Automatically fetch .csi index from file name

[skranz0]

Is your feature request related to a problem? Please describe.

I am working with rather big genomes which cannot be indexed as a .bai and need .csi. While jbrowse automatically fetches index files when you load a .bam, it does not detect .csi files.

Describe the solution you'd like

When loading a alignment.bam, look for a alignment.bam.csi automatically.

Describe alternatives you've considered

I can explicitly load the .csi index, but it would save a few clicks and be a quality of life change if that wasn't necessary.

Additional context

I use JBrowse 2.17.0

[cmdcolin]

This is generally a nice idea but it would be a little tricky to make this work properly. Just curious, are you generally using the GUI or the CLI for loading tracks? Ideally we would handle either case similarly, but currently they are sort of separate systems

[skranz0]

Naively, I would have thought it would just need to extend some regex for the new file type. I don't know how the internals work, though.
I usually use the GUI, but I'm also not using JBrowse to its full extent, just to double-check coordinates and gene positions from time to time.

[cmdcolin]

it currently does something like this to automatically fetch .tbi files. to handle .csi it would probably have to first try the .tbi file path, detect a 404, and then try .csi, which could also 404, and then report an error to the user. i think samtools does something like this

[cmdcolin]

note that my above is just my limited understanding of the issue. if you have a different sequence of operations that you are envisioning, please lay them out in as much detail as possible.