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torognes / swarm

A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
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Add support for unseekable pipes #86

Closed frederic-mahe closed 7 years ago

frederic-mahe commented 8 years ago

Like vsearch, swarm would benefit from a broader support of pipes and stdin/stdout redirections. As of now:

# unlikely example
swarm --output - input.fas > output.swarms

produces an empty output.swarms and write OTUs to a file named -.

frederic-mahe commented 7 years ago

Perfect, swarm 2.1.13 can now read from process substitutions, which allows for more flexible pipelines.

swarm <(printf ">s_1\nAAAA\n")