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,
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]]
_
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
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
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
(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 defaults for ScanVcfParam() to a
minimal subset I'm fine with that.
The reason why 'y' and 'z' are different is the same reason why
readVcfAsVRanges exists. It was meant to be a convenience so that users
could get the minimal information needed into the VCF. But maybe that was
just being too helpful, and the user ends up confused. So I agree with
Julian that we sho
Hi,
Can we harmonize the default parameters for =ScanVcfParam= and
=VRangesScanVcfParam=? It even seems that we could drop
=VRangesScanVcfParam= since it is mainly a wrapper for =ScanVcfParam=.
Currently, the defaults for importing fields from a VCF are:
ScanVcfParam: fixed = character(), inf
