Deal with gibson designs
Add dry-run option to just print out command
Name work folders after gene and exon if we have a exon id
add a rm_dir option to delete work dir if it already exists before re-creating it
Show reasons primer3 failed to to find oligos
Check for primers in all regions, do not just throw exception after the first failure
Store reasons that a primer failed validation and print out into log file
add a design_fail.yaml file to store details on why a design failed to run, make the gibson design command write to this file for now
parse out the template sequence from the primer3 input so it can be written to the design_fail file if needed
add a as_hash method to the base DesignCreate::Exception class, this will be used to grab the data needed to write into the design_fail.yaml file
augment the as_hash methods in these 2 exception sub-classes
add 2 new expection classes, one for failed primer3 run, another for failed oligo validation
throw a oligo validation error instead of a generic error class
throw a more useful error message when we can not retrieve a exon
throw a custom exception when we can not find any valid oligos for a given oligo type
add a comment about the string ref being passing around
fix typo, gene type is HGNC not HGCN
update tests to deal with new variable we are passing back from the run_primer3 subroutine
add option to set number of threads bwa aln step uses
mouse as well as human gibson designs
update script name
move script back into bin dir
skip columns with no headers when working out design parameters