Closed samuelruizperez closed 10 months ago
Hi @samuelruizperez , thank you so much for this issue and the pull request! It would be fine for me to force the use of CSI, but for backwards compatibility, I made a fix for uropa 4.0.3
which automatically checks for the largest coordinates and uses CSI if the chromosomes are too large. It's available on PyPI now - I hope this solves your issue! I will close your pull request but feel free to contribute again in the future, thanks! 🥳
Hi, @msbentsen:
Thank you for the quick reply and fix! Sounds good to me. 🥳
Hi!
Thank you for developing such a great tool!
I tried to run UROPA 4.0.2 and I got these error messages:
I think the issue is that my GTF has some pretty large chromosomes, and they cannot be stored in a TBI index. Is there an easy way to index as CSI instead of TBI or any other way to handle large chromosomes in the GTF file for UROPA?
Thank you!