GitLab

[ENSCORESW-264] Can now handle odd sequence region names involving . - _ now. The supercontig names seemed to be a good source of these

[ENSCORESW-217] & [ENSCORESW-263]. Added automatic generation of the primary assembly file and cleaned up the readme slightly pending full re-design.

[ENSCORESW-262]. Customised the Exon summary as hash, gene and transcript summaries have been improved. Biotype mapper can ask objects for their SO term and knows Variation objects are already annotated with a code. BioType mapper caches SO retrieval so it is a massive speed increase for large result sets.

[ENSCORESW-261]. Edits to allow for easier regulation adaptor creation. Grab the species name from the DB if it wasn't given to the adaptor and make sure we avoid returning the coord system core adaptor if the group was funcgen

will get unique regions with variation_feature, stops it from counting snps twice on chromosome Y

The old way was possibly the WORST way to blank a LRU cache by replacing it for a bare hash. Possible memory leak fixed ...

rather than return all toplevel slices, returns all slices with genes
does not affect much species with a reduced number of toplevel slices but increases things considerably for large number of toplevel slices

Adding patch from James Allen where a copy/paste bug has meant the incorrect setting of end_Exon to be on the $translation and not alternative $translation

when counting features, do not use strict lower/higher