Skip to content
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.

Sign up for GitHub

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

Jump to bottom

Fail to read read groups when PG is in header #72

Open
mgymrek opened this issue Mar 3, 2016 · 1 comment
Open

Fail to read read groups when PG is in header #72

mgymrek opened this issue Mar 3, 2016 · 1 comment

Comments

@mgymrek
Copy link
Owner

mgymrek commented Mar 3, 2016

Pointed out by Isidro Cortes. When a @pg line is in the header, we report an error that no read groups are found "ERROR: No read groups found". This could be an issue in the underlying BamTools library.
@jmonlong
Copy link

Hi, I'm also getting this error. Good to know that the @pg is at fault.
Any recommendation on how to handle that ?
I'll try to reheader the bam files, but is there another way that doesn't require rewriting the whole bam ?
Thanks,

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@mgymrek @jmonlong