Optimised code around option parsing and removed short options where they would be confusing.
Optimised code around file path assembly, by no longer specifying the default value of the file.path fsep option.
Changed options --instance to --biomart-instance, --data_set to --biomart-data-set, --host to --biomart-host, --port to --biomart-port, --path to --biomart-path and --genome_directory to --genome-directory.
The boolean result vector of file.symlink is now directly evaluated and a warning gets issued upon an error.
R objects are now removed, as soon as they are no longer required.
Added a symbolic link to the TopHat unmapped.bam file.
Added data frames for replicate count matrices on both, genes and isoforms.