C. Titus Brown
C. Titus Brown
Note: PR into https://github.com/sourmash-bio/sourmash/pull/2598.
https://github.com/mr-eyes/sourmash_plugin_extract_errors by @mr-eyes ref https://github.com/sourmash-bio/sourmash/issues/2383#issuecomment-1922765919 From the README: # sourmash_plugin_extract_errors ## Motivation Illumina's sequencing errors are unique per sample. If you are working on a pool of samples and you...
As I was thinking about the ANI stuff #1967 https://github.com/sourmash-bio/sourmash/issues/2001 I came up with an idea. 💡 right now, search outputs largely useless CSV files, with minimal information. (see https://github.com/sourmash-bio/sourmash/issues/1390...
NOTE: all of the functionality for this plugin has been implemented in [the `manysearch` command from the branchwater plugin](https://github.com/sourmash-bio/sourmash_plugin_branchwater), which is fast, low-memory, and multithreaded. We suggest you use that...
```python def add_scaled_arg(parser, default=None): parser.add_argument( '--scaled', metavar='FLOAT', type=check_scaled_bounds, help='downsample to this scaled; value should be between 100 and 1e6' ) ``` here, `default` should be used in `add_argument` to provide...
e.g. `self.sum_abunds = (generator expression)` could maybe just become `self.sum_abunds = self.orig_query_mh.sum_abundances` could be good to add these methods to the Rust FFI interface too 🤔
after https://github.com/sourmash-bio/sourmash/issues/2812 and https://github.com/sourmash-bio/sourmash/pull/2954, it seems like it might be nice to group the information in the files a bit more - categories like, * comparisons and containment values *...
In https://github.com/sourmash-bio/sourmash/pull/1837, we change `sourmash sig extract` to identify signatures to extract using manifest rows, and then have to convert the manifest rows into a manifest and then from there...
turns out [we've supported windows](https://github.com/sourmash-bio/sourmash/issues/1004#issuecomment-635708595) for a little while, which I'd forgotten! So people have been downloading `sourmash-minimal` on conda-forge (which supports Windows builds) and then installing extra deps themselves!...
do you use `-o` or use stdout redirect or ...? It seems to differ from output format to output format, too?