[BioC] Rsamtools: Sorting BAM files

Martin Morgan mtmorgan at fhcrc.org
Tue Jul 20 19:12:15 CEST 2010


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



More information about the Bioconductor mailing list