change name of startReadIds and endReadIds to unflippedReadIds and flippedReadIds.
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.