On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
> 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:
> 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
> I'm wondering if this is common enough to justify adding "-A" to the wrapper,
> or is it rare enough and can be ignored.
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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