Pipe and filter model with bfast+bwa 0.6.4e

[James W. MacDonald]

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.

[drio]

Please, use the git version and try again:

$ git clone git://bfast.git.sourceforge.net/gitroot/bfast/bfast
$ git checkout -b bfast+bwa origin/bfast+bwa
$ sh ./autogen.sh && ./configure && make

[James W. MacDonald]

Retracted. Never mind.