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
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