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Bugfix for SqlHelper which caused it to rerun a transaction even if it succeeded; test case added. Bugfix to gene.t which had a syntax error.

ensembl-62'.

Sprout from master 2011-04-01 15:03:13 UTC Ian Longden <ianl@sanger.ac.uk> 'Changed order of vega xrefs to check and added a test that the transcript has a logic_name of havana.'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Changed order of vega xrefs to check and added a test that the transcript has a logic_name of havana.

Changed order of vega xrefs to check and added a test that the transcript has a logic_name of havana, plus made sql easier to read.

to ens-staging2.

Change one instance of $dbport to $mport to connect to the right port
on the master server.

server port.

for a few releases but that I've ignored.

Parser to create an HTML documentation from the table.sql file.

Added SQL wildcard support to GeneAdaptor, TranscriptAdaptor and TranslationAdaptor -> fetch_all_by_external_name()
Actual modifications in DBEntryAdaptor. Features tested through gene.t