I'm not too familiar with Rsamtools::pileup() but I know it does
handle indels. I also remember that last time I tried it was very
fast, very flexible, and has a very extensive man page.
H.
On 10/12/2018 09:09 AM, Tim Triche, Jr. wrote:
can it handle indels reasonably well? It might be a reason
can it handle indels reasonably well? It might be a reasonable substitute,
especially if it can spit out a VRanges somehow
--t
On Thu, Oct 11, 2018 at 10:14 AM Hervé Pagès wrote:
> Sounds good.
>
> I should also mention that Rsamtools has pileup() that is available
> on all platforms. Don't k
Sounds good.
I should also mention that Rsamtools has pileup() that is available
on all platforms. Don't know how easy it would be to use to achieve
the kind of variant calling you're doing in MTseeker though...
Cheers,
H.
On 10/11/2018 04:35 AM, Tim Triche, Jr. wrote:
This makes sense. Window
This makes sense. Windows users won’t be easily able to call variants across
thousands of samples but at least the plotting, impact prediction, etc will
work fine for them.
I will need to define things such that the variant calling is optional, which
is not too absurd — I’ll add loading of MVR
And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.
Otherwise the trick below will make MTseeker available on
Hi Tim,
No platform-specific dontrun capabilities AFAIK but you can use
something like:
if (requireNamespace("gmapR", quietly=TRUE)) {
...
...
}
in your man pages.
You would also need to move gmapR from Imports to Suggests.
Then make sure that MTseeker passes 'R CMD check' **w
There is .BBSoptions, which can be placed in the root of your package,
but this is insidious, as evidenced by your own use case -- gmapR
doesn't support windows, so your package doesn't support windows, so any
package that Depends: or Imports: your package doesn't support windows,
so actually 1
it looks like gmapR does not support Windows, and as a result, my MTseeker
package cannot build on tokay1, so the Data package which requires it also
cannot build on tokay1. Are there platform-specific dontrun capabilities?
http://bioconductor.org/spb_reports/MTseekerData_buildreport_201810101032
