-
Since the user has the power to `sig rename` or generates signatures without `.sig` or `.sig.gz` extension. And since the zipStorage implementation expects `.sig` or `.sig.gz` extension as per https:/…
-
The following will use [GNU parallel](https://www.gnu.org/software/parallel/) to calculate sketches in parallel - 8 at a time.
```
for i in *.fa
do
echo sourmash sketch dna $i -o demo/$i.sig
…
-
Over in https://github.com/sourmash-bio/sourmash/issues/2128, I wrote
>>Also while I am at it, any speed/memory advantage using FrozenHashes?
>Not a big one. The main goal of FrozenMinHash is to…
-
In https://github.com/sourmash-bio/sourmash/pull/1936, I'm adding tests for basic features of the `Index` class, and `RevIndex` doesn't pass them. (`RevIndex` is the rust-based reverse index added in …
-
(Some of this might be 5.0 material, because they change the file format in backwards-incompatible ways)
A few issues --
* in https://github.com/dib-lab/sourmash/pull/1346#pullrequestreview-6108…
ctb updated
10 months ago
-
First, it doesn't pick up the k-mer size from the available signatures, so you have to specify it explicitly on the command line (unlike `sourmash index`, where you only need to specify -k if it's not…
-
In #1808 I'm adding a `LCA_SqliteDatabase` class that supports on-disk LCA databases. These can be built directly with `sourmash lca index ... -F sql`, but it is also very easy to convert them from JS…
-
see https://github.com/ctb/2021-sourmash-greymake2 -- README in sum,
# 2021-sourmash-greymake2
parallelize containment searches of large sourmash databases using
manifests, picklists, and snake…
-
The identities of the query genome and the metagenome database are not matching. I am getting an error message indicating the genome is not present in the database when it is. Error message shown belo…
-
I have a suggestion that may be considered for a future version of sourmash. The current Minhash includes `hashes` and `abundances`. I propose adding an optional array called `positions`, which would …