[BioC] Rsamtools: Sorting BAM files

Thomas Unterthiner thomas.unterthiner at students.jku.at
Tue Jul 20 19:06:55 CEST 2010


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?)

Cheers

Thomas



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