Is it no longer possible to use the pipe and filter model with this version of bfast? If I pipe from bfast match to bfast localalign, I get a complaint that I am missing a -O and -T. Adding an -m - doesn't help either. The manual says that the default input for localalign is stdin, but maybe that isn't correct for bfast+bwa?
I am aligning single end reads now, but the next set will be paired end and I wanted to use the same version of bfast for both.
I am aligning single end reads now, but the next set will be paired end and I wanted to use the same version of bfast for both.
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