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Invalid BGZF block header #1131
I am using JBrowse to visualize data stored on a remote server over ssh port forwarding and have run into an issue with BGZF headers. However, I have also reproduced this issue running my setup locally too.
When first running JBrowse on a bam it seemed to work successfully (I could be wrong, but I don't think anything in the console is cause for concern. I think the two errors in the console are just because I didn't run generate-names.pl since I'm not using index features, and the warnings are because chrome doesn't cache things over a MB).
Upon trying JBrowse with other bams, I got the same error. Interestingly, some of the reads are displayed, but others are not.
According to #552, this error is because of incorrect binary formatting. However, I am able to open the aforementioned bams with samtools, view them in IGV, manipulate them with Bio.bgzf, and I also manually checked that the first two 8-bit ints in the files are 31 and 139 respectively.
Additionally, #552 was closed because of a known Apache fix, but I am using python's simple http server module (
The issue is very likely that python http.server does not handle byte-range requests (HTTP Range header)!