For direct reading of the sequence, the skip.non.fasta idea sounds good. An
alternative for the name would be "skip.to.first.record". Up to you.
Michael
On Mon, Mar 17, 2014 at 5:33 PM, Hervé Pagès wrote:
> Hi Michael,
>
>
> On 03/17/2014 04:15 PM, Michael Lawrence wrote:
>
>> Hi Herve,
>>
>>
Hi Michael,
On 03/17/2014 04:15 PM, Michael Lawrence wrote:
Hi Herve,
What would be a clean way for rtracklayer to extract the (optional) FASTA
data embedded in a GFF3 file and parse it as an XStringSet? Is there a
low-level way to pass in-memory data to the parser in Biostrings?
Not that it
Hi Herve,
What would be a clean way for rtracklayer to extract the (optional) FASTA
data embedded in a GFF3 file and parse it as an XStringSet? Is there a
low-level way to pass in-memory data to the parser in Biostrings?
In terms of the API, import,GFFFile could return a GRanges with the
DNAStrin
This was my oversight. I didn't think of using a BStringSet for the
structural variants.
Taking a quick look at how this might work.
> fl <- system.file("extdata", "structural.vcf",
package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> alt(vcf)
CharacterList of length 7
[[1]]
[[2]] C
[
Hi Vince,
On 03/16/2014 06:11 PM, Vincent Carey wrote:
It seems that there is diversity in the classes assigned for ALT in results
of readVcf, and there was some discussion of this in 1/2013.
Was this discussion on the mailing list?. Can't find it.
If using diverse/unpredictable classes for A
Hi Valerie & Hervé,
Thanks a lot, I will try adding the new alias!
I am still baffled by the other half of the mystery, i.e. that the build
check warning appeared to the reports about a week ago and I still
cannot see it on my own R-3.1.0 alpha build.
Any ideas why this would work differentl
Hello, bioc-devel community,
This is a reminder that when you make changes to your Bioconductor packages in
our Subversion repository, those changes do not propagate to our
website/repository, or to users, unless you bump (increment) the version number.
So for example, if you discover a bug in
Hi Antti,
Yes it's a little bit surprising (and questionable) that
'R CMD check' requires you to define an alias that is inconsistent
with:
- Your setMethod statement:
setMethod("[", signature(x="scoreList"), ...
- The output of showMethods:
showMethods("[")
Function: [
Hi Antti,
It's looking for
\alias{[,scoreList,ANY-method}
The generic '[' can dispatch on arguments 'x', 'i' and 'j'.
getGeneric("[")
standardGeneric for "[" defined from package "base"
function (x, i, j, ..., drop = TRUE)
standardGeneric("[", .Primitive("["))
Methods may be defined for
Hi Vince,
ALT is a CharacterList when the variants are 'structural', i.e., when
the ALT field has non-nucleotide characters. Otherwise, ALT is a
DNAStringSetList.
It looks like ALT is a CharacterList in x[[1]] and is probably a
DNAStringSetList in x[[3]]. So you are trying to combine GRanges
Hi all,
The latest build check report shows one warning for 'tigre':
---
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'scoreList,ANY'
---
As far as I can tell th
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