I have a question regarding the parameters available at the command line version but not in R.
Is there a possibility to for example alter the minMatch value (Minimum ratio of bases that must remap)?
Apparently this value adapts automatically from 0.95 default to 0.1 when using a chain for different species (in my case hg19ToMm10.over.chain) in R like it does on the webpage.
Anyways it would be great to manually adjust this value in R.
(I am aware that pslMap is maybe a better idea)