[Debian-med-packaging] Bug#1021675: ariba: autopkgtest regression and ftbfs with samtools 1.16

[Étienne Mollier]

Source: ariba
Version: 2.14.6+ds-3
Severity: serious
Tags: ftbfs upstream help
Justification: fails to build from source (but built successfully in the past)

Greetings,

Following the upgrade of htslib, samtools and bcftools from
versions 1.13 to 1.16, ariba hits autopkgtest regressions which
are preventing migration of python-pysam to testing.  The test
failures are also present during the build time test suite,
causing the package to fail to build from source.

I attempted to begin wrapping up a patch fixing/working around
the problem which looks to be caused by the migration of mpileup
functionalities from samtools to bcftools, but the test suite
then chokes on non-matching command output, for which I don't
know whether the new results are sound and simply need
adjustments, or if errors could have been left over.  Temporary
patch is below for reference, but is not sufficient on his own
to fix the failure:

-------8<--------------8<--------------8<--------------8<-------
--- a/ariba/samtools_variants.py
+++ b/ariba/samtools_variants.py
@@ -1,6 +1,7 @@
 import os
 import sys
 import pysam
+import pysam.bcftools
 import pyfastaq
 import vcfcall_ariba
 
@@ -36,13 +37,11 @@
 
         tmp_vcf = self.vcf_file + '.tmp'
         with open(tmp_vcf, 'w') as f:
-            print(pysam.mpileup(
+            print(pysam.bcftools.mpileup(
                 '-t', 'INFO/AD,INFO/ADF,INFO/ADR',
                 '-L', '99999999',
                 '-A',
                 '-f', self.ref_fa,
-                '-u',
-                '-v',
                 self.bam,
             ), end='', file=f)
 
-------8<--------------8<--------------8<--------------8<-------

I already provided upstream with my findings on their issue
tracker[1] in a related entry, but I don't know for sure how
much active they are these days.  This note in debbugs is mostly
to document the issue for Med team members before they spend too
much time debugging this issue in parallel (and also seeking
help if possible).

[1]: https://github.com/sanger-pathogens/ariba/issues/327

Have a nice day,  :)
Étienne.

-- System Information:
Debian Release: bookworm/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.19.0-2-amd64 (SMP w/12 CPU threads; PREEMPT)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/5, please excuse my verbosity.
On air: Gazpacho - Valerie's Friend
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