Hi Paul, I implemented the method I described for limiting the maximum number of files open at any time. I have only performed very limited testing (on sacCer3 multiz7way MAF files), which simply showed that using this feature (by passing low value maxOpenFiles2=5 to NLMSA constructor) yielded identical index files vs. the standard mode not applying this limit.
Maybe you could test this on your data. You don't need to change anything in the parameters you pass to NLMSA construction, since its new default values should work OK for you: * maxOpenFiles=1024 default is used only for requesting the OS to permit us to have up to 1024 open files; * maxOpenFiles2=1000 default will limit readMAFfiles() to 1000 open files at any one time, which should work for you. The code is available from my rebuf branch of my pygr repo on github: https://github.com/cjlee112/pygr/tree/rebuf Let me know whatever problems you run into... Yours, Chris On Tuesday, April 30, 2013 12:38:05 PM UTC-7, Paul Rigor wrote: > > Hi Chris, thanks so much for taking care of this. Looking forward to > testing the feature. Cheers, > Paul > -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to pygr-dev+unsubscr...@googlegroups.com. To post to this group, send email to pygr-dev@googlegroups.com. Visit this group at http://groups.google.com/group/pygr-dev?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
