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.

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

Strand specific behavior is broken #1103

Open
Thomas1664 opened this issue Aug 21, 2024 · 0 comments
Open

Strand specific behavior is broken #1103

Thomas1664 opened this issue Aug 21, 2024 · 0 comments

Comments

@Thomas1664
Copy link

This problem can be observed for example for shift. The documentation states that the flags -m and -p can be used for strand-specific shifting. The documentation also provides an example but when I try the example with the latest version of bedtools (2.31.1), I get this output instead:

$ bedtools shift -i a.bed -g my.genome -p 2 -m -3
chr1    7       102     +
chr1    802     982     -

It seems like the problem is not limited to shift. The problem also exists for example in the window command.

I also observed this issue with my own data.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant