Re: [Bioc-devel] [devteam-bioc] Very slow when operate GRangesList

2013-08-27 Thread Ou, Jianhong
Dear Valerie, Great improvement. Thanks a lot for your work. I am greatly appreciated for this. Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 8/27/13 4:49 PM, "Valerie Obenchain" wrote: >Thanks Jianhong for repor

Re: [Bioc-devel] [devteam-bioc] Very slow when operate GRangesList

2013-08-27 Thread Valerie Obenchain
Thanks Jianhong for reporting this. Changes implemented in IRanges 1.19.27: - RleList() constructor now has default 'compress=TRUE'. - seqselect,Vector-method lapply() loop was replaced with direct subset. New timings: ## generic subset function fun0 <- function(x) x[500:1] ## GRangesList with

Re: [Bioc-devel] [devteam-bioc] Very slow when operate GRangesList

2013-08-23 Thread Michael Lawrence
On Fri, Aug 23, 2013 at 8:41 AM, Valerie Obenchain wrote: > Hi Michael, > > Martin and I have been discussing this. In addition to the fix you > suggest, what do you think of changing the default to compressed=TRUE for > the RleList constructor? Rle is the only one of the AtomicLists with > defaul

Re: [Bioc-devel] [devteam-bioc] Very slow when operate GRangesList

2013-08-23 Thread Valerie Obenchain
Hi Michael, Martin and I have been discussing this. In addition to the fix you suggest, what do you think of changing the default to compressed=TRUE for the RleList constructor? Rle is the only one of the AtomicLists with default FALSE. Was there a reason for this when it was first implemented