[Bioc-devel] VariantAnnotation: Harmonize default readVcf params

[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 <stvjc at channing.harvard.edu>
wrote:

>
>
> On Mon, Dec 8, 2014 at 9:18 PM, Valerie Obenchain <vobencha at fredhutch.org>
> 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 defaults for ScanVcfParam() to a
>> minimal subset I'm fine with that.
>>
>
> It might be time to have a GUI widget that helps people construct a
> ScanVcfParam.
>
>
>>
>> Valerie
>>
>>
>>
>> On 12/08/14 13:32, Michael Lawrence wrote:
>>
>>> 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 should just drop VRangesScanVcfParam and have
>>> readVcfAsVRanges just be an alternative syntax to as(readVcf(),
>>> "VRanges").
>>>
>>> Michael
>>>
>>> On Mon, Dec 8, 2014 at 10:48 AM, Valerie Obenchain
>>> <vobencha at fredhutch.org <mailto:vobencha at fredhutch.org>> wrote:
>>>
>>>     Michael, how would you feel about dropping VRangesScanVcfParam? I'm
>>>     open to changing the defaults in ScanVcfParam; the current 'read all
>>>     fields' default is probably not the best approach.
>>>
>>>     Valerie
>>>
>>>
>>>
>>>     On 12/04/2014 02:47 AM, Julian Gehring wrote:
>>>
>>>         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(), info = character(), geno =
>>>             character()
>>>
>>>             VRangesScanVcfParam: fixed = "ALT", info = NA, geno = "AD"
>>>
>>>         When using
>>>
>>>             readVcfAsVRanges(vcf_path, genome_name)
>>>
>>>         with default parameters, that yields a VRanges object only the
>>> 'AD'
>>>         metadata column.  If 'AD' is not present in the VCF file (which
>>> is
>>>         perfectly fine because it is not essential), it throws a warning.
>>>
>>>         My main motivation behind all of this is that I would expect
>>>
>>>             x = readVcf(vcf_path, genome_name)
>>>             y = as(x, "VRanges")
>>>
>>>         and
>>>
>>>             z = readVcfAsVRanges(vcf_path, genome_name)
>>>
>>>         to give an equal object.  I added some code below to make the
>>>         case more
>>>         concrete:
>>>
>>>             library(VariantAnnotation)
>>>
>>>             vcf_path = system.file("extdata", "ex2.vcf",
>>>         package="VariantAnnotation")
>>>
>>>             ## read VRanges (implicit conversion)
>>>             z = readVcfAsVRanges(vcf_path, "ncbi37")
>>>
>>>             ## read VCF, convert to VRanges (explicitly)
>>>             x = readVcf(vcf_path, "ncbi37")
>>>             y = as(x, "VRanges")
>>>
>>>             ## harmonize it
>>>             vr_param = VRangesScanVcfParam(fixed = character(), info =
>>>         character(), geno = character())
>>>
>>>             z2 = readVcfAsVRanges(vcf_path, "ncbi37", param = vr_param)
>>>
>>>             all.equal(unname(y), unname(z2))
>>>
>>>
>>>         Best
>>>         Julian
>>>
>>>         _________________________________________________
>>>         Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>>         mailing list
>>>         https://stat.ethz.ch/mailman/__listinfo/bioc-devel
>>>         <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>
>>>
>>>
>>>
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