recover all tests in EdgeMap
small teaks
find bug in neighbor of node
Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into nanzhang/recover_tests_EdgeMap

# By Anbang Xu (14) and others
# Via JArod (7) and others
* 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks: (39 commits)
  remove unnecessary cast
  Remove some wrong tab
  create the log directory if it doesn't exist
  Remove .crc file
  Refactor based on code review
  move MapReduceVertex and BFSVertex to src/test
  rename BackedArray to MashToByte
  Refactor Scaffoling again
  fix switch break statement
  jobGenerator uses getConfiguredJob
  fix regression introduced by output format change
  removing in-place update
  catch more cases for logging
  fix the issue found by Genomix P4 algorithm
  make update tests more extensive
  move debug messages for Node into VertexValue
  Delete ScaffoldingAggregator and use multiple bins to store fake nodes and do group by
  BFSearch passes test
  Need to fix ouputFormat
  Add ByteArrayListWritable and EnumArrayList
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
	genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeTest.java
Complete all tests For Genomix Node
Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into nanzhang/recover_tests_EdgeMap

# By Anbang Xu (34) and others
# Via Jake Biesinger (8) and others
* 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks: (61 commits)
  bubble merge offsets use relative length rather than relative offset
  another :clap: for @Nan-Zhang! node offsets were wrong for flipped merges
  print usage if given the empty arguments or wrong type of arguments
  fix Node.addCoverage. :clap: @Nan-Zhang
  clean up graphstatistics; add maximum counter values
  output name of stats is prev + "-STATS"
  don't forget to remove previous shutdown hooks from our map
  write STATS graph output to HDFS
  start a hadoop cluster before running STATS
  travis allows local ssh'ing
  Reset deleteSet after each loop
  add 1k reads for testing; travis runs basic pipeline
  allow running pipelines without saving intermediate results
  fix for connection refused errors: go back to `getip.sh`
  Create README.md
  remove check permission
  polished by comments
  Make BasicMapReduceVertex to abstract class to empty the compute() method
  change JobGen to jobgen in .travis.yml
  Change to 6, to be consistent with increment number
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
	genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeTest.java
delete old NodeTest
Merge branch 'genomix/fullstack_genomix' into nanzhang/recover_tests_EdgeMap

# By Anbang Xu
# Via Anbang Xu (3) and anbangx (1)
* genomix/fullstack_genomix:
  typo
  GenomixJobConf.RANDOM_RANDSEED should be GenomixJobConf.RANDOM_SEED
  Use the whole directory in .gitignore
  Add some comments and some refactors based on code review
  Exclude text and graphviz output in .gitignore
  Make constant DISSIMILAR_THRESHOLD uppercase
  Merge pathmerge-randomSeed and splitrepeat-randomSeed into the same randomSeed
  Add restrict split neighbor condition
  Add LongRead testcase for SplitRepeat
  Fix Split repeat: leave tandem repeat off
  Print out NeighborInfo
recover nodetest
consistent with genomix_fullstack
format EdgeMap test
Merge branch 'genomix/fullstack_genomix' into nanzhang/recover_tests_EdgeMap

# By Anbang Xu (42) and Nan Zhang (6)
# Via Anbang Xu (3) and others
* genomix/fullstack_genomix: (48 commits)
  Move default to fillMiss
  remove the start/end readIds in graphStatistics
  remove un-used "else" branch
  format node Test
  change name of startReadIds and endReadIds to unflippedReadIds and flippedReadIds.
  Make default value more readable
  Provide numerical value for users but deal with Enum under the hook
  Fix the Low-Coverage
  Fix LOW_COVERAGE bug
  Forget to save....
  Fix again
  Fix again
  Fix a bug in folder name
  GenerateGraphViz should be applied to given types
  Provide numerical value for users to choose among different GRAPH_TYPE
  Try to make plot_subgraph as a seperate job
  In debug mode, dirrectly using if(debug); if(verbose) is for special vertex debugging
  small tweaks
  Complete all Tests for Genomix Node, Now Genomix node is safe temparally
  resolve app.home themselves using pwd and parent dirs
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
	genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeTest.java
	genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
Merge branch 'genomix/fullstack_genomix' into nanzhang/recover_tests_EdgeMap

# By Jake Biesinger (24) and others
# Via Jake Biesinger (7) and Anbang Xu (3)
* genomix/fullstack_genomix: (49 commits)
  Fix compiler error
  Delete abstract in base clas
  Use inheritance in MESSAGE_FILEDS instead of indicating mutually exclusive bits.
  Reformat and dont't forget to use bit 0 =-=
  remove hard-coded logging and restore readFields verbose check and print
  Reduce message communication in Scaffolding
  Reduce message communication in BubbleMerge
  Reduce message communication in SymmetryCheck
  Reduce message communication in SplitRepeat
  Reduce message communication in pathmerge
  Add byte class VALID_MESSAGE
  subGraph has default value; stores as string in conf
  Allow subgraph to plot the entire graph if no seeds are specified
  If don't specify startSeed, plot the whole graph
  add standard and extended pipelines to travis testing
  remove .settings
  fix the HadoopVSHyrack test comparison by increase Xmx to 1G
  Clean up code
  Fix a symmentry bug in pathmerge
  Correct SymmetryCheck
  ...
small change
Merge pull request #45 from uci-cbcl/nanzhang/recover_tests_EdgeMap

recover tests edge map for genomix-data