use Path:Class to deal with dir names, avoid over-writing work directories if multiple designs target the same gene, trim arguments of whitespace
do not need to log a error message if we can not find alt design file
store design parameters in file
make fetch-olig-regions-sequence command grab chromosome name from design parameters file instead of the oligo_region_coords.yaml file, remove the chromosome name from that file, fix tests
add oligos attribute to Action.pm
stop using Oligos Role, expected oligos can now be called from base Action.pm class
mimic addition of oligos attribute to test Action.pm class
remove TargetSequence and Oligos roles, start using design parameters hash in all commands
fix consolidate design tests
remove Oligos role
Move design_method attribute out of base Action class into the oligo
region definition classes. Access the design_method via the
design_parameters hash in other modules
remove design_method attribute from test Action class, fix consolidate design test to deal with new way of setting design method
fix fetch oligo regions sequence test, move design_method into design params file
fix filter oligos tests, now use design_parameters.yaml file
fix find oligos tests, now use design_parameters.yaml file
fix pick block oligos tests, now use design_parameters.yaml file
fix pick gap oligos tests, now use design_parameters.yaml file
code tidy
split common attributes and methods for commands not related to the MooseX::App::Cmd framework out of Action.pm base clase and into new role, this will mean the test base class can now consume this this
throw error if trying to set design parameter from non existant attribute