Question: [devteam-bioc] parallel BAM sorting with Rsamtools
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gravatar for Jens Reeder
5.0 years ago by
Jens Reeder40
Jens Reeder40 wrote:
Hi Martin, while you are at it, Do you think you could also expose the samtools cat command at the R level? (from the samtools help: http://samtools.sourceforge.net/samtools.shtml) samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ] While functionally this can already be done using mergeBam(), samtools cat is way faster. This is e.g. useful when you already have sorted bam files per chromosome and want to combine them. thanks Jens On Fri, Aug 29, 2014 at 1:36 PM, Jens Reeder <jens.reeder at="" gmail.com=""> wrote: > That's great to hear. > I'll keep an eye open for the new Rhtslib. > > Hopefully the windows issues will not keep it out of the next bioc release. > > thanks > Jens > > > On Fri, Aug 29, 2014 at 1:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > >> 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. >> >> Martin >> >> >>>> thanks >>>> Jens >>>> >>>> -- output of sessionInfo(): >>>> >>>> . >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane. >>>> science.biology.informatics.conductor >>>> >>> >>> __________________________________________________________________ ______ >>> devteam-bioc mailing list >>> To unsubscribe from this mailing list send a blank email to >>> devteam-bioc-leave at lists.fhcrc.org >>> You can also unsubscribe or change your personal options at >>> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc >>> >>> >> >> -- >> Computational Biology / Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> >> Location: Arnold Building M1 B861 >> Phone: (206) 667-2793 >> > > [[alternative HTML version deleted]]
cancer rsamtools biocparallel • 779 views
ADD COMMENTlink written 5.0 years ago by Jens Reeder40
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