[Bioc-sig-seq] ScanBamParam suggestion

[Janet Young]

Hi,  

I have a suggestion to make ScanBamParam easier to use for coding amateurs like myself (I'm still sometimes confused with the many ways to encode genomic regions):

Is it easy/possible to change bamWhich function to accept GRanges objects, rather than requiring RangesList?  See below...

thanks, as usual,

Janet



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library(Rsamtools)
myGR <- GRanges(seqnames="chr1",ranges=IRanges(start=1,end=100))

# I can use GRanges as the "which" argument if I do it when I create the ScanBamParam object
myparams1 <- ScanBamParam(which=myGR)

#but not if I try to set later
myparams2 <- ScanBamParam()
bamWhich(myparams2) <- myGR
### Error in checkSlotAssignment(object, name, value) : 
###   assignment of an object of class "GRanges" is not valid for slot "which" 
### in an object of class "ScanBamParam"; is(value, "RangesList") is not TRUE

## it's OK, though coercion does work.  
bamWhich(myparams2) <- as(myGR,"RangesList")

sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

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_1.4.3     Biostrings_2.20.4   GenomicRanges_1.4.8 IRanges_1.10.6     

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