* If AltEst plugin is activate, EuGene creates two files: one for the initial prediction
(.gff3) and one including the variant prediction (.variants.gff3)
* The -k option (equivalent to AltEst.reference=1) allows to predict splicing variants
from a reference annotation.
* New parameter 'AltEst.IncompatibilityExonBorderMatchThreshold'. EuGene will perform a
variant search only for the AltEst where one of the exons shows at one of its borders
a difference of at least x nucleotides with a reference gene.
* Improve performance of splicing variant prediction
* Allow to predict only variant from a reference annotation with the -k option
* If AltEst plugin is activate, create two files: one for the initial prediction and one for the variant prediction. (File with the suffix ".variants")
* New parameter 'AltEst.IncompatibilityExonBorderMatchThreshold'. Only AltEst with an exon showing
...his is the margin used to select the AtEst for which an alternative prediction would be launched.
An EST is considered a potential variant if one of its exon show a difference with a length upper or equals to that value with a reference gene.
