[Bioc-sig-seq] strandedness bug in Rsamtools?

[Steve Lianoglou]

Hi all,

I think there might be a bug in Rsamtools. I have reason to believe
that the strand information that's being returned from
scanBam(...)$strand is flipped, ie. a read that should be on the '+'
strand is being reported as aligning to the '-' strand.

Can someone else conform/deny?

Thanks,
-steve

sessionInfo()
R version 2.11.0 Under development (unstable) (2009-12-28 r50849)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] Rsamtools_0.1.28   BSgenome_1.15.4    Biostrings_2.15.19 IRanges_1.5.39

loaded via a namespace (and not attached):
[1] Biobase_2.7.0


-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact