Adds check that ref sequence names do not contain semicolon during index #16
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
…with XA:Z If a user's input reference sequences have a semicolon in the name, this clashes with the use of the semicolon as a delimiter in the XA:Z tag. It may be useful to warn users of this potential issue during the bwa index step. For example, if users use xa2multi.pl to make multiple entries from the XA tag and pass to samtools view, samtools view will only look for the refname prior to the semicolon.
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Outdated suggestions cannot be applied.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.
If a user's input reference sequences have a semicolon in the name, this clashes with the use of the semicolon as a delimiter in the
XA:Ztag. It may be useful to warn users of this potential issue during the bwa index step. For example, if users usexa2multi.plto make multiple entries from the XA tag and pass to samtools view, samtools view will only look for the refname prior to the semicolon.