[ensembl-dev] bgzf_read_block message in stderr

andrew126 at mac.com andrew126 at mac.com
Mon Dec 4 17:30:51 GMT 2017


In using API 90, when recovering all available allele frequencies for a particular variation feature, occassionally this message is shown in stderr:

	[W::bgzf_read_block] EOF marker is absent. The input is probably truncated

That message seems to correlate with some allele frequencies not being found/reported by my script (in my case, the gnomAD frequencies).

That is, when that message is not seen in stderr, I recover gnomAD frequencies for a particular variation feature; but when the message is seen, then it can look like that same variation feature doesn't have any gnomAD frequencies (even though it does).

Is there any way to make such an event fatal to any API script?  I'd much rather have my script fail/exit under such errors, than to not have it fail and risk believing such allele frequencies don't exist.


Please let me know if any other information would be useful.



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