[Bioc-devel] inconsistent results from applyPileups and pileLettersAt

James W. MacDonald jmacdon at uw.edu
Fri May 27 17:31:16 CEST 2016

The Bioc-devel list is intended for people who are developing packages.
Your question should be posted on the bioconductor support site,


On Fri, May 27, 2016 at 11:05 AM, Jesper Gådin <jesper.gadin at gmail.com>

> Hello everyone,
> I find inconsistent results from applyPileups and pileLettersAt. I have a
> placed a full example on github, so you can try the code with data that
> will reproduce what I am suspecting is a "bug".
> #Repo with reproducible example
> https://github.com/pappewaio/ExampleData
> #Here a short summary of what is happening
> One version requires the user to use readGAlignments first and then use
> pileLettersAt, here I can read in 450 reads into R, but after using
> pileLettersAt I am left with only 413 counts. What could possibly explain
> this difference? Is it because some reads are spanning the position I am
> piling letters at, but not having any sequence information for the
> position?
> The second version uses applyPileups and summarize straight from the bam
> file, and here I would expect to have at least the 413 counts found by
> pileLettersAt. But instead I can only find 385 counts. Why is it so?
> Until now I have been using version one to get allele counts. But version
> two is very much faster, so would be very nice to be able to switch to it,
> without losing counts.
> looking forward to hearing your thoughts,
> Jesper
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list