On 07/20/2010 10:06 AM, Thomas Unterthiner wrote: > On 07/20/2010 06:28 PM, Martin Morgan wrote: >> On 07/20/2010 06:50 AM, Thomas Unterthiner wrote: >> >>> Hi there! >>> >>> I need to sort BAM files. I am aware of 'samtools sort ...', but >>> being able >>> to do this in R (w/o dependence on an external tool like samtools) would >>> suit >>> my workflow much better. >>> >>> Are there any plans to integrate this sorting functionality into >>> Rsamtools? >>> >> Thanks for the feedback; I wasn't sure whether users would find this >> convenient, or would have samtools installed anyway, and so was not sure >> how useful this would be. I'll implement this, but it will not be >> immediate. >> >> Martin >> >> > > That is awesome news! :) > I will probably hack together some workaround until the functionality > is available in Rsamtools. OTOH I could instead try to implement > this decently within the Rsamtools codebase myself and then send you > the patches. But since I'm neither familiar with interfacing R and C nor > with the Rsamtools-codebase, my solution might not be on par with yours. > So is this something you'd rather implement yourself anyways, or would > the help be appreciated? > (And last but not least: would this help in speeding up the process > of getting this feature in Rsamtools?) Thanks for the offer; of course patches are welcome but there's likely a fairly steep learning curve (but learning is fun, so if you're looking for an opportunity...). I'll definitely make use of you as a tester... Also, samtools is not difficult to download and build on a standard Linux machine; by the time you were able to write code in Rsamtools you'd have everything needed to build samtools yourself. Martin > > Cheers > > Thomas -- Martin Morgan 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