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
add version of tipremove that doesn't require graph compression
stop tipremove search if max length is surpassed
rename previousNodes to visitedNodes
fix bug where MIN_LENGTH_TO_KEEP isn't kept between iterations
make TipSearch consistent with other msgs: use Integer, not int for length
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
rename TIP_WITH_SEARCH to TIP; old version to TIP_SINGLE_NODE