On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:

> Hello,
> Question for galaxy maintainers: have you encountered situations where BWA 
> jobs run 'forever' (for days) ?
> A little digging shows that it's the "bwa sampe" step, and SEQanswers thread 
> mention it's somewhat common:
> http://seqanswers.com/forums/showthread.php?t=11652
> http://seqanswers.com/forums/showthread.php?t=6340
> One suggested work-around is to add "-A" to "bwa sampe", but there's no way 
> to do it in the current BWA wrapper.
> (On the command-line with the same input files it does make things much 
> faster).
> I'm wondering if this is common enough to justify adding "-A" to the wrapper, 
> or is it rare enough and can be ignored.
> -gordon

Can it be added as an optional argument?  So that if it is selected, the 
setting is passed to the tool, otherwise not.


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