genebuilder-standard optional options added ( -host || -dbhost etc.)
-additinal option -dbname added

treeshrew and hedgehog added

minor problems (e.g. whitespace after a line-continuation \)

from the sequence-match xref pipeline (they are too for this to be
sensible)

addition to ensure attached protein features are stored

platypus stuff

additional option-names added -dbhost -dbuser -dbname -dbport ...

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