Insertion directly before CDS start should not be included in CDS
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/39 Original date: 2011/02/25 Original reporter: m DOT vermaat DOT hg AND lumc DOT nl
In contrast to insertions directly in exon/intron boundaries, insertion directly before CDS start should not be included in CDS. Instead, the CDS start should just get a positive shift of the insertion size.
For example, NM_000143.3:c.-1_1insCAT should not change the predicted protein product.
Internally, this means we don't want to apply the -1+1 fix in Mutator.newSplice for CDS start. It is probably also okay to skip this fix for the first 'splice site' (really translation start), so the solution may be to always skip this fix in newSplice for the first element in the given list of sites.