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Sadly, there is neither documentation nor a python interface, and it will probably be painful to get external code to link to this stuff - I've put no effort into even thinking about exporting a library.
The only feasible approach would be to add a new tool in https://github.com/marbl/meryl/tree/master/src - for example, copy meryl-lookup to fancy-processing (renaming files and adding targets to main.mk) then modifying that to do what you want.
Are there any draft docs available for the Meryl C++ API?
Or, very optimistically, has anyone written any python bindings for doing kmer set operations with Meryl?
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