[BioC] [devteam-bioc] parallel BAM sorting with Rsamtools

Martin Morgan mtmorgan at fhcrc.org
Fri Aug 29 22:26:00 CEST 2014

On 08/29/2014 10:36 AM, Maintainer wrote:
> 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...

Hi Jens --

There are two developments likely before the next Bioconductor release in October.

First, an 'Rhtslib' package will be developed to wrap the recently released 
1.0.0 version of the htslib. I've been working on this recently, and will make a 
public version available on github.org/Bioconductor toward the end of next week. 
One aspect that is causing a little slow-down (not insurmountable) is that 
htslib seems to have had minimal development / testing on Windows.

Second, Rsamtools will be modified to use Rhtslib; htslib is a dependency for 
the updated parallel samtools code. It's not clear whether Rhtslib will be 
reliably cross-platform in time for the next Bioconductor release.


>> thanks
>> Jens
>>    -- output of sessionInfo():
>> .
>> --
>> Sent via the guest posting facility at bioconductor.org.
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