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So https://github.com/dib-lab/sourmash/pull/1046 added a `clear` option to `set_abundances`, but setting abundances to zero doesn't delete the hash, which seems nonintuitive.
code:
```python
impo…
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I.e. any switch that tracks which k-mer sequence is present in the signature?
Thank you.
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e.g. `--scaled 0` works => produces a num sketch, which is technically ok but...
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example command:
```
sourmash prefetch SRR7186547.abundtrim.sig databases/pl-genomes.dna-k31-scaled100.sbt.zip \
-k 31 --dna -o results/hangtest.sbt-prefetch.csv
```
```
== …
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Running the demo data in [charcoal](https://github.com/dib-lab/charcoal/) produces a `ValueError` for `threshold_bp`.
I added a print statement to the charcoal file `charcoal/contigs_list_contaminant…
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I've recently been working on building sourmash taxonomy databases built on the GTDB alternate taxonomy (c.f. https://github.com/Ecogenomics/GtdbTk, etc.). This has about 25,000 genomes, most of which…
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**Note:** updated in https://github.com/dib-lab/sourmash/issues/1525
when taking in DNA sequence to translate into protein, how should sourmash treat the k-mer size?
right now,
1. sourmash on D…
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`git log --oneline v4.0.0..latest`:
## 4.1.0 release notes
This release provides several convenient features for users, including zipfile collections on input and output and a new `prefetch` comma…
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Example:
```python
# load one signature "sig"
mh = MinHash(ksize=21, scaled=100, n=0)
assert len(mh) == 0
newmh = mh.merge(sig.minhash)
assert len(mh) == 0
AssertionError:
```
Is this b…
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**Note:** Updated in https://github.com/dib-lab/sourmash/issues/1524, which contains the unresolved parts of this issue.
#936 added `Index.select(ksize=ksize, moltype=moltype, ...)` and with #1059 …