Functionality suggested by Ensembl Genomes, used when building a variation DB.
New flag: start_equals_end which controls the simplified sql for 1bp slice.

(defaults to 200).

Test will fail if run on non-deterministic data storage engines as we have 2 features with the queried for ditag_id

Introduced Utils::IO namespace along with serializer code for GFF3 and human-readable formats. Pre-release, not intended for public use.
Also added Utils::BiotypeMapper that performs ontology mappings.

	formatting

	safe use of @aliases (don't expect registry to make copy of the list)

	quote argument names and values

(zero by default in the code, but set to 0.125 in the default.conf
configuration file).

found in get_adaptor().  Suggested by jm18 on dev.

Also reformat get_alias() and get_DBAdaptor().

Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype
to plugins to run.

EnsemblGeneGeneric.pm

method in GeneScoreBuilder.pm

than {}.

Bit of error checking/throwing put in to stop bad file system paths from being produced when we lack a CS version

Bringing in the DataFile infrastructure. First pass implementation can perform CRUD and has associated test cases. Currently lacks a good way of passing the base directory in. Will be addressed.

Bringing in a new method which allows us to retrieve the last inserted identifier into the table this adaptor is working with via DBI. Should be called from within an execute block so we do not need to wrap this in a work_with_dbh call

Brought in a new method for getting single value meta items from the meta table. This is then used in MetaContainer for just about every call reducing duplicated logic.