Allow pass_through in GetOpt::Long some circumstances.
Allow pass_through in GetOpt::Long some circumstances.

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