removed warning in store_alt_alleles when none of the alt_alleles in a set is on reference sequence - this is a valid case and doesn't require a warning

Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas

does not store density feature with value of 0

updated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.

no clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse either

Assignment bug; we did not want the cache assigned to the ID of the seq region but wanted the seq region id into a local variable. Fixed.

Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.

Using the "best" HTTP client available i.e. avoid making people install LWP if they are on a late enough version of Perl. HTTP::Tiny is very nice

Asking if a dereferenced array ref is undefined is not testing what you think it is and is deprecated in Perl 5.16.0. You are seeing if the first element was defined when in actual fact you needed to assert if the array reference was undefined and act accordingly.