Good day, countOverlaps doesn't work for a GAlignmentPairs object with strandMode set to 0. This is because of an oversight in the grglist function. It has an if statement that checks whether the strand mode is 1 or 2. Then, it tries to subset the variable 'x_unlisted'. However, if strand mode is 0, neither of the conditional sections of code are executed and Error in .local(x, use.names, use.mcols, ...) : object 'x_unlisted' not found happens because the 'x_unlisted' variable has not been created. It's a surprise no one else has encountered this bug before.
-------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
