Changed sanity-check comparison to be case-insensity#157
Closed
travc wants to merge 1 commit into
Closed
Conversation
Closed
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
bcfools merge was failing due to a case (as in upper/lower) difference between the REFs.
The fix is inserting 4 characters on 1 line.
I'm not 100% on how the case difference is getting in there. My guess is that...
Our reference genome fasta is soft-masked with lower-case, which seem to be preserved sometimes but not others. IMO, the preferred behaviour would be to always preserve the case of the REF allele as it is in the reference, but it isn't important enough for me to track it down at the moment.