Seperate firstKmer case out of loop
Some tweaks on scaffolding
No distinction between prev and next and so make a loop to iterate through it
Merge branch 'genomix/fullstack_genomix' into anbangx/genomix-scaffolding-refactor

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
	genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
	genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
Modify BFSVertex to be test code and Scaffolding use its utility function
fix generic input formatsand derived class to use derived objects
fix generic input formatsand derived class to use derived objects
Merge
Add ByteArrayListWritable and EnumArrayList
Need to fix ouputFormat
BFSearch passes test
Delete ScaffoldingAggregator and use multiple bins to store fake nodes and do group by
Merge branch 'genomix/fullstack_genomix' into anbangx/genomix-scaffolding-refactor

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BFSTraverseMessage.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessage.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/ComplexBubbleMergeVertex.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/ScaffoldingVertex.java
fix regression introduced by output format change
jobGenerator uses getConfiguredJob
Refactor Scaffoling again
rename BackedArray to MashToByte
move MapReduceVertex and BFSVertex to src/test
Refactor based on code review
Remove .crc file