all ensembl species should now have the same list of 14 sources, + any species-specific ones they may have

tested on GRCh37 to GRCh38 mappings, where patch fixes in GRCh37 have been integrated into the reference assembly in GRCh38

using current_schema_no_cvs everywhere now

[ENSCORESW-385]. The go statement handle was missing the binding of external db id. This was a bug introduced in 1.36 due to re-appropriated execute call

when running stable id mapping, exons are projected onto reference chromosome
added method in GeneScoreBuilder and EnsemblGeneGeneric to distinguish genes depending on their initial slice
added method in EnsemblExonGeneric to distinguish exons according to the mapped transcript they belong to

The big post-merge alt allele commit. Changes to alt_allele table, new tests, and a couple of new objects.

now closing file with same name as well

rolling back as we migrate back to old farm. new farm lacks exonerate 0.9 binary. sort this out later on

adding a version flag to ping ensembl. users should not use this but it is very useful for developers

removing deprecated/duplicated/unused scripts

switching to farm3 means that memory specification for bsub is in MB not KB i.e. -M and rusage need the same value

Ontology db updated to 73. Mouse ones updated as well but they do not really need it as it is not being rerun this release

Ok that was dumb. Do not under any circumstances add /xms to a regex that really depends on whitespace. Oddly enough it will not match anything

Slight change in logic. Do not skip a UniProt reecord because it is Ensembl derived annotation. Choose not to import the Gene Name into our system

- sub_Slice_same (does not weaken adaptor)
- seq_region_Slice_same (does not weaken adaptor)
- get_seq_region_id_same

This means that CoordSystem, DensityType, Map::Marker, Map::Ditag, Map::Qtl,
MiscSet, OntologyTerm and SeqRegionSynonym have now a fast constructor available.

Accordingly, new_fast is removed from Analysis, Feature, DataFile, DBEntry, RepeatConsensus,
Translation and UnmappedObject together with the import of weaken and isweak from
Scalar::Util.