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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
88 stars 12 forks source link

CRAM support #38

Closed willhooper closed 1 year ago

willhooper commented 1 year ago

Hi,

Thanks for developing this great tool! It seems like nanomonsv doesn't currently support CRAM input. Would it be possible to add this? I think many would find this useful.

Thanks! Will

friend1ws commented 1 year ago

Hi, thank you very much for your interest in our software. Supporting CRAM is an option. But I'm still not sure whether people often use CRAM format for Nanopore sequence data or not so.

Supporting CRAM is technically not very challenging, But the challenge for supporting CRAM input is that we use random access in the validation phase, and the computational cost may increase significantly. I will try to optimize Nanomonsv so that in near future we may accept CRAM format.

willhooper commented 1 year ago

Thank you! We use CRAM for our nanopore data stored in the cloud to save on storage costs, I suspect anyone else working in the cloud would find this useful as well.

friend1ws commented 1 year ago

OK, I will support CRAM format and try to release it in the next version.

friend1ws commented 1 year ago

We have almost finished the CRAM support in the devel branch. It seems that there is not so much computational overhead because of CRAM. I will release it after additional tests hopefully next week.

willhooper commented 1 year ago

That's great to hear. Thank you for adding this feature!

friend1ws commented 1 year ago

We have now pre-released the CRAM-supported version. We will provide a stable release after intensive testing. So I would like to close this issue once.