Setting up embedded database for cluster use.
fixed maven issue
fixing minor bugs
derby works, but the database as is currently setup is far too slow.  mysql is much faster.
Merge remote-tracking branch 'origin/embedded-db-setup'

Conflicts:
	assembly.xml
	database/normal-genome.sql
	figg/src/main/java/org/lcsb/lu/igcsa/database/sql/JDBCFragmentDAO.java
	figg/src/main/java/org/lcsb/lu/igcsa/database/sql/JDBCGCBinDAO.java
	figg/src/main/java/org/lcsb/lu/igcsa/variation/fragment/Substitution.java
	figg/src/main/java/org/lcsb/lu/igcsa/variation/fragment/TandemRepeat.java
	figg/src/main/java/org/lcsb/lu/igcsa/variation/structural/Inversion.java
	figg/src/main/resources/genome.properties.example
	figg/src/main/resources/log4j.properties
	figg/src/main/resources/start-igcsa.sh
	pom.xml
	src/dist-resources/genome.properties.example
	src/main/java/org/lcsb/lu/igcsa/variation/fragment/Inversion.java
	src/main/java/org/lcsb/lu/igcsa/variation/structural/Inversion.java
	src/main/resources/genome.properties.example