[Bioc-devel] inconsistent results from applyPileups and pileLettersAt

[Jesper Gådin]

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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