[BioC] bug: subsetByOverlaps(GRangesList, GRanges)

[Cei Abreu-Goodger]

Hello,

I think I've found another bug. If you use subsetByOverlaps with a 
GRangesList as query, the full object is returned, instead of the subset 
that overlaps:

library(GenomicRanges)
gr1 <- GRanges(seqnames=c("a","b"),ranges=IRanges(c(1,11), c(5,15)))
gr2 <- GRanges(seqnames=c("a","b"),ranges=IRanges(c(1,11), c(5,15)))
gr3 <- GRanges(seqnames=c("a"),ranges=IRanges(1,5))
grl <- GRangesList(gr1,gr2)

identical(grl,subsetByOverlaps(grl, gr3))
[1] TRUE

To get the behavior that I was expecting, you can do:
endoapply(grl, subsetByOverlaps, gr3)

Cheers,

Cei

 > sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0

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

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

other attached packages:
[1] GenomicRanges_1.0.6 IRanges_1.6.8       Biobase_2.8.0

loaded via a namespace (and not attached):
[1] tools_2.11.0