[Bioc-devel] VariantAnnotation: Harmonize default readVcf params

(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.

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