[Bioc-devel] GRangesList Conversion Fails For Unstranded Sequencing Data

[Dario Strbenac]

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.

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia