Complete all Tests for Genomix Node, Now Genomix node is safe temparally
small tweaks
change name of startReadIds and endReadIds to unflippedReadIds and flippedReadIds.
format node Test
remove un-used "else" branch
remove the start/end readIds in graphStatistics
Merge branch 'genomix/fullstack_genomix' into nanzhang/change_start_end_reads_name

# By Anbang Xu
# Via Anbang Xu (3) and anbangx (1)
* genomix/fullstack_genomix: (42 commits)
  Move default to fillMiss
  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
  resolve app.home themselves using pwd and parent dirs
  don't commit changes to some stuff
  Rename to PLOT_SUBGRAPH and provide simple numeric value for users to choose
  Ctrl + Shift + F
  Add some comments for some functions and some parameters
  Move extractSubgraph.sh to right place
  Add different options to graphviz for different levels of details
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenerateGraphViz.java
Merge pull request #44 from uci-cbcl/nanzhang/change_start_end_reads_name

change name of start/endReadIds to unflippedReadIds and flippedReadIds.
Merge branch 'genomix/fullstack_genomix' into nanzhang/genomix_node_test

# By Anbang Xu (53) and Nan Zhang (2)
# Via Anbang Xu (5) and others
* genomix/fullstack_genomix: (55 commits)
  Move default to fillMiss
  remove the start/end readIds in graphStatistics
  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
  resolve app.home themselves using pwd and parent dirs
  don't commit changes to some stuff
  Rename to PLOT_SUBGRAPH and provide simple numeric value for users to choose
  typo
  GenomixJobConf.RANDOM_RANDSEED should be GenomixJobConf.RANDOM_SEED
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
Merge pull request #41 from uci-cbcl/nanzhang/genomix_node_test

Complete all Tests for Genomix Node, Now Genomix node is safe temparally
Clean up code
Merge branch 'genomix/fullstack_genomix' into anbangx/debug-split-repeat2