Great, thanks!
On Tue, Sep 27, 2016, at 09:10 PM, Dan Tenenbaum wrote:
> Seems like that was a transient error. I was able to kick off another
> build that did not have this problem.
>
> https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650
>
> Dan
>
>
> - Origina
Seems like that was a transient error. I was able to kick off another build
that did not have this problem.
https://github.com/Bioconductor/Contributions/issues/155#issuecomment-250036650
Dan
- Original Message -
> From: "Tyler Smith"
> To: "bioc-devel"
> Sent: Tuesday, September 27,
I think the basic problem is that each range requires a separate query
through tabix. BAM and tabix are designed to be fast for single
queries, like what a genome browser might generate, but not for
querying thousands of regions at once. At least that's the way it
seems to me. The index is only at
Good day,
file <- system.file("extdata", "chr22.vcf.gz", package = "VariantAnnotation")
anotherFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package =
"VariantAnnotation")
aSet <- readVcf(file, "hg19")
system.time(commonMutations <- readVcf(anotherFile, "hg19", rowRanges(aSet)))
Hi,
I've just submitted a new package. The automated build generated an
error which I think (?) is a problem on one of the build servers (SSL
connect error in querying the bioc-devel list). I'm not sure if I'm far
enough along in the process for my assigned human to be alerted to this,
or if they'
Hi Dario,
On 09/27/2016 01:00 AM, Dario Strbenac wrote:
> Good day,
>
> When importing a VCF file from VariantAnnotation's data directory into R, a
> warning is emitted.
>
> library(VariantAnnotation)
> aFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package =
> "VariantAnnotation")
Good day,
When importing a VCF file from VariantAnnotation's data directory into R, a
warning is emitted.
library(VariantAnnotation)
aFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", package =
"VariantAnnotation")
aSet <- readVcf(aFile, "hg19")
Warning message:
In .bcfHeaderAsSimple