Stand-alone Sedaka consensus and stitch

[christopher-vollmers]

Hi,

I've been using medaka as part of our bc1 pipeline. I did a fresh install recently and now "medaka consensus" and "medaka stitch" are no longer available. They are still mentioned in the README though.

Did those options go away?

Best,
Chris

[iiSeymour]

Hey @christopher-vollmers

These where changed in the v2.0.0 release of Medaka.

• The medaka consensus command has been renamed to medaka inference to reflect
  its function in running an arbitrary model and avoid confusion with medaka_consensus.
• The medaka stitch command has been renamed to medaka sequence to reflect its
  function in creating a consensus sequence.

See https://github.com/nanoporetech/medaka/releases/tag/v2.0.0

[christopher-vollmers]

Got it! Thank you. I will give it a try.

[christopher-vollmers]

Working as intended again. Will have to update bc1. Thank you for the tool and advice!