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

[Frank Heimes]

** Patch removed: "debdiff vcftools focal from 0.1.16-1build1 to 0.1.16-1ubuntu0.1"
   https://bugs.launchpad.net/ubuntu/+source/vcftools/+bug/1983867/+attachment/5607371/+files/debdiff_vcftools_focal_from_0.1.16-1build1_to_0.1.16-1ubuntu0.1.diff

** Changed in: vcftools (Ubuntu Focal)
       Status: In Progress => Invalid

** Description changed:

- 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 focal-proposed
-    migration now pointed to vcftools on top.
- 
-  * vcftools contains (yet) another bgzf.c implementation.
- 
-  * Hence PR #1258 is needed to fix bgzf.c as part of vcftools.
- 
-  * 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 'vcftools' (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/lp1983867; apt update; apt -y upgrade; apt install -y \
-       vcftools=0.1.16-1ubuntu0.1" vcftools_0.1.16-1ubuntu0.1.dsc \
-       -- lxd autopkgtest/ubuntu/focal/s390x
- 
-  * Without PR #1258 in place, the error: 'bgzf.c:<line-number>: bgzf_open:
-    Assertion `compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE'
-    will occur.
- 
- [Where problems could occur]
- 
-  * The bgzf.c implementation as it is in 'vcftools' is very outdated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.
+ invalid, please ignore
  __________
  
  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.

** Tags removed: focal s390x

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https://bugs.launchpad.net/bugs/1983867

Title:
  vcftools misses 'Remove compressBound assertions' (PR #1258) fix

Status in vcftools package in Ubuntu:
  Invalid
Status in vcftools source package in Focal:
  Invalid

Bug description:
  invalid, please ignore
  __________

  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.

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