Hello, I really like this new ability to index into an RleList via a GRanges: rl <- RleList(chr1=1:100) gr <- GRanges(ranges=IRanges(10, 20), strand="+", seqnames="chr1") rl[gr] # RleList of length 1 # $chr1 # integer-Rle of length 11 with 11 runs # Lengths: 1 1 1 1 1 1 1 1 1 1 1 # Values : 10 11 12 13 14 15 16 17 18 19 20 Would it be possible to make it strand-aware so that the values are reversed for ranges on the negative strand? Currently, the strand of each range appears to have no effect: strand(gr) <- ?-? rl[gr] # RleList of length 1 # $chr1 # integer-Rle of length 11 with 11 runs # Lengths: 1 1 1 1 1 1 1 1 1 1 1 # Values : 10 11 12 13 14 15 16 17 18 19 20 This would make it more consistent with things like getSeq(), which are aware of negative-stranded GRanges. Thanks! Jeff > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.16.0 GenomeInfoDb_1.0.1 IRanges_1.22.2 BiocGenerics_0.10.0 setwidth_1.0-3 loaded via a namespace (and not attached): [1] XVector_0.4.0 stats4_3.1.0