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lgautier avatar lgautier commented on May 26, 2024

For the sake of global efficiency, a temp solution might be to work out a simple adapter mashing-pumpkins <-> sourmash and rely on that export (see sourmash-bio/sourmash#99 (comment) )

The adapter would also make it easy to plug the heap+set-based implementation into sourmash if the 1.5x-3x speedup is holding with real data.

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lgautier avatar lgautier commented on May 26, 2024

The adapter is now in the code base (module mashingpumpkins.sourmash) and appears to be working (very) well.

The first release will not include specific JSON capabilities (and may never include any as long as sourmash_lib is providing the feature).

**edit: ** sourmash-bio/sourmash#99 (comment) is only about reading the interop JSON exchange format. Time permitting, I'll throw writing into the mix.

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