On 27 May 2016, at 06:14, Peter Johansson <[email protected]> wrote:
> Seems the problematic entry had a negative QUAL (-2147480064), which looks
> very suspicious. Need to go upstream and look for the source of that.
QUAL is Phred-scaled, so by definition valid values are non-negative. So the
upstream source might be interesting!
> I have no idea why negative QUAL causes a segfault and whether it would make
> sense with a more gracious exit. I have attached the problematic entry, if
> you are want to test further.
BCFtools stats rounds QUAL to integers 0..998 and displays totals for those
bins. Negative QUAL was crashing as it was trying to increment a negative bin.
I've fixed it to increment the 0 bin instead of crashing, just as it
increments the 998 bin for QUALs beyond a thousand. Thanks for the test case.
John
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