Hide reads with unmapped flag by default in alignments tracks #2204
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
github-actions
bot
added
the
needs label triage
cmdcolin
added
enhancement
cmdcolin
changed the title
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Outdated suggestions cannot be applied.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.
This is a small change to have "unmapped reads" included in the default set of flags hidden on alignments tracks
Unmapped reads can be weird in that they can exist at a given coordinate but be shown still
1540 can be seen here https://broadinstitute.github.io/picard/explain-flags.html
read unmapped
read fails platform/vendor quality checks
read is PCR or optical duplicate
This is true in jbrowse 1 and igv by default. Had run into this with a hand crafted sam file that had unmapped reads that displayed in jbrowse but not in igv by default.