small-fixes
change-aggregate-and-request-score-msgs-to-hashmaps
move-the-seed-loops-outside
Merge remote-tracking branch 'origin/elmira/test-mutual-overlap' into genomix/fullstack_genomix

Conflicts:
	genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding2/RayVertex.java
Merge branch 'genomix/fullstack_genomix' of github.com:uci-cbcl/genomix into genomix/fullstack_genomix