complete the GetFastaStata Parallel, wait for test
refactor gage to map reduce job
remove un-nessacery files
add some comments
use counter to get fast stats
Merge commit '41238e19b16a842aac4519aca40ffb01a977d49f' into nanzhang/genomix_gage_feature

# By Anbang Xu
# Via Anbang Xu
* commit '41238e19b16a842aac4519aca40ffb01a977d49f':
  If using Enum, change byte/boolean to it. Temporarily P2 code for clean code
  Refactor the SimpleBubbleMerge
add gageStats with map reduce counters
modify statsCode
remove unrelated file
add MUMMer
small teaks for genomic node
Merge remote-tracking branch 'origin/genomix/fullstack_genomix' into nanzhang/genomix_gage_feature

# By Anbang Xu (59) and others
# Via Jake Biesinger (12) and others
* origin/genomix/fullstack_genomix: (120 commits)
  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
  bubble merge offsets use relative length rather than relative offset
  Make constant DISSIMILAR_THRESHOLD uppercase
  Merge pathmerge-randomSeed and splitrepeat-randomSeed into the same randomSeed
  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
  Add restrict split neighbor condition
  Add LongRead testcase for SplitRepeat
  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
  Fix Split repeat: leave tandem repeat off
  Print out NeighborInfo
  ...

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
	genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
	genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/gage/source/GetScaffoldStats.java
	genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/converttofasta/ConvertToFasta.java
	genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GraphStatistics.java
remove "old-style" in genomic-conf
change the usage message for minContigLength
combine two for loop into one loop for Function getFastaStatsForGage
clean all stuff related to oldStyle
change the gage test hadoop starter to use Genomix Manager
Merge branch 'genomix/fullstack_genomix' into nanzhang/genomix_gage_feature

# 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/config/GenomixJobConf.java
	genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GraphStatistics.java
remove un-use files
change stringbuffer to stringBuilder