Add a warning for samtools fastq on coordinate sorted data.#2176
Merged
Conversation
There can be legitimate cases of samtools fastq/fasta being run on such data, for example when it is single ended, and we do not wish to reorder the file. So making this a hard error may be problematic for existing pipelines. However it is also a cause of confusion and mistakes to users, so a warning is necessary. Fixes samtools#2169
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
2 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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
There can be legitimate cases of samtools fastq/fasta being run on such data, for example when it is single ended, and we do not wish to reorder the file. So making this a hard error may be problematic for existing pipelines.
However it is also a cause of confusion and mistakes to users, so a warning is necessary.
Fixes #2169