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 reasonable
substitute, especially if it can spit out a VRanges somehow
--t
On Thu, Oct 11, 2018 at 10:14 AM Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
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. 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
MVRanges/MVRangesList objects from VCFs and move gmapR to suggests.
>
> Personally I use the variant calling functionality regularly, but
I have my doubts as to whether someone on Windows would even have
enough RAM to call variants across 2000+ samples in a shot, so this
is a good compromise. Everything else is, I believe, platform
agnostic. This should work.
>
> --t
>
>> On Oct 11, 2018, at 1:41 AM, Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>> wrote:
>>
>> 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 Windows
>> but Windows users won't be able to accomplish anything meaningful
>> with it. In that case, marking the package as unsupported on Windows
>> would be preferable.
>>
>> Hope this makes sense,
>>
>> H.
>>
>>> On 10/10/2018 10:26 PM, Hervé Pagès wrote:
>>> 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' **without**
>>> the gmapR package being installed. You'll need to define and set
>>> environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
>>> Do it with:
>>> export _R_CHECK_FORCE_SUGGESTS_=0
>>> on Linux or Mac, or with:
>>> set _R_CHECK_FORCE_SUGGESTS_=0
>>> on Windows.
>>> Once MTseeker is accepted, we'll add a .BBSoptions file with
special
>>> directive:
>>> CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
>>> This will have the effect to set the environment variable on the
>>> Windows build machines before running 'R CMD check' there.
>>> So MTseeker will be supported and available on all platforms.
>>> For MTseekerData: the package doesn't seem to make any use of gmapR
>>> so you can probably remove gmapR from its Suggests field.
>>> Hope this helps,
>>> H.
>>>> On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
>>>> 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?
>>>>
>>>>
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw&e=
>>>>
>>>> Short of somehow forcing gmapR to build on Windows, which I
believe is
>>>> beyond my control, is there a way to declare that parts of the
MTseeker
>>>> package are unsupported/unsupportable on Windows?
>>>>
>>>> I suppose I could cleave off the variant-recalling portions
but that seems
>>>> a little ridiculous. The original goal was to take the
non-NuMT reads from
>>>> a given alignment, realign (only) those to rCRS/RSRS, and call
against
>>>> that, for better mitochondrial haplogroup inference. We're
still working
>>>> towards the full version, but even just calling variants
against rCRS with
>>>> indels is hugely useful, and the ability to screen out
haplogroup-specific
>>>> variants while retaining indels, SNVs, etc. turns out to be
VERY handy.
>>>> More generally, there isn't any equivalent (AFAIK) in BioC, at
all.
>>>>
>>>> --t
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
mailing list
>>>>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM&e=
>>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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