Remove the dataloader mask #216
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Previously, when creating the dataloader, Vamb would create a mask, signifying which contigs were unsuitable for encoding due to having no TNFs or a depth of zeros. However, with the recent changes in commit 5c1dc3e, sequences with zero depth can be encoded just fine. And it was always unrealistic that a sequence would have zero TNFs - if it did, it was probably due to a serious user mistake. Now, do not mask sequences at all, and throw an error if a sequence has no TNFs.
|
CC @Paupiera not important ATM - I looked through the AVAMB workflow to see if this would effect anything but I couldn't find any. Nonetheless, before merging, it would be nice to check that the workflow still runs with this PR. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Previously, when creating the dataloader, Vamb would create a mask, signifying which contigs were unsuitable for encoding due to having no TNFs or a depth of zeros.
However, with the recent changes in commit 5c1dc3e, sequences with zero depth can be encoded just fine. And it was always unrealistic that a sequence would have zero TNFs - if it did, it was probably due to a serious user mistake. Now, do not mask sequences at all, and throw an error if a sequence has no TNFs.