hi there,
in my package VariantFiltering i have an example VCF file from a Hapmap
CEU trio including three chromosomes only to illustrate its vignette.
i've come across a problem with the function readVcf() in
VariantAnnotation that may be specific of the situation of a VCF file
not having
Hi Robert,
Thanks for the bug report and reproducible example. Now fixed in release
1.12.2 and devel 1.13.4.
I've also updated the docs to better explain how the Seqinfo objects are
propagated / merged when supplied as 'genome'.
Valerie
On 10/23/2014 06:45 AM, Robert Castelo wrote:
hi
Hi,
I just found a tiny bug in .guessSpeciesStyle(). Basically, if the
style name has a dot, this function incorrectly returns the name of
the style.
See below:
## Lets guess the species and style for 'T'
GenomeInfoDb:::.guessSpeciesStyle('T')
$species
[1] Populus trichocarpa
$style
[1] JGI2
It's been a while since I worked with experimental packages. Where
can I find documentation on how to (Subversion) update our
AffymetrixDataTestFiles package with additional data files? All I
know is that the SVN repository only contains a stub of the package
and
There is a README.txt in the pkgs folder.
I will attach it. I think this is accurate, but there may be something
else on the site.
On Thu, Oct 23, 2014 at 10:23 PM, Henrik Bengtsson h...@biostat.ucsf.edu
wrote:
It's been a while since I worked with experimental packages. Where
can I find
- Original Message -
From: Vincent Carey st...@channing.harvard.edu
To: Henrik Bengtsson h...@biostat.ucsf.edu
Cc: bioC-devel bioc-de...@stat.math.ethz.ch
Sent: Thursday, October 23, 2014 7:45:13 PM
Subject: Re: [Bioc-devel] Documentation on how to update a BioC experimental
Hi Henrik,
FWIW there is some additional information here:
https://stat.ethz.ch/pipermail/bioc-devel/2014-January/005156.html
In particular the section starting at One important difference with
the svn software repository provides some useful hints on how to
commit changes to the data (see
