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

Reading BAM files #40

Open
mikael-s opened this issue Jul 19, 2021 · 4 comments
Open

Reading BAM files #40

mikael-s opened this issue Jul 19, 2021 · 4 comments

Comments

@mikael-s
Copy link

Hi!

Is there any possibility to read a BAM file as a bank of sequences? Do you know of any software relying on GATB which would have done that?

Thanks!

@rizkg
Copy link
Contributor

rizkg commented Jul 19, 2021

Hi,

I did that some time ago using htslib, but did not push it to GATB master branch because of the added dependency to htslib that I thought would bother some people. Let me see if I can put that in a branch or fork.

@rchikhi
Copy link
Member

rchikhi commented Jul 20, 2021

another way would be a wrapper script with named pipes? e.g. COMBINE-lab/salmon#29 (comment)

@mikael-s
Copy link
Author

I did that some time ago using htslib, but did not push it to GATB master branch because of the added dependency to htslib that I thought would bother some people. Let me see if I can put that in a branch or fork.

Awesome, thanks!

another way would be a wrapper script with named pipes? e.g. COMBINE-lab/salmon#29 (comment)

Named pipes are nice but unfortunately I may need to read the input file more than once.

@rchikhi
Copy link
Member

rchikhi commented Jul 21, 2021

yes exactly, I came back to post this, sorry this pipe solution can't work in gatb as it already reads the file more than once internally

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

3 participants