First patch file for 38->39. Adds 'KNOWN_BY_PROJECTION' to enumerations for status in gene and transcript.

Note new patch file naming convention.

Added code to remove anything in parens from the RefSeq entry sequence line. E.g. s/Oryza sativa (ssp. japonica)/Oryza sativa/

Added logic_name option, get_mysql_command method, and a warning in direct_xref if the source does not map to an entry in the target database external_db table

Fixed typo in fetch_all_byProbe [ db() -> dbID() ]

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