Note that there is already an import,TabixFile that handles indexed
restriction via the "which" arg. rtracklayer autodetects tabix files,
so the user just calls import("my.bed.bgz", which=gr).
Michael
On Thu, Jul 21, 2016 at 1:17 PM, Martin Morgan
wrote:
> On 07/21/2016 02:12 PM, Simon Anders (
On 07/21/2016 02:12 PM, Simon Anders (by way of
Simon Anders wrote:
Hi Hervé, Martin, Wolfgang, and anybody else who might be interested
this post is stimulated by a discussion Martin Morgan and I had last
week at the CSAMA course. It is on how to improve in Bioconductor the
handling of large g
I agree that supporting out of core representations is the way to go.
Implementations should push the iteration as far down as possible, so
that the user does not have to worry about it for common operations.
The DelayedArray package is a good example of this. The GenomicRanges
data structures are
Hi Hervé, Martin, Wolfgang, and anybody else who might be interested
this post is stimulated by a discussion Martin Morgan and I had last
week at the CSAMA course. It is on how to improve in Bioconductor the
handling of large genomics data files like GFF or BED files with many
millions of lines.
