When I try to use the queryLoc2refLoc() function I get the error message "NOT IMPLEMENTED YET, SORRY!".

Am I missing something or is this not yet available? 

Take a look at the function definition:

R> GenomicAlignments::queryLoc2refLoc
{
    stop("NOT IMPLEMENTED YET, SORRY!")
}
<environment: namespace:GenomicAlignments>

I think you got the right idea :-)