Gitiles
Code Review Sign In
asterix-gerrit.ics.uci.edu / hyracks / 9c01d098f621a79fd1fff4ed22eec22f7bc89ddd / genomix
  1. 9c01d09 Fix mergeReadID RF and RR by Jake Biesinger · 12 years ago
  2. 569945a add RF/FR with/without head test for pathmerge by Anbang Xu · 12 years ago
  3. 7a75b07 add updateEdges for pathmerge. Issue: mergeWithStartreads by Anbang Xu · 12 years ago
  4. 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
  5. 6fc84f1 Add additional merge info to pathmerge by Anbang Xu · 12 years ago
  6. d06c50f add testcase for pathmerge by Anbang Xu · 12 years ago
  7. 56e291f Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  8. ced394a Make pathmerge robost by Anbang Xu · 12 years ago
  9. ca15771 UnrollTandemRepeat is completed by Anbang Xu · 12 years ago
  10. b37b705 Add UnRollTandemRepeat. TODO: add the corresponding MSG and update edges by Anbang Xu · 12 years ago
  11. fc7d4b8 fix the positionWritable unionUpdate(), and add automatic test case by Nan Zhang · 12 years ago
  12. 6efa434 Completed P2 debugging by Anbang Xu · 12 years ago
  13. c00e007 add graphviz by Nan Zhang · 12 years ago
  14. a4e850d add license header for hyracks by Nan Zhang · 12 years ago
  15. ca84702 Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  16. a3c0538 Clean up P2 code and prepare to deep debug it by Anbang Xu · 12 years ago
  17. feec5be Fix BubbleMerge by Anbang Xu · 12 years ago
  18. de3a280 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  19. 15306ff small modification by Nan Zhang · 12 years ago
  20. 4903be0 add expected file by Nan Zhang · 12 years ago
  21. 5e01f76 Adapt RemoveLowCoverageVertex to new graph structure. Finally, all the patterns are adapted to new graph by Anbang Xu · 12 years ago
  22. df21153 complete hyracks graph building Junit4 Testing normalization by Nan Zhang · 12 years ago
  23. e7856d5 Adapt ScaffoldingVertex to new graph structure by Anbang Xu · 12 years ago
  24. c970d65 Adapt BTSTraverseVertex to new graph structure by Anbang Xu · 12 years ago
  25. 000fa26 getReadIDs added to EdgeWritable by Jake Biesinger · 12 years ago
  26. 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
  27. 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
  28. 37a8489 Adapt MergeBubbleVertex to new graph structure. TODO: check if bubble flip and merge all metadata except kmer by Anbang Xu · 12 years ago
  29. c69d141 Add node to BubbleMessage by Anbang Xu · 12 years ago
  30. 14de2c6 save current state by Anbang Xu · 12 years ago
  31. 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  32. 4370b2b adapt TipAddVertex and TipRemoveVertex to new graph structure by Anbang Xu · 12 years ago
  33. 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago
  34. e7885ee Pregel TestSuite is completed by Anbang Xu · 12 years ago
  35. 0e037c1 Prepare to clean up pregel testSuite by Anbang Xu · 12 years ago
  36. 6f88379 save current state and prepare to clean up hadoop test result by Anbang Xu · 12 years ago
  37. 5d431a1 temporary save modified state by Anbang Xu · 12 years ago
  38. 3786935 hyracks graph building test complete. by Nan Zhang · 12 years ago
  39. b02033e BasicPathMergeVertex is completed by Anbang Xu · 12 years ago
  40. 0d72095 Make generic message class for all patterns by Anbang Xu · 12 years ago
  41. 128eb0e Revert "update hyracks_genomix branch" by Nan Zhang · 12 years ago
  42. 9a664b7 update hyracks_genomix branch by Nan Zhang · 12 years ago
  43. a5a1e63 Make basic msg class: MessageWritable and subclasses: PathMergeMessage, BubbleMergeMessage, BFSMessage by Anbang Xu · 12 years ago
  44. 7401944 test cases again :) by Jake Biesinger · 12 years ago
  45. 585dbb5 fastq parser for hadoop graphbuild by Jake Biesinger · 12 years ago
  46. 6bdf197 add EdgeList[dir].getKeys() by Anbang Xu · 12 years ago
  47. 58875bf delete SelfPath.txt~ by Anbang Xu · 12 years ago
  48. 9296bb6 Add EdgeList.getKeys for iterating over keys by Jake Biesinger · 12 years ago
  49. 202f2ab Hadoop graphbuild uses filename for mateid; tests by Jake Biesinger · 12 years ago
  50. 6266614 Simplify edgewritable interface by Jake Biesinger · 12 years ago
  51. 2d17c5b Complete the Graph construction(Hadoop) by Anbang Xu · 12 years ago
  52. 60782f4 Add test cases; reinstate compareTo function use Hadoop's version by Jake Biesinger · 12 years ago
  53. 35875ce removed cursed autogen stub that was breaking hadoop by Jake Biesinger · 12 years ago
  54. e73873e merge with new argmented graph by Anbang Xu · 12 years ago
  55. dfd2e0f added shallower interface for readIDs by Jake Biesinger · 12 years ago
  56. ab3d8f4 add interface for edgewritable.appendReadID by Jake Biesinger · 12 years ago
  57. c448987 refactoring edgelists; still some to do by Jake Biesinger · 12 years ago
  58. 034979c Partial refactor following edge type changes in NodeWritable by Jake Biesinger · 12 years ago
  59. 82aca33 Refactor merging into NodeWritable and add tests by Jake Biesinger · 12 years ago
  60. 2b9ba78 Starting on NodeWritable merge by Jake Biesinger · 12 years ago
  61. 473c225 Consolidate edges and threads into a single element by Jake Biesinger · 12 years ago
  62. 76f4101 add license header to NodeWritable (can't we just have it in ONE place?) by Jake Biesinger · 12 years ago
  63. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  64. 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
  65. 13348bf Graph construcion is completed by Anbang Xu · 12 years ago
  66. 67c7e22 debuging SplitRepeatVertex by Anbang Xu · 12 years ago
  67. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  68. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  69. 1de8032 Half done BFSTraverseVertex Framework by Anbang Xu · 12 years ago
  70. b965efd modify pom by Nan Zhang · 12 years ago
  71. 88d6cb5 modify the pom by Nan Zhang · 12 years ago
  72. f010494 adapt new NodeWritable and extends it in VertexValue by Anbang Xu · 12 years ago
  73. 361916b save current state by Anbang Xu · 12 years ago
  74. 7f3e343 add the unmerged graph job by Nan Zhang · 12 years ago
  75. 52bda5c add new graph result to PathMergeTestSet by Anbang Xu · 12 years ago
  76. 813f143 adapt pregel package to new graph by Anbang Xu · 12 years ago
  77. 7812d08 Augment graph construction(hadoop) -- add ThreadList and 5PReaedId by Anbang Xu · 12 years ago
  78. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  79. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  80. 2065960 NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  81. 9c6fe97 starting changes to NodeWritable by Jake Biesinger · 12 years ago
  82. 580f6cd add vertex.activate() to notice update and change DirectionFlag to 2 bits by Anbang Xu · 12 years ago
  83. e35e302 add driver by Nan Zhang · 12 years ago
  84. b4c6e09 Complete the Argumented graph building by Nan Zhang · 12 years ago
  85. 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  86. 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  87. 47fc29c NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  88. b6122b5 starting changes to NodeWritable by Jake Biesinger · 12 years ago
  89. 8ded1a3 Clean genomix package and complete mergeing with Master by Anbang Xu · 12 years ago
  90. c5e5abc remove dependency on hyracks-hdfs-core test-jar by Jake Biesinger · 12 years ago
  91. 05fc10d clean pregel package for latest master by Anbang Xu · 12 years ago
  92. 1afcd2b add graph package by Anbang Xu · 12 years ago
  93. dfd2e50 fix genomix pom.xml's to use 0.2.10-SNAPSHOT by Jake Biesinger · 12 years ago
  94. e0b35ce Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  95. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  96. ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
  97. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  98. 153c2d5 add expected results by Nan Zhang · 12 years ago
  99. 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
  100. 61bfb93 add computeSimilarity and mergeAverageCoverage to MergeBubbleVertex by Anbang Xu · 12 years ago