[Bug 1983867] [NEW] vcftools misses 'Remove compressBound assertions' (PR #1258) fix

Launchpad Bug Tracker 1983867 at bugs.launchpad.net
Mon Aug 8 16:24:09 UTC 2022


You have been subscribed to a public bug by Ubuntu Foundations Team Bug Bot (crichton):

vcftools comes with it's own (bundled) version of bgzf.c (src/cpp/bgzf.c);
which misses the fix for 'compressBound() returns an incorrect result on z15'.
(this fix is required in all bgzf.c implementations, like htslib, bedtools or even samtools-legacy)

Since the vcftools autopkgtest is triggered by the zlib proposed-migration,
the missing fix vcftools lets the autopkgtest fails and with that blocks the zlib proposed migration LP#1961427.

Problematic is that the code differs quite a bit from the one where the PR#1258 was designed for and that is used in the htslib or bedtools package (no bgzf_hopen - looks a bit out of date), so it does not apply cleanly.
But it is very close (one line differs) to the backport of PR#1258 that is already used by samtools-legacy.

** Affects: vcftools (Ubuntu)
     Importance: High
         Status: New


** Tags: focal patch s390x update-excuse
-- 
vcftools misses 'Remove compressBound assertions' (PR #1258) fix
https://bugs.launchpad.net/bugs/1983867
You received this bug notification because you are a member of Ubuntu Sponsors Team, which is subscribed to the bug report.



More information about the Ubuntu-sponsors mailing list