[Bug 1983255] Re: samtools-legacy misses 'Remove compressBound assertions' (PR #1258) fix

[Olivier Gayot]

Hi @fheimes!
I stumbled upon this bug when looking at proposed-migrations (i.e., zlib vs libbio-samtools-perl).

I ran autopkgtest on s390x against proposed and pinned libbam-dev to the
version in your ppa
(https://launchpad.net/~fheimes/+archive/ubuntu/lp1983255) but
unfortunately the test is still red for me.

Would you mind having a quick glance and let me know if you think I
overlooked or missed something?

I'm attaching the logs.

Best regards,
Olivier

** Attachment added: "autopkgtest-logs"
   https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5607043/+files/autopkgtest-logs.tar.xz

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https://bugs.launchpad.net/bugs/1983255

Title:
  samtools-legacy misses 'Remove compressBound assertions' (PR #1258)
  fix

Status in samtools-legacy package in Ubuntu:
  In Progress

Bug description:
  samtools-legacy is the source package for libbam-dev,
  which is used by libbio-samtools-perl (autopkgtests),
  that is for example triggered by a zlib update (proposed-transition).

  zlib requires a fix for 'compressBound() returns an incorrect result
  on z15' LP#1961427 that again requires the 'Remove compressBound
  assertions' (PR #1258) fix in all bgzf.c implementations, like htslib,
  bedtools or even samtools-legacy.

  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  bedtools package (no bgzf_hopen - looks a bit out of date), so it does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.

  According to upstream 'https://github.com/lh3/samtools-legacy' the project
  is "For testing only." and marked as "DON'T USE!" and it's last update
  is from Nov 9, 2013.

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