Better hit counting to prevent counting situations where the same probe hits a transcript multiple times - thanks to Ian Sealy for the suggestion

Remove crash when get_all_complete_names() was called by initialising $probeset to be blank for arrays that don't have the concept of probesets (e.g. Agilent probes in Zebrafish)

Changed release to source_release as row name for table source as release became a reserved word in MySQL5

Row name change from release to source_release in source table, this change is done because release became a reserved word in MySQL5

Modifed to code to make it MySQL5 friendly, the changes made were the addition of parenthesis in the LEFT JOIN queries, without the parenthesis the queries will just not work or give unexpected results

Added writing of unmapped entries to unmapped_object and unmapped_reason tables in xref database. Old entries are deleted (if -delete is specified).

added locus_tag for the gene synonym or more generally known name and also added a note that contains the description. This is all just for the gene.

added new type: complex_indel, for long variations affecting different coding regions in the same transcript

Added optional argument to get_all_DBEntries and get_all_DBLinks which is the database name. Use like in sql statment so percentage sign can be used for wild cards etc.