Fix the following: - now works when the verbose option isn't specified - doesn't complain about uninitialized values when not transforming - copies canonical transcripts
Fix the following:
- now works when the verbose option isn't specified
- doesn't complain about uninitialized values when not transforming
- copies canonical transcripts

Ensembl/ensembl-analysis,Ensembl/ensembl-analysis,Ensembl/ensembl-analysis,mn1/ensembl-analysis,kiwiroy/ensembl-analysis,james-monkeyshines/ensembl-analysis,james-monkeyshines/ensembl-analysis,kiwiroy/ensembl-analysis,mn1/ensembl-analysis,mn1/ensembl-analysis,james-monkeyshines/ensembl-analysis