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

ggsashimi can easy read from remote BAMs if allowed to do it #95

Open
diekhans opened this issue Aug 21, 2023 · 0 comments
Open

ggsashimi can easy read from remote BAMs if allowed to do it #95

diekhans opened this issue Aug 21, 2023 · 0 comments

Comments

@diekhans
Copy link

New feature

Allow ggsashimi to access BAMs remotely via HTTP like many other tools operating on regions of BAMs.

Usage scenario

I want to render images on my laptop so I can look at them immediately, however downloading large BAMs just to render small ranges of the BAMs.
This is inefficient of my time.

Suggest implementation

pysam can read BAMs remotely by HTTP,. however ggsashimi disallows it by checking if there is a file present. Just deleting these two lines and ggsashimi works find on HTTP URLs to indexed BAMs

                if not os.path.isfile(bam):
                        continue

This check is also problematic as it causes ggsashimi to ignore BAMs without telling you which one is bad or why. Just let pysam generate an error.

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

No branches or pull requests

1 participant