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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Missing --output-mlst #99

Closed apetkau closed 5 years ago

apetkau commented 5 years ago

It looks like the parameter --output-mlst was missed in release 0.6.0. This should allow you to specify an output file for the MLST results, similar to --output-plasmidfinder.

See line https://github.com/phac-nml/staramr/blob/2d882b4547e4838c368391be8a3679d445bdc793/staramr/subcommand/Search.py#L133

jennifertran commented 5 years ago

This is abit strange, I was sure I did add the --output-mlst command at some point. If you were to look in the development branch, the command for mlst is there https://github.com/phac-nml/staramr/blob/development/staramr/subcommand/Search.py#L145

I noticed that in version 0.6.1 the --output-mlst command was eventually added but for some reason not included in 0.6.0.

Takadonet commented 5 years ago

Been fixed in version 0.6.1