Allow SAM-style flags to be passed through to output from FASTQ comments #4451
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
jeizenga
changed the title
jeizenga
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Outdated suggestions cannot be applied.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.
Changelog Entry
To be copied to the draft changelog by merger:
vg map,vg mpmap, andvg giraffecan now annotate output with SAM-style flags from FASTQ comments with--comments-as-tagsDescription
Resolves #4370.
The tags get stored in the annotation field of the GAM and then interpreted in the BAM and GAF output.
I ended up not pulling in the full up-to-date master branch of libvgio because there's a recent PR in there that introduced a progress option, which leads to all sorts of crashes in the integration tests. I don't exactly know what's causing it, but @adamnovak might want to take a look.