[BioC] suppressing reduce() function when applying set operations to GRanges

[Bill Gibb]

Hello,

I noticed that when applying set operations to GRanges objects, the returned range is reduced (by default), e.g.

	r1 <- GRanges(seqnames=c(1,1,1), ranges=IRanges(start=c(1,3,5), end=c(1,3,5)), strand='*')
	length(r1)
	r2 <- GRanges(seqnames=c(1,1,1), ranges=IRanges(start=c(1,3,4), end=c(1,3,4)), strand='*')
	length(r2)
	r3 <- union(r1,r2)
	length(r3)
	sum(width(ranges(r3)))

Both r1 and r2 have length 3, whereas r3 has length 2, due to the implicit reduce applied to the result of union(). I can see that reducing the ranges would normally be desired when applying set operations, however there are occasions when one might want to keep a list of singleton ranges (e.g. when sub-sampling at the genomic coordinate level). Is there a way to suppress the reduce() operation when applying set operations to GRanges? Something like union(r1, r2, reduce.ranges=FALSE) would be nice.

I also tried:

	resize(r3,width=1)

however it appears to simply truncate multi-base sequences.

Thank you.

Bill Gibb
Genomic Health, Inc.
Redwood City, CA

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