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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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Gzipped files get cutoff when loading from google cloud #1579

Open lbergelson opened 2 months ago

lbergelson commented 2 months ago

bed.gz files are sometimes incompletely loaded when accessing them from google cloud.

It's unclear what set of conditions causes this to happen, but it seems to be deterministic and repeatable.

image

Strangely, copying the same file to a public google bucket caused it to load correctly. There is no error message or obvious sign that something went wrong when loading, the file just gets cutoff at chromosome 10.

The user reports that they've seen similar things with other files including gzipped vcf.

lbergelson commented 2 months ago

This is caused by https://github.com/samtools/htsjdk/issues/1691.