v0.012

	Fixed bug where dual synthetic cassette features created.
Added exon rank into exon feature tag
added script that will generate the eng-seq for a given lims2 well
ignore tmp dir
Merge branch 'devel' into andrew_exon_ranks
Added clear of EnsEMBL registry in config to prevent conflicts with other systems e.g. LIMS2
	Added exon feature ranks. Added clear step when creating EnsEMBL registry.