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

Hervé Pagès hpages at fredhutch.org
Wed Mar 15 07:33:19 CET 2017


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


> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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