Re: [Bioc-devel] Google hangout on Wed December 10th for new package authors

2014-12-09 Thread Sonali Arora
Hi everyone, Please be reminded that we are inviting you to join a webinar tomorrow(Dec 10th, 2014) at 8:00AM PST. You can "tune in" at: http://youtu.be/QfqaK_BHebU Please feel free to chat and ask questions, they will be collectively answered at the end of a short presentation. A recordin

Re: [Bioc-devel] VariantAnnotation: Harmonize default readVcf params

2014-12-09 Thread Michael Lawrence
I think GUIs like this are more the domain of the IDE (in-line auto-prompting and completion) rather than something needing a shiny-style interface, which just takes you out of the programming workflow. On Tue, Dec 9, 2014 at 10:06 AM, Vincent Carey wrote: > Yes, based on the query to the list,

Re: [Bioc-devel] VariantAnnotation: Harmonize default readVcf params

2014-12-09 Thread Vincent Carey
Yes, based on the query to the list, it seemed to me someone was having trouble finding out what can be/needs to be specified. There are a lot of options and the little widget you've sketched is going to be useful. ​ [[alternative HTML version deleted]] _

Re: [Bioc-devel] VariantAnnotation: Harmonize default readVcf params

2014-12-09 Thread Julian Gehring
I guess Vince was more thinking of a GUI for constructing the ScanVcfParam object itself, given a VCF file. Have a look at https://gist.github.com/julian-gehring/978ff86691bd87e95daf (https://gist.github.com/julian-gehring/978ff86691bd87e95daf) Quick and dirty prototype, a shiny app to interact

Re: [Bioc-devel] VariantAnnotation: Harmonize default readVcf params

2014-12-09 Thread Michael Lawrence
It would be nice to have a high-level GUI that allowed the user to specify a query and then showed a sample of the query result, perhaps along with some plotting capabilities. Julian is somewhat close to something like that, I think. On Tue, Dec 9, 2014 at 2:50 AM, Vincent Carey wrote: > > > O

Re: [Bioc-devel] VariantAnnotation: Harmonize default readVcf params

2014-12-09 Thread Vincent Carey
On Mon, Dec 8, 2014 at 9:18 PM, Valerie Obenchain wrote: > (Resend - last message didn't post to the list.) > > OK, sounds good. In 1.13.18 I've deprecated VRangesScanVcfParam() and > changed the signature of readVcfAsVRanges() to use ScanVcfParam(). > > If at some point we want to revise the def