add function to return repeat masked sequence
make mask by lower case option for AOS default to yes
get repeat masked sequence when building oligo target region fasta files
find oligos now checks if entire oligo target region is masked, if it is throws error, only checks if the mask by lower case option is set to yes
throw a better error exception when aos does not produce any oligos for given oligo type
update TODO
improve logging in filter oligo command
make sure oligo seq is uppercase, also only set phase it its been calculated
update create multiple design script to be more useful
fix test, check for new exception
pass sequence to check_masked_seq subroutine, not bioseq object
add test for upper casing the oligo sequence
add test for check_masked_seq subroutine, as well as checking for error thrown when one or more oligo regions is entirely masked
update tests for getting sequence from ensembl