Skip to content
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

BUG: Empty samples #167

Merged
merged 2 commits into from
Aug 8, 2024
Merged

BUG: Empty samples #167

merged 2 commits into from
Aug 8, 2024

Conversation

Oddant1
Copy link
Member

@Oddant1 Oddant1 commented Jul 25, 2024

We attempt to concatenate the empty samples dropped by dada2 in R back onto the table. If no samples are dropped we attempt to concat an empty 0x0 table onto the table produced by dada2 in R.

Bug introduced here

Came up on the forum here

Should be resolved by ensuring we have dropped samples before attempting to concat them back on.

OK so I went down a bit of a rabbit hole here, and the explanation is not actually as simple as I originally believed. The user on the forum specifically has 1 OTU and no dropped samples, so we try to instantiate a 1x0 biom table. We end up with a 0x0 biom table because of this line of code here. The guard I implemented in this PR should still work, but not quite for the reason I thought.

@Oddant1 Oddant1 assigned Oddant1 and colinvwood and unassigned Oddant1 Jul 25, 2024
@Oddant1 Oddant1 requested a review from colinvwood July 29, 2024 21:38
@colinvwood
Copy link
Contributor

Is this awaiting a test?

@lizgehret lizgehret changed the title Empty samples bug BUG: Empty samples Aug 8, 2024
@lizgehret lizgehret assigned Oddant1 and unassigned colinvwood Aug 8, 2024
@colinvwood colinvwood merged commit ae3a2df into dev Aug 8, 2024
5 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
No open projects
Status: Completed
Development

Successfully merging this pull request may close these issues.

2 participants