exception message.

times for writing.

second argument was being ignored

Added just a test for the new method filter_dir at the moment.

content of a directory.

corrupting multiple entries file.

Slice sequence is written into chunks (as specified by the chunk_factor
parameter given to the constructor) in method write_embl_seq, which now
returns the base counts.
Methods dump_embl has been modified accordingly. A template for a sequence
header is written, then the sequence, then we seek backwards to the
position of the sequence header to write it with the actual base counts
which have been figured out during the writing of the sequence.

Pros: memory efficiency
Cons: cannot dump to a file for which a compressed fh has been obtained,
      i.e. cannot call dump_embl method in a callback provided to
      Bio::EnsEMBL::Utils::IO::gz_work_with_file.

stable_id_lookup is a separate public method
added archive_id_lookup method, which will look for the stable id in the archive_id_lookup table
the generic lookup method now calls stable_id_lookup
if no stable_id is found and $use_archive argument is given, the generic lookup will attempt to find the stable id
in the archive_id_lookup, ie amongst the retired ids
if a stable id is found using this, a 'retired' flag is returned as well

this works similarly to the stable_id_lookup table, but is populated with stable ids which are not current any more
the populate_stable_id_lookup.pl script has been updated to populate that table along with the other ones

updated test cases to check integrity of api once deprecated tables, columns and methods have been removed
test databases patched to schema 74

ApiVersion has been updated to 74
method and column calls for deprecated tables/columns have been removed
this includes:
- dnac table
- qtl, qtl_feature and qtl_synonyms tables
- unconventional_transcript_association table
- pair_dna_align_feature_id column in dna_align_feature table
- canonical_annotation column in gene table

this API is backwards compatible, it can be used to query databases in release 73 or before
the 73 API is not forward compatible, if you want to use databases on schema 74 or beyond, use the 74 API

includes removal of deprecated tables/columns
the following have been removed:
- table dnac
- tables qtl, qtl_feature, qtl_synonym
- table unconventional_transcript_association
- column pair_dna_align_feature_id in dna_align_feature table
- column canonical_annotation in gene table

leaving the Orphanet parsing options in in case they are needed again later in history

Seems that the ConfigRegistry code was not picking up on the right ontology
database object type. Added what I think is the right one and lets see
if it stops the website from warning so much.

SliceAdaptor has been changed to bring back the karyotype rank and
the karyotype boolean when retriving karyoptype slices. The Slice object
now caches the rank locally. AssemblyAdaptor now adds the list of
karyotype regions for the rest API.

Committing since we are now beyond the branch point in the API. This
allows a FullIdCache to key on various alternative identifiers/keys
generated by the implementing class. It means that if you want this
functionality you need to sub-class FullIdCache.

now supports schema_version and schema_type retrieval

not used directly in the ontology database but allows for compatibility with the core MetaContainer and release version tracking

is not required for ontology database but allows for compatibility with metacontainer and schema version control like other databases

allows for future schema patching
added single table.sql file, replaces the need for individual sql files for each table

successfully tested on farm3 settings