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Right, for our network BAM file reading, we assume the .bai file is located at file.bam.bai rather than file.bai.

I'm sorry that that assumption doesn't hold up in your situation.

For local BAM files, we can look at the file system and see if there is no file.bam.bai but there is a file.bai we can find the index file and move on.

We can not generate .bai files for remote sources as that requires reading the entire BAM file (which is as much work as downloading the file).