[BioC] pileup function in ShortRead package

[Nora Rieber]

Hi there,

I'm using the pileup function in the ShortRead package and it seems I
call it with the wrong arguments, or that there is some kind of bug in
the function. All my reads are piled up in forward direction only, even
if they were actually mapped to the backward strand.

Here's a small (nonfunctional since I assume I cannot append data to
this e-mail) example of how I call the pileup function:

#read in the MAQ alignment file:
aln_s_7_MCIP4<-readAligned("/home","sequenceALN.txt", type="MAQMapview")
aln_Pat_subset<-aln_Pat[1:10]
pos_Patient_subset<-position(aln_Pat_subset)
str_Patient_subset<-strand(aln_Pat_subset)
#use only a small subset (all positions are on the same chromosome 1)

subset_pileuptest<-pileup(pos_Patient_subset, 36,
max(pos_Patient,na.rm=TRUE)+37,dir=str_Patient_subset)

Is there anything wrong with my dir argument? I checked several places
all over the genome for the complete alignment and my reads all seem to
be considered on the + strand, even when they are not. Can anybody help?

This is my session info:

> sessionInfo()
R version 2.9.2 (2009-08-24)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ShortRead_1.2.1   lattice_0.17-25   BSgenome_1.12.3   Biostrings_2.12.9
[5] IRanges_1.2.3

loaded via a namespace (and not attached):
[1] Biobase_2.4.1 grid_2.9.2    hwriter_1.1

Thanks,
Nora