- 9ac0dda Modify mergeWithKmer to mergeWithNode by Anbang Xu · 12 years ago
- 6fc84f1 Add additional merge info to pathmerge by Anbang Xu · 12 years ago
- d06c50f add testcase for pathmerge by Anbang Xu · 12 years ago
- ced394a Make pathmerge robost by Anbang Xu · 12 years ago
- b37b705 Add UnRollTandemRepeat. TODO: add the corresponding MSG and update edges by Anbang Xu · 12 years ago
- 6efa434 Completed P2 debugging by Anbang Xu · 12 years ago
- a3c0538 Clean up P2 code and prepare to deep debug it by Anbang Xu · 12 years ago
- feec5be Fix BubbleMerge by Anbang Xu · 12 years ago
- 5e01f76 Adapt RemoveLowCoverageVertex to new graph structure. Finally, all the patterns are adapted to new graph by Anbang Xu · 12 years ago
- e7856d5 Adapt ScaffoldingVertex to new graph structure by Anbang Xu · 12 years ago
- c970d65 Adapt BTSTraverseVertex to new graph structure by Anbang Xu · 12 years ago
- 6212780 BTS almost done and wait for EdgeListWritable[dir].getReadIds(Key key) by Anbang Xu · 12 years ago
- 0217e7e Adapt SplitRepeatVertex to new graph structure. TODO: test AdjSplitRepeat by Anbang Xu · 12 years ago
- 37a8489 Adapt MergeBubbleVertex to new graph structure. TODO: check if bubble flip and merge all metadata except kmer by Anbang Xu · 12 years ago
- c69d141 Add node to BubbleMessage by Anbang Xu · 12 years ago
- 14de2c6 save current state by Anbang Xu · 12 years ago
- 977a413 Adapt BridgeAddVertex and BridgeRemoveVertex to new graph structure by Anbang Xu · 12 years ago
- 4370b2b adapt TipAddVertex and TipRemoveVertex to new graph structure by Anbang Xu · 12 years ago
- 112cdf7 Adapt MapReduceVertex and P4 to new graph structure by Anbang Xu · 12 years ago
- e7885ee Pregel TestSuite is completed by Anbang Xu · 12 years ago
- 0e037c1 Prepare to clean up pregel testSuite by Anbang Xu · 12 years ago
- 6f88379 save current state and prepare to clean up hadoop test result by Anbang Xu · 12 years ago
- 5d431a1 temporary save modified state by Anbang Xu · 12 years ago
- b02033e BasicPathMergeVertex is completed by Anbang Xu · 12 years ago
- 0d72095 Make generic message class for all patterns by Anbang Xu · 12 years ago
- a5a1e63 Make basic msg class: MessageWritable and subclasses: PathMergeMessage, BubbleMergeMessage, BFSMessage by Anbang Xu · 12 years ago
- 6bdf197 add EdgeList[dir].getKeys() by Anbang Xu · 12 years ago
- 58875bf delete SelfPath.txt~ by Anbang Xu · 12 years ago
- c448987 refactoring edgelists; still some to do by Jake Biesinger · 12 years ago
- 14df82f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
- 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
- 67c7e22 debuging SplitRepeatVertex by Anbang Xu · 12 years ago
- bb8e581 Complete NaiveBFSTraverse and make more test cases by Anbang Xu · 12 years ago
- d282e07 argumented graph building pass test successfully by Nan Zhang · 12 years ago
- 1de8032 Half done BFSTraverseVertex Framework by Anbang Xu · 12 years ago
- f010494 adapt new NodeWritable and extends it in VertexValue by Anbang Xu · 12 years ago
- 361916b save current state by Anbang Xu · 12 years ago
- 52bda5c add new graph result to PathMergeTestSet by Anbang Xu · 12 years ago
- 813f143 adapt pregel package to new graph by Anbang Xu · 12 years ago
- 399fc4a NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
- 211d79c use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
- 2065960 NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
- 580f6cd add vertex.activate() to notice update and change DirectionFlag to 2 bits by Anbang Xu · 12 years ago
- 62a61f6 NodeWritable: refactor getListFromDir to getEdgeList by Jake Biesinger · 12 years ago
- 64f07c9 use direction flag as only public interface for nodewritable edges and threads by Jake Biesinger · 12 years ago
- 47fc29c NodeWritable: Remove nodeIdList, refactor edges, add threads, add start/end reads by Jake Biesinger · 12 years ago
- 8ded1a3 Clean genomix package and complete mergeing with Master by Anbang Xu · 12 years ago
- 05fc10d clean pregel package for latest master by Anbang Xu · 12 years ago
- dfd2e50 fix genomix pom.xml's to use 0.2.10-SNAPSHOT by Jake Biesinger · 12 years ago
- be39f91 Add AverageCoverage to graph construction(hadoop) and make graphviz more pretty by Anbang Xu · 12 years ago
- ac6b1a6 RemoveBridge pass test and add RemoveLowCoverage and Scaffolding by Anbang Xu · 12 years ago
- 4a5ee49 Hadoop TestSuite is completed and P2 pass test by Anbang Xu · 12 years ago
- 18c032a make TestSuite for graph building(hadoop) by Anbang Xu · 12 years ago
- 61bfb93 add computeSimilarity and mergeAverageCoverage to MergeBubbleVertex by Anbang Xu · 12 years ago
- cb4391e clean pregel package for build by Anbang Xu · 12 years ago
- c4961c9 complete MergeBubbleVertex & wait for compute fracSimilarity by Anbang Xu · 12 years ago
- 3986b17 debugging BubbleMergeVertex by Anbang Xu · 12 years ago
- 3e3144b cleanning continue by Nan Zhang · 12 years ago
- 8e8e99f Merge branch 'nanzhang/hyracks_genomix' into genomix/fullstack_genomix by Nan Zhang · 12 years ago
- 6ad60bf fix bug in readFields of KmerListWritable by Anbang Xu · 12 years ago
- 6981f1c adapt graph construction(hadoop) to VKmer by Anbang Xu · 12 years ago
- ad800e8 more cleanup of setByRead interface by Jake Biesinger · 12 years ago genomix/before-nodeid-graph-cleanup-Aug2013
- b8626fd make GraphViz for test by Anbang Xu · 12 years ago
- 79c5ccf Merge branch 'wbiesing/genomix/VKmers' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
- 9f949c4 MergeBubbleVertex half done by Anbang Xu · 12 years ago
- 39f1cf1 Merge commit '07acebba2c4470834919a82092faec0c982411e5' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
- 07acebb Merge MergeBubbleMessageWritable to MessageWritable by Anbang Xu · 12 years ago
- ac6a090 Fix BubbleAddVertex and pass test by Anbang Xu · 12 years ago
- 6d8afff fix RemoveBridgeVertex and update for merge by Anbang Xu · 12 years ago
- ec095b2 RemoveTipVertex pass test by Anbang Xu · 12 years ago
- 95c432c BridgeAddVertex pass test by Anbang Xu · 12 years ago
- 6f81b59 small update by Anbang Xu · 12 years ago
- 714d906 adapt BridgeAddVertex to new graph construction by Anbang Xu · 12 years ago
- d1075a0 adapt TipAddVertex to new graph construction by Anbang Xu · 12 years ago
- aac7732 SimpleSplitRepeat is completed. An issue in graph building(hadoop): KmerList.appendList() doesn't check existed element by Anbang Xu · 12 years ago
- 0b9da1e Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
- c68e510 finish the debugging by Nan Zhang · 12 years ago
- 1259632 refactor KmerList -> VKmerList by Jake Biesinger · 12 years ago
- 34d3d73 there is an issue in KmerListWritable and try to fix it by Anbang Xu · 12 years ago
- 5eaa799 Merge commit '94e075b5c3db9aa613ef61c2581430a143b17bc8' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
- ceab4c1 Merge branch 'wbiesing/genomix/VKmers' into nanzhang/hyracks_genomix by Nan Zhang · 12 years ago
- 94e075b update for merge by Anbang Xu · 12 years ago
- 6ee7bdf fix HashSet in SplitRepeat by Anbang Xu · 12 years ago
- 0049eac refactor 'NaiveAlgorithm' to 'P1' and add test case for SplitRepeat by Anbang Xu · 12 years ago
- d57d7e5 add CreatedVertex and ConnectedTable by Anbang Xu · 12 years ago
- 37c6933 start coding SplitRepeat by Anbang Xu · 12 years ago
- 5412086 refactor LogAlgorithm to P2 by Anbang Xu · 12 years ago
- 9db1ea8 merge MapReduceVertex to p2 and p2 is completed by Anbang Xu · 12 years ago
- d94f5f9 refactor 'BasicPathMergeVertex' to 'BasicGraphCleanVertex', make it more general by Anbang Xu · 12 years ago
- 29ebdc8 Map/Reduce version in pregel is completed by Anbang Xu · 12 years ago
- 0f06660 start dependency refactor by Jake Biesinger · 12 years ago
- 5dfa7b6 add MapReduceVertex for mapper/reducer in pregel by Anbang Xu · 12 years ago
- d6276e7 p2 pass test by Anbang Xu · 12 years ago
- a9e482e update KmerListWritable to use fixed-length kmers by Jake Biesinger · 12 years ago
- b8e0097 p2 pass test9 by Anbang Xu · 12 years ago
- 9e00650 p2 pass all the tests except 9 by Anbang Xu · 12 years ago
- 2990977 debugging p2 by Anbang Xu · 12 years ago
- b811143 Refactor KmerBytesWritable to use internal length by Jake Biesinger · 12 years ago
- 1307443 P2 pass test1,2,3,4 by Anbang Xu · 12 years ago
- d253d8f fix mergeWithRFKmer by Anbang Xu · 12 years ago