Can now specify old and new mapping files on command line.
Can now specify old and new mapping files on command line.

muffato/ensembl,muffato/ensembl,at7/ensembl,willmclaren/ensembl,danstaines/ensembl,mjg17/ensembl,Ensembl/ensembl,Ensembl/ensembl,Ensembl/ensembl,mjg17/ensembl,mjg17/ensembl,muffato/ensembl,willmclaren/ensembl,james-monkeyshines/ensembl,james-monkeyshines/ensembl,mjg17/ensembl,danstaines/ensembl,muffato/ensembl,james-monkeyshines/ensembl,at7/ensembl,at7/ensembl,at7/ensembl,Ensembl/ensembl,james-monkeyshines/ensembl,danstaines/ensembl