Fix export_fasta_from_regions to output one header per region#259
Open
nsheff wants to merge 1 commit into
Open
Fix export_fasta_from_regions to output one header per region#259nsheff wants to merge 1 commit into
nsheff wants to merge 1 commit into
Conversation
Previously wrote one header per chromosome and concatenated region sequences without separators. Now correctly outputs standard FASTA with one header per BED region in the format >chr:start-end.
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Summary
export_fasta_from_regionswas outputting one header per chromosome, concatenating sequences from multiple regions without separators>chr:start-endThe bug
Before this fix, extracting 5 regions from 2 chromosomes would produce output like:
After this fix:
Test plan