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Actually, this is an issue with the old .bai format. BigWigs support up to 4 GB and I've tested up to 2GB myself. There may be an issue with older versions of pysam or something.
Xref: deeptools/deepTools#761
I should also propose a new bigWig version to handle longer chromosomes. It'd "just" be a matter of changing the sizes of all the ints.
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