added optional argument of a compara dbadaptor to get_all_compara_DnaAlignFeatures and get_all_compara_Syntenies to make it easier for users who may not have configured the databases properly

Converted o use pod2usage for the documentation. Added logicname parameter (optional) to allow the analysis type for genes to be specified

added Uniprot/Varsplic to the list of those to get descriptions from. Insert after uniprot but before refseq

unmapped_reasons not generated on the fly now, but have to be uploaded with the update_unmapped_reason.pl script. similar to external_db so that they ids remain the same

Improved statistics output.

to fetch ungapped_features from DNA-PEP transcript_supporting_features
(due tothe presence of Insertions that are non modulo-3 in length, which is
common for introns).

Added -delete_unmapped option to only delete stuff from the unmapped_object table if the option is specified. This makes it easier to do "patch" xref runs without clobbering the unmapped data from a previous full run.

Added temporary(?) OTTT source for Havana-Ensembl transcript mappings

try to fall back to gene analysis when storing transcript that doesn't have an analysis object attached

Some sources (e.g. TIGR Gene Index) reuse accessions between species. I have therefore altered the "insert_or_select" and "get_xref_id_by_accession_and_source" functions so that they accept a species arg. The UNIQUE key on the xref table has also been updated with the addition of the species field

Add join with seq_region to allow output of chromosome name when -locations option is used. Seems to slow things down, so could be removed again if -locations is removed in future.