added another scalar_attribute rapper get_first_scalar_attibute which gets first non-null value from a list of IDs

Comment out 'print' commands as they bork the web code :(

Added fetch_all_by_logic_name method - "Returns a listref of features created from the database. Only features with an analysis of type $logic_name will be returned."

fetch_by_stable_id_version() now checks if this stable_id.version is actually in the database, and retrieves dbname, release and assembly of latest incarnation of this ID

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