Comments (2)
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.
from mashing-pumpkins.
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.
from mashing-pumpkins.
Related Issues (12)
- Fix ngrams at junction of batches between `hashfun` calls. HOT 1
- Codecov stopped reporting coverage
- Default seed not programmatically accessible
- Make default seed value 42 ? HOT 1
- Current implementation is computing MaxHash sets HOT 1
- Error pickling XXHash hashing function HOT 1
- Add Dockerfile w/ command line HOT 3
- Implement in-place add operator `__iadd__` as an alias to existing method `update`.
- Move tests to directory / submodule `tests/` HOT 1
- Additional example / notebook showing how easily alternative minhash approaches can be compared HOT 1
- Ensure it builds on OS X
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from mashing-pumpkins.