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asterix-gerrit.ics.uci.edu / hyracks / 9c01d098f621a79fd1fff4ed22eec22f7bc89ddd / genomix / genomix-data
  1. 9c01d09 Fix mergeReadID RF and RR by Jake Biesinger · 12 years ago
  2. 7a75b07 add updateEdges for pathmerge. Issue: mergeWithStartreads by Anbang Xu · 12 years ago
  3. 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
  4. 6fc84f1 Add additional merge info to pathmerge by Anbang Xu · 12 years ago
  5. 56e291f Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  6. ced394a Make pathmerge robost by Anbang Xu · 12 years ago
  7. b37b705 Add UnRollTandemRepeat. TODO: add the corresponding MSG and update edges by Anbang Xu · 12 years ago
  8. fc7d4b8 fix the positionWritable unionUpdate(), and add automatic test case by Nan Zhang · 12 years ago
  9. de3a280 Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  10. c970d65 Adapt BTSTraverseVertex to new graph structure by Anbang Xu · 12 years ago
  11. 000fa26 getReadIDs added to EdgeWritable by Jake Biesinger · 12 years ago
  12. 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago
  13. 3786935 hyracks graph building test complete. by Nan Zhang · 12 years ago
  14. b02033e BasicPathMergeVertex is completed by Anbang Xu · 12 years ago
  15. 0d72095 Make generic message class for all patterns by Anbang Xu · 12 years ago
  16. 128eb0e Revert "update hyracks_genomix branch" by Nan Zhang · 12 years ago
  17. 9a664b7 update hyracks_genomix branch by Nan Zhang · 12 years ago
  18. 9296bb6 Add EdgeList.getKeys for iterating over keys by Jake Biesinger · 12 years ago
  19. 6266614 Simplify edgewritable interface by Jake Biesinger · 12 years ago
  20. 2d17c5b Complete the Graph construction(Hadoop) by Anbang Xu · 12 years ago
  21. 60782f4 Add test cases; reinstate compareTo function use Hadoop's version by Jake Biesinger · 12 years ago
  22. 35875ce removed cursed autogen stub that was breaking hadoop by Jake Biesinger · 12 years ago
  23. e73873e merge with new argmented graph by Anbang Xu · 12 years ago
  24. dfd2e0f added shallower interface for readIDs by Jake Biesinger · 12 years ago
  25. ab3d8f4 add interface for edgewritable.appendReadID by Jake Biesinger · 12 years ago
  26. 034979c Partial refactor following edge type changes in NodeWritable by Jake Biesinger · 12 years ago
  27. 82aca33 Refactor merging into NodeWritable and add tests by Jake Biesinger · 12 years ago
  28. 2b9ba78 Starting on NodeWritable merge by Jake Biesinger · 12 years ago
  29. 473c225 Consolidate edges and threads into a single element by Jake Biesinger · 12 years ago
  30. 76f4101 add license header to NodeWritable (can't we just have it in ONE place?) by Jake Biesinger · 12 years ago
  31. 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  32. 13348bf Graph construcion is completed by Anbang Xu · 12 years ago
  33. bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
  34. d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
  35. f010494 adapt new NodeWritable and extends it in VertexValue by Anbang Xu · 12 years ago
  36. 361916b save current state by Anbang Xu · 12 years ago
  37. 7812d08 Augment graph construction(hadoop) -- add ThreadList and 5PReaedId by Anbang Xu · 12 years ago
  38. 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  39. 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  40. 2065960 NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  41. 9c6fe97 starting changes to NodeWritable by Jake Biesinger · 12 years ago
  42. e35e302 add driver by Nan Zhang · 12 years ago
  43. b4c6e09 Complete the Argumented graph building by Nan Zhang · 12 years ago
  44. 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
  45. 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
  46. 47fc29c NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
  47. b6122b5 starting changes to NodeWritable by Jake Biesinger · 12 years ago
  48. 8ded1a3 Clean genomix package and complete mergeing with Master by Anbang Xu · 12 years ago
  49. dfd2e50 fix genomix pom.xml's to use 0.2.10-SNAPSHOT by Jake Biesinger · 12 years ago
  50. be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
  51. 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
  52. 8edaabd Add fracDissimilar to VKmer by Jake Biesinger · 12 years ago
  53. 7dc9400 clean the useless code for project by Nan Zhang · 12 years ago
  54. 3fc4fef Please enter the commit message for your changes. Lines starting by Nan Zhang · 12 years ago
  55. 8e8e99f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
  56. 96465fb Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  57. 6ad60bf fix bug in readFields of KmerListWritable by Anbang Xu · 12 years ago
  58. 9dc35e0 fix merge test case by Jake Biesinger · 12 years ago
  59. d235865 catch too-short kmers when trying to merge by Jake Biesinger · 12 years ago
  60. 078e20a catch attempts at merging empty kmers by Jake Biesinger · 12 years ago
  61. b072b75 Add edit distance computation for VKmers by Jake Biesinger · 12 years ago
  62. 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
  63. def02ee clean up interface for VKmer setByRead by Jake Biesinger · 12 years ago
  64. 1df93be Bugfix for Hadoop bug in VKmer and PositionList by Anbang Xu · 12 years ago
  65. 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  66. 999f6ac add coverage for hyracks graph building by Nan Zhang · 12 years ago
  67. 07011c1 Merge commit '164cc8091571ad11261a91eed68e06d2e73ea490' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  68. 164cc80 add compare-by-coverage Comparator for NodeWritable by Jake Biesinger · 12 years ago
  69. 39f1cf1 Merge commit '07acebba2c4470834919a82092faec0c982411e5' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  70. 42036c1 add methods for node coverage merge/add; serialize coverage by Jake Biesinger · 12 years ago
  71. 6ffdef2 add 3 SplitRepeat TestCases and fix the PositionListWitable: UnionUpdate HashSet by Nan Zhang · 12 years ago
  72. b01f330 Merge commit '50e9f8614b4124288f606d90c3417caa2b5f80de' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  73. 016df5f finish the debugging by Nan Zhang · 12 years ago
  74. 50e9f86 add conversions for Kmer <-> VKmer by Jake Biesinger · 12 years ago
  75. 0b9da1e Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  76. c68e510 finish the debugging by Nan Zhang · 12 years ago
  77. ff02e22 Use VKmers in lists by Jake Biesinger · 12 years ago
  78. 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
  79. 34d3d73 there is an issue in KmerListWritable and try to fix it by Anbang Xu · 12 years ago
  80. 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  81. ceab4c1 Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
  82. 94e075b update for merge by Anbang Xu · 12 years ago
  83. 6ee7bdf fix HashSet in SplitRepeat by Anbang Xu · 12 years ago
  84. 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
  85. d57d7e5 add CreatedVertex and ConnectedTable by Anbang Xu · 12 years ago
  86. 5a69e16 refactor graph building in hyracks using new genomix-data code by Nan Zhang · 12 years ago
  87. f2507bf debugging for hyracks by Nan Zhang · 12 years ago
  88. 844d774 update the genomix-data by Nan Zhang · 12 years ago
  89. d94f5f9 refactor 'BasicPathMergeVertex' to 'BasicGraphCleanVertex', make it more general by Anbang Xu · 12 years ago
  90. 29ebdc8 Map/Reduce version in pregel is completed by Anbang Xu · 12 years ago
  91. b89e7dc allow references in all variable-length elements by keeping track of originally allowed space by Jake Biesinger · 12 years ago
  92. 1e68c8f PositionListWritable passes tests by Jake Biesinger · 12 years ago
  93. b92f4e5 add copy-based byte array serialization for NodeWritable by Jake Biesinger · 12 years ago
  94. d907eb4 remove reference code for variable-length lists. We don't keep track of onwership of our data block by Jake Biesinger · 12 years ago
  95. d6276e7 p2 pass test by Anbang Xu · 12 years ago
  96. 11b2760 Kmer factory uses VKmers by Jake Biesinger · 12 years ago
  97. bd58f1a .hashcode and .equals need to use storage with offsets; no more super methods. by Jake Biesinger · 12 years ago
  98. a9e482e update KmerListWritable to use fixed-length kmers by Jake Biesinger · 12 years ago
  99. 9ba730c no more inherited Kmers by Jake Biesinger · 12 years ago
  100. 5fb6805 use global, static length for fixed-length kmers by Jake Biesinger · 12 years ago