-
Notifications
You must be signed in to change notification settings - Fork 80
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[MRG] report both weighted and unweighted % recovered in gather #2301
Conversation
Codecov Report
@@ Coverage Diff @@
## latest #2301 +/- ##
==========================================
+ Coverage 84.83% 92.14% +7.31%
==========================================
Files 131 100 -31
Lines 15676 11414 -4262
Branches 2252 2253 +1
==========================================
- Hits 13298 10517 -2781
+ Misses 2083 602 -1481
Partials 295 295
Flags with carried forward coverage won't be shown. Click here to find out more.
📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
Ready for review & merge @sourmash-bio/devs |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
lgtm! It'll be pretty helpful to have both weighted and unweighted results printed.
This PR changes
sourmash gather
to report both weighted and unweighted k-mer identification per #1818; the changes in #2249 made this a pretty easy fix, and the conversation in dib-lab/genome-grist#197 made it obvious that we should support it for genome-grist purposes!This PR also updates the docs on % recovered in response to #2300 (comment).
example output
If
--ignore-abundance
is specified or abundances are not available, only the unweighted number is reported.Fixes #1818.
TODO items
sourmash gather
output #1850, reporting threshold more clearly