On 5/19/17 12:15 PM, Michael Lawrence wrote:
That could work, also.
On Fri, May 19, 2017 at 10:27 AM, Martin Morgan
<martin.mor...@roswellpark.org> wrote:
On 05/19/2017 12:14 PM, Michael Lawrence wrote:
Since SeqArray already imports SummarizedExperiment and
VariantAnnotation, why can't it just move them to Depends and use
their generics?
do they need to be moved to Depends? Or simply import the generic export the
new method(s) (and generic)?
We used to do this, but Xiuwen just moved SummarizedExperiment and
VariantAnnotation from Imports to Suggests, because it was taking too
long to load the package with them attached. So now we are redefining
the generics.
In our daily use of SeqArray we almost never use VariantAnnotation or
these generics, so the change improves our pipeline performance without
any immediate downsides for us. But it does add annoyance for any
(potential) users of both SeqArray and VariantAnnotation in the same
session, as they would have to add the package name with "::" to
disambiguate the methods.
Martin
On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten
<sdmor...@u.washington.edu> wrote:
Dear Core Team,
What do you think about adding the following generics to BiocGenerics?
colData
rowRanges
ref
alt
qual
filt
header
fixed
info
geno
They are currently defined by both VariantAnnotation/SummarizedExperiment
and SeqArray. Given the increasingly widespread use of VCF files, it
seems
likely that other packages may want to use them in future also.
Stephanie
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