[ENSCORESW-395]. Addition of -eg and -ue options to get people to ping different database servers for ensembl genomes and useast respectively. Also allow users to specify the species used.

first, test all the cases and add seq_region_mapping entries when necessary
then, update the mapping_set table
prevents us from skipping a species where a previous run might have failed

[ENSCORESW-448]. new overlap algorithm and better test cases. supports overlaps when you do not want to normalise WRT the backing slice

[ENSCORESW-445]. Fixes an issue with transformed and transfered transcripts. Attribute arrays are shallowed copied so attributes meant for the transformed object go back into the parent object. This causes more issues when you start to do multiple transformations from the same transcript. Regression test case added

There are some circumstances where exon coordinate recalculation is not the right thing to do and the user has them correctly set out (ori spanning transcription models). Rather than tie this directly into the coordinate recalculations we are allowing skipping this procedure. It is up to the user to do the right thing if using this module. It also does not alter any existing functionality

was giving it an exon mapping list where a transcript mapping list was required

[ENSCORESW-438]. Fixed API when someone can specify a _rna_edit where the substring length was not equal to the substituting string length

better testing of meta_coord and the container object. Now testing if updates work to existing data sets

Finished up some queries that are left hanging when an early exit is made. This was causing weirdness when fetching supercontigs and projecting them. ENSCORESW-429

9593 corresponds to gorilla gorilla, also known as Western gorilla, the species
9595 corresponds to gorilla gorilla gorilla, also known as western lowland gorilla, the genus of the animal represented in ensembl

also has a unigene species-specific source

if the production database value is NULL, we do not overwrite the existing value in the core-like database
this allows us to keep information like db_version which is database specific and should not be centrally held