C. Titus Brown

I got: ``` picking column 'ident' of type 'ident' from 'outputs.ath/host/picklist-exclude.csv' loaded 46123 distinct values into picklist. loaded 33759 signatures total, from 1 files loaded 33759 signatures total. for given...

Over in `classifying-signatures.md` [link](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html#appendix-d-gather-csv-output-columns) I wrote: >`f_orig_query`: The fraction of the original query represented by this match. Approximates the fraction of metagenomic reads that will map to this genome. but...

key word: cosmopolitan k-mers ```python #! /usr/bin/env python import sys import argparse import sourmash from collections import Counter import csv def main(): p = argparse.ArgumentParser() p.add_argument('sigs', nargs='+') p.add_argument('-o', '--output', required=True)...

support name output from `sig grep`

4

right now `sig grep` outputs either count or the sketch; would be nice to be able to see just the sketch names.

see https://github.com/ctb/2025-sourmash-gather-inquisition ---- Usage: `inquisite.py` Take the metagenome 'SRR606249', the query genome '47.fa.sig', and the gather results against 'podar-ref.zip', and show relevant overlaps between the query genome and genomes found...

per @luizirber: it works, only issue is for really big sigs (like some SRA metagenomes) that go over the 2GiB limit per list/array in parquet (it's only 32-bit indexing). I...

``` sourmash sketch dna --name SRR15057930.assembly SRR15057930.d/final.contigs.fa -o SRR15057930.unmapped.assembly-singletons.sig.zip -p dna,k=31,k=51 --singleton ``` produced only a single sketch, despite 'singleton'.

WIP: add exception for unkown manifest output format

1

A minor fix to add error message for unknown output format. Noticed during https://github.com/sourmash-bio/sourmash/issues/3801

script: options for shuffling the order in which sketches are searched in a database

2

for straight up sourmash zipfiles, it turns out to be surprisingly hard to change the order in which sketches are loaded. some options for @bettafische - - update the actual...

sourmash compute/sketch doesn't recognize signature files when erroneously provided on command line

2

`sourmash compute *` will error on signature files. Which is technically correct, but surprising from a UX perspective!