[Bioc-devel] VariantAnnotation: Harmonize default readVcf params

[Vincent Carey]

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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