[Debian-med-packaging] Bug#1029202: Wrong calls of snpEff in snippy (Was: Could some SnpEff user from the community please ping authors)

[Andreas Tille]

Control: reassign -1 snippy
Control: retitle -1 Wrong calls of snpEff
Control: tags -1 upsteam
Control: forwarded -1 https://github.com/pcingola/SnpEff/issues/510

Thanks to snpEff upstream I've found a solution[1] for the problem
reported above.  I've also added a conscise test case[2] which was
exposing the problem above (which is solved) but in a later call to
snpEff with a different command a new problem occures.

I have reported this to snpEff[3] since I hope to get quick help there
for another patch to snippy to simply get rid of some single line in
some output file.  If all fails we can remove this manuall inside the
snippy Perl code but I'm striving for a clean solution here.

Kind regards
    Andreas.

[1] https://salsa.debian.org/med-team/snippy/-/blob/master/debian/patches/snpeff_v5.1%2B.patch 
[2] https://salsa.debian.org/med-team/snippy/-/blob/master/debian/tests/test_for_working_snpeff_v5.1%2B
[3] https://github.com/pcingola/SnpEff/issues/510

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