How can I activate multitasking with Rbwa when creating a reference index or alignment?
The "-t" parameter doesn't work...
There is no -t argument for bwa_build_index, so if that's what you are basing your question on, that's the reason. There is a -t argument for bwa_aln, and it looks like Rbwa just calls bwa_aln directly, so it should work.
Indeed, one can pass additional arguments to the bwa_aln function in Rbwa:
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