[ENSCORESW-499]. schemaPatches.t checks that the table.sql patch set matches what is in the patched database

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this

[ENSCORESW-478] and [ENSCORESW-467]. Brought in a Perl::Critic test being run on the lowest level. Tests are only run when we have the ENV TEST_AUTHOR is set to a true value. Otherwise it does not impact on the current test cases. Also had to fix a number of issues associcated with these flags. Mostly were due to not using warnings or strict. Anything I felt was ok or not my call has been annotated with a no critic flag.

[ENSCORESW-479]. Making this module better at handling homologue Compara errors and also get it to die when you try to get homologues without a compara adaptor configured

Added a method that lists the species in available databases. Ancestral_ are ignored, and the list is filtered to a group type, defaulting to core dbs. Testcase is less than perfect, because the test db has so few species in it.

[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

[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

Introducing a proxy Feature class to allow custom limitation of the boundaries of the feature. This implementation influences the get_all_ methods while leaving the standard methods unaffected.

removing the adding of species if they are in the force_speices list. unintented side effect of limiting it to just those force species

We do not need proxies for this test. Having them actually causes it to go wrong. Deleted HTTP_PROXY and http_proxy from Perl ENV hash

New method store_batch_on_ for faster bulk storage of attributes. New modules GeneGCBatch and PepStatsBatch use this method. Updated test to include use of this method.

[ENSCORESW-377]. Fixing the seq region synonym as mentioned by Steve S. Also added a test case which looks for synonyms with a coordinate system not as before which only worked when we had no coordinate system)

Added constrain_to_seq_region for web rendering reasons, where requested slice->expand were flying off the end of chromosomes.