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

Update __init__.py #216

Merged
merged 1 commit into from
Jan 18, 2024
Merged

Update __init__.py #216

merged 1 commit into from
Jan 18, 2024

Conversation

rraadd88
Copy link
Contributor

Hi, I added a command to convert gzip to bgzip in the error message of UnsupportedCompressionFormat. It should be helpful for those who encounter this error.

Added the command to convert gzip to bgzip.
@mdshw5
Copy link
Owner

mdshw5 commented Jan 18, 2024

Thanks for the thoughtful contribution. I do think this will help a few people, since "how to bgzip a file" is still a common bioinformatics question!

@mdshw5 mdshw5 merged commit aa6b59b into mdshw5:master Jan 18, 2024
8 checks passed
@jmarshall
Copy link

However samtools bgzip is not a samtools subcommand so this will not in fact work.

I would recommend instead

For example: gunzip file.fa.gz; bgzip file.fa

This is simpler, avoids shell redirection, and avoids confusion about the file name extension used.

@mdshw5
Copy link
Owner

mdshw5 commented Jan 19, 2024

@jmarshall are you like Beetlejuice but for samtools? 😂

Of course this is a great recommendation and I’ll make the change.

@jmarshall
Copy link

🤣 First time I've ever got any value out of the GitHub dashboard feed — it showed you had made a new release surprisingly soon after the last one, so I had a look…

mdshw5 added a commit that referenced this pull request Jan 19, 2024
@mdshw5
Copy link
Owner

mdshw5 commented Jan 19, 2024

I truly appreciate it. I thought I had just fallen behind in the latest block gzip compression methodology!

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

Successfully merging this pull request may close these issues.

3 participants