BUILD-profile optimize: use static final EDGETYPE.values not values()
BUILD-profile optimize: only compile regex once
BUILD-profile optimize: copy reference rather than deep copy in build
reformat
BUILD-profile optimize: remove getLengths() and return offsets from copy ops
MERGE-profile optimize: in/out formats use tmp references
MERGE-profile optimize: less reading from conf; use global debug vals
MERGE-profile optimize: random uses hash, not many calls, to break correlation
MERGE-profile optimize: don't send unnecessary edges in MERGE
MERGE-profile optimize: only send non-overlapping parts of kmers
fix coverage bug form short kmers in MERGE messages
fix bug in coverage; simplify merging with truncated kmers in messages
Merge remote-tracking branch 'origin/genomix/fullstack_genomix' into wbiesing/optimizations-from-profiling-BUILD_HYRACKS

Conflicts:
	genomix/genomix-
pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
	genomix/genomix-
pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/DeBruijnGraphCleanVertex.java
Merge pull request #68 from uci-cbcl/wbiesing/optimizations-from-profiling-BUILD_HYRACKS

optimizations from profiling build_hyracks