Hi,
On 03/13/2017 11:00 PM, Dario Strbenac wrote:
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.
Thanks for catching and reporting this. Should be fixed in
GenomicAlignments 1.11.12.
It's a surprise no one else has encountered this bug before.
Maybe because few people know they can set the strandMode to 0. I think
most people with unstranded protocol just use the default strandMode
(i.e. 1) and specify ignore.strand=TRUE when calling countOverlaps() or
summarizeOverlaps().
H.
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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