[Bioc-devel] inconsistent results from applyPileups and pileLettersAt

[James W. MacDonald]

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Jim



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

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

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