I ran Mitosalt on a sample with a deletion, and it was mistakenly called as a dup.
In delplot.R, should lines 269-275 change from:
OLD:
if(dloop == 'yes'){
Ds<-res$del.start.median[i]
De<-res$del.end.median[i]
Dsr<-res$del.start.range[i]
Der<-res$del.end.range[i]
}
NEW:
if(dloop == 'yes'){
# BUG / Pauline fxed on Sep 29, 2025, need to switch coordinates, like OriH below
Ds<-res$del.end.median[i]
De<-res$del.start.median[i]
Dsr<-res$del.end.range[i]
Der<-res$del.start.range[i]
}
Otherwise, the dloop if statement has no effect because Ds, De, Dsr, Der were assigned in the previous lines.