more SQL changes
master merge of db changes
Updated SQL tables in pangenome.
removed loop over strain name, now just contig

Also checked to make sure we are not looking up NA in the SQL DB
getting the output from the DB to be useful as text format.
SQL output is good. Fixed novelIterator when numberOfCores=1.

Still need to update phylip file creation based on SQL.
Phylip file creation from SQL DB.

Need to convert to/from 10 char limit.
SQL DB update complete.
Resolved merge conflict; kept DB version.

Conflicts:
	lib/Modules/Alignment/SNPFinder.pm
	lib/Modules/PanGenome/PanGenome.pm
ignore
Build updated for SQL.