New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add option to show CDR3 AA translation for export alignments #192

Closed
wants to merge 1 commit into
base: develop
from

Conversation

Projects
None yet
2 participants
@bbimber

bbimber commented Jan 25, 2017

This proposed patch adds an option to show the CDR3 AA translation above the NT sequence in ExportAlignmentsPretty. We've found this useful when looking at many reads. I'm open to implementation suggestions - one weakness of this approach is that it only seems to report AA if we have full-length CDR3. I'm extracting this using:

NSequenceWithQuality cdr3NT = vdjcObject.getFeature(GeneFeature.CDR3);

and it's possible another route would also give us a result for partial overlaps.

dbolotin added a commit that referenced this pull request Dec 26, 2017

@dbolotin dbolotin closed this Dec 26, 2017

dbolotin added a commit that referenced this pull request Dec 26, 2017

This adds amino acid sequence in exportAlignmentsPretty output. (#317)
* This fixes #316
* This supersedes #192
* Repseqio update.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment