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

[Frank Heimes]

** Patch removed: "debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff"
   https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+attachment/5606313/+files/debdiff_kinetic_samtools-legacy_from_0.1.19+dfsg-5_to_0.1.19+dfsg-5ubuntu1.diff

-- 
You received this bug notification because you are a member of Ubuntu
Sponsors Team, which is subscribed to the bug report.
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  bedtools package (no bgzf_hopen - looks a bit out of date), so it does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.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/samtools-legacy/+bug/1983255/+subscriptions