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Implement JSON format discussed in MASH #1

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lgautier opened this issue Jan 10, 2017 · 2 comments
Open

Implement JSON format discussed in MASH #1

lgautier opened this issue Jan 10, 2017 · 2 comments

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@lgautier
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While the format is still discussed (see marbl/Mash#44), the design should already make the implementation of JSON signature both easy and sufficiently performant.

@lgautier lgautier changed the title Implement JSON format discussin in MASH Implement JSON format discussed in MASH Jan 10, 2017
@lgautier
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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.

@lgautier
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lgautier commented Jan 21, 2017

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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