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Jim On Fri, May 27, 2016 at 11:05 AM, Jesper Gådin <jesper.ga...@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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel