago
  64. b679646 Add more test cases for path merge by Jake Biesinger · 12 years ago
  65. ac4a3fb add script for simple random read generation by Jake Biesinger · 12 years ago
  66. 4bb565e use argparse for python plotting by Jake Biesinger · 12 years ago
  67. 67e67aa more test cases by Jake Biesinger · 12 years ago
  68. c408358 Add python script for visualizing graphs by Jacob Biesinger · 12 years ago
  69. 2049ae8 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jacob Biesinger · 12 years ago
  70. 5c0184f Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  71. 8eac65c Add data for few test cases by Jake Biesinger · 12 years ago
  72. 6a6f6bc Fix old merge leftovers by Jacob Biesinger · 12 years ago
  73. b5c8428 test cases by AnbangX · 12 years ago
  74. 0fd527e Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  75. 8c8f194 test cases by Jake Biesinger · 12 years ago
  76. 5c31812 Add expected outputs for a few simple tests by Jake Biesinger · 12 years ago
  77. 15d0a8f Add sequences for simple test cases by Jake Biesinger · 12 years ago
  78. 8e4fbc3 test cases and fixes for H4 by Jake Biesinger · 12 years ago
  79. 1dea1ea PathNodeInitial uses 2 output bins instead of 3 by Jake Biesinger · 12 years ago
  80. d31a1b4 use local maximum (not min) for h4 by Jake Biesinger · 12 years ago
  81. 93e9c22 debugging p4 and fix random seed issue by AnbangX · 12 years ago
  82. 98dae20 H4 complete; fix probBeingHead by Jake Biesinger · 12 years ago
  83. 21ad290 Code review with Jake on H4 by AnbangX · 12 years ago
  84. 26d9f46 Fix nodewritable merge logic by Jake Biesinger · 12 years ago
  85. af826b9 gc optimize h4 reduce by Jake Biesinger · 12 years ago
  86. 64ae953 Add mergeInDir for kmers by Jake Biesinger · 12 years ago
  87. db5d564 WIP H4 1 mapper + 2 reducers by Jake Biesinger · 12 years ago
  88. 974c47f refactor h4 update mapper to use update messages by Jake Biesinger · 12 years ago
  89. 5adaeec add merge and update utility functions by Jake Biesinger · 12 years ago
  90. 3cda435 Remove tests using MRUnit (whose old API doesn't work with MultipleOutputs) by Jake Biesinger · 12 years ago
  91. 1f0b7d5 refactor MergePaths message types to use directions and message types by Jake Biesinger · 12 years ago
  92. 3e70ffe PathNodeInitial updateable optimization by Jake Biesinger · 12 years ago
  93. 24e076f PathNodeInitial identifies nodes needing updates by Jake Biesinger · 12 years ago
  94. 1920264 refactor: MessageFlag is now MergeMessageFlag by Jake Biesinger · 12 years ago
  95. 7c1d870 H4 driver works with multipleOutputs by Jake Biesinger · 12 years ago
  96. f20a7e7 Fix path separators in test cases by Jake Biesinger · 12 years ago
  97. 76cc619 simplify graphbuilding driver by Jake Biesinger · 12 years ago
  98. 86e8c3a simplify driver and test case for h4 graph building by Jake Biesinger · 12 years ago
  99. 87a1029 mergepaths uses multipleoutputs properly (prep for update code) by Jake Biesinger · 12 years ago
  100. c0e90ce simplify hadoop graphbuilding test case by Jake Biesinger · 12 years ago