[Debian-med-packaging] Bug#1021557: jellyfish: Performance regression in 2.3.0 (orders of magnitude for some inputs)

[J Nisbet]

Package: jellyfish
Version: 2.3.0-10
Severity: normal
Tags: upstream
X-Debbugs-Cc: ksnp-dev at kissake.net

Dear Maintainer,

   * What led up to the situation?

I observed this issue through normal use of jellyfish.  For some values of -m
and -t, and for a variety of input genomes, performance of 2.3.0 is
significantly (orders of magnitude) worse than other available revisions.
Specifically, jellyfish versions 2.2.10 and 1.1.2 were tested for comparison.

   * What exactly did you do (or not do) that was effective (or
     ineffective)?

For -m values of 13 and 15, -t should be set to 1 for best performance.  This
performance is still noticeably worse than performance at the same settings for
previous versions, but not by an order of magnitude.

This issue has also been reported at the upstream GitHub page here:
https://github.com/gmarcais/Jellyfish/issues/192

You can probably find more details in that report.


-- System Information:
Debian Release: 11.5
  APT prefers stable-security
  APT policy: (500, 'stable-security'), (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.10.0-18-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_CRAP, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not
set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages jellyfish depends on:
ii  libc6               2.31-13+deb11u4
ii  libgcc-s1           10.2.1-6
ii  libhts3             1.11-4
ii  libjellyfish-2.0-2  2.3.0-10
ii  libstdc++6          10.2.1-6

jellyfish recommends no packages.

jellyfish suggests no packages.
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