Re: parallel BAM sorting with Rsamtools

Hi Jens,

Note that if you have a large number bam files, you can already sort 
them in parallel using BiocParallel or your favorite parallel variant 
of lapply. It's not multi-threaded sorting of single bam files, but it 
will still make use of all your cores.

-Ryan

On Fri Aug 29 10:32:34 2014, Jens Reeder [guest] wrote:
> Hi,
>
> samtools now allows the sorting of bam files using several threads. This is incredibly useful for large BAM files, e.g. from whole-genome projects.
> Are there any plans of exposing the parallel sorting via Rsamtools' sortBam() and  asBam(..., indexDestination=TRUE)?
>
> I couldn't find any mention of this in the mailing lists or elsewhere...
>
> thanks
> Jens
>
>   -- output of sessionInfo():
>
> .
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

_______________________________________________
Bioconductor mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor