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In the ZipFileLinearIndex PR https://github.com/dib-lab/sourmash/pull/1349#issuecomment-787191222, I'm thinking about signature manifests that provide some kind of metadata about the signature - ksize…
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There have been a number of requests for getting at the k-mers behind the hashvalues (#211 #483 #678), and it turns out that there is no simple way to do this - ref code in #724, which only works for …
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per @luizirber, on running gather on a gigantic signature --
>Right now it is spending all the time inside sum_abunds = sum(( orig_query_abunds[k] for k in orig_query_hashes)), because it is pullin…
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Over in #1392, I implement a code block that retrieves abundances from a sketch using hashes; in `src/sourmash/commands.py`, function `gather`:
```python=
if is_abundance:
…
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I am trying to calculate hashes for all kmers in a certain space. I found a [script]() in this repo that was used to calculate this independent of sourmash using the `mmh3` library. Now I try this:
…
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I am trying to create a custom database and some of my reference genomes have ambiguous base pairs `N`
When computing the minhash from the python API I get the following error:
```
File ".../so…
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I'd like to be able to calculate ONE "deep" signature of e.g. 10k kmers for each sample and then adjust the scaling factor to 5k kmers, 1k kmers, 500 kmers, 100 kmers, see how that affects the similar…
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I ran into a panic when working on doctests for #1695, but foolishly did not stop to save the exact code. I'm leaving it here so that @mr-eyes or I can return to it later to figure out what probably h…
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As I write more/deeper code around search and prefetch and so on, I am starting worry about accidentally modifying `MinHash` objects.
In brief -
* *most* of the time, `MinHash` objects loaded from…
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If we have 2 sequences containing 4 kmers each, they are different in only one kmer. Shouldn't the similarity be 75% instead of 60%?
**Reproduce:**
```python
from sourmash import MinHash
mh1…