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

[Launchpad Bug Tracker]

You have been subscribed to a public bug by Steve Langasek (vorlon):

SRU Justification:
==================

[Impact]

 * zlib requires a fix for 'compressBound() returns an incorrect result
   on z15' (described at LP#1961427 in more detail).

 * But the above patch expects that another fix 'Remove compressBound
   assertions' (PR #1258) is in place for all bgzf.c implementations.

 * The packages htslib and bedtools are covered in LP#1961427.

 * Unfortunately more 'embedded' or better 'bundled' bgzf.c implementations
   exist, that are difficult to find upfront, hence the zlib proposed migration
   now pointed to libbio-samtools-perl.

 * libbio-samtools-perl is linked to libbam-dev from samtools-legacy;
   and samtools-legacy contains another bgzf.c implementation.

 * Hence PR #1258 is needed to fix bgzf.c as part of samtools-legacy.

 * And libbio-samtools-perl needs then rebuild to like against the
   fixed libbam-dev.

 * PR #1258 removes the Assert lines and modifies bgzf_compress.

[Test Plan]

* An IBM zSystem (LPAR, z/VM guest or KVM virtual machine)
  with Ubuntu Server 20.04 (or 22.04 or 22.10).

* Having the zlib version from -proposed installed or from PPA:
  ppa:fheimes/lp1961427

* The easiest way to test this is based on the autopkgtest of the affected
  package, here 'samtools-legacy' (here a manual autopkgtest execution):
      autopkgtest --no-built-binaries --apt-pocket=proposed --apt-upgrade \
      --shell-fail --setup-commands="apt -y -q install \
      software-properties-common; apt-key adv --keyserver \
      hkp://keyserver.ubuntu.com:80 --recv-keys \
      73E9E91F16C43C45C621AE3EDF0A28DEFAFEB468; add-apt-repository -y \
      ppa:fheimes/lp1983255; apt update; apt -y upgrade; apt install -y \
      libbam-dev=0.1.19+dfsg-5ubuntu1" samtools-legacy_0.1.19+dfsg-5ubuntu1.dsc \
      -- lxd autopkgtest/ubuntu/kinetic/s390x
      (for focal and jammy adjust the versions accordingly)

 * Without PR #1258 in place, the error: 'bgzf.c:<line-number>: bgzf_open:
   Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE'
   will occur.

 * If the above test is successful one can rebuild 'libbio-samtools-perl',
   and run the autopkgtest of 'libbio-samtools-perl' on top.

[Where problems could occur]

 * The bgzf.c implementation as it is in 'samtools-legacy' is very outdated
   and the code was not touched for close to 10 years.

 * Hence PR #1258 could not directly be applied, and a backport was
needed.

 * Issues could be that checks (due to missing asserts) are now
insufficient,

 * or (un-)compress does not work properly anymore, due to the changes in
   bgzf_compress.

 * But the autopkgtest(s) will be helpful to ensure proper
functionality.

[Other Info]

 * The different bgzf.c versions that are bundled are almost all
   slightly different implementations, hence the backport of PR #1258
   needs to be a bit adjusted here and there.
__________

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.

** Affects: libbio-samtools-perl (Ubuntu)
     Importance: Undecided
         Status: Fix Released

** Affects: samtools-legacy (Ubuntu)
     Importance: High
         Status: Fix Released

** Affects: libbio-samtools-perl (Ubuntu Focal)
     Importance: Undecided
         Status: New

** Affects: samtools-legacy (Ubuntu Focal)
     Importance: Undecided
         Status: Fix Committed

** Affects: libbio-samtools-perl (Ubuntu Jammy)
     Importance: Undecided
         Status: New

** Affects: samtools-legacy (Ubuntu Jammy)
     Importance: Undecided
         Status: Fix Committed

** Affects: libbio-samtools-perl (Ubuntu Kinetic)
     Importance: Undecided
         Status: Fix Released

** Affects: samtools-legacy (Ubuntu Kinetic)
     Importance: High
         Status: Fix Released


** Tags: focal kinetic patch s390x update-excuse verification-needed verification-needed-focal verification-needed-jammy
-- 
samtools-legacy misses 'Remove compressBound assertions' (PR #1258) fix
https://bugs.launchpad.net/bugs/1983255
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