[BUFIX] fail when passed fastas with duplicate sequence ids#555
Merged
Conversation
skothenhill-nv
requested review from
cspades,
edawson,
jstjohn and
malcolmgreaves
as code owners
…o hillst/nvfaidx-restrictions
Collaborator
Author
|
/build-ci |
cspades
approved these changes
Dec 24, 2024
edawson
approved these changes
Dec 25, 2024
Contributor
edawson
left a comment
edawson
left a comment
There was a problem hiding this comment.
Looks good, and appreciate the tests - approved.
nvdreidenbach
pushed a commit
to nvdreidenbach/bionemo-framework
that referenced
this pull request
Jan 2, 2025
…ioNeMo#555) When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry. This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead. Signed-off-by: Danny <dreidenbach@nvidia.com>
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry.
This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead.