[Debian-med-packaging] Bug#843621: mummer: serious bug?

[Andreas Tille]

Package: mummer
Version: 3.23~dfsg-3
Severity: important

Dear Ivan,

thanks for the bug report you've sent via private e-mail.  While we try
to care for this as well it is strongly recommended to use reportbug to
report bugs against packages on Debian systems since we get all needed
information.  So please next time use

     reportbug mummer

to inform us about problems (please note that you need to have a proper
SMTP configuration to enable reportbug sending an e-mail.  If this is
not the case you can copy the text created by reportbug to your
favourite mail program and send it to control at bugs.debian.org).  I'm
just trying to simulate this here now to save you the work - please
subscribe to this bug to get new information and send more information
to the bug e-mail address to keep others informed as well.

Thanks again

       Andreas.

Here comes the original mail from Ivan.


Dear Andreas,

I got your email from here:
metadata.ftp-master.debian.org/changelogs/main/m/mummer/mummer_3.23+dfsg-1_changelog
.

We noticed a somewhat serious bug in the latest MUMmer version on the Apt
repository (version 3.23~dfsg-3) and would like to let you know in case you
haven't noticed it before.

When aligning and comparing two sequences using dnadiff, where one is an
identical (or very similar) subset of another, we get strange results
(however not on all genomes).
For example, taking only the first chromosome of the S. Cerevisiae S288c
reference and comparing it to the entire reference:
dnadiff saccharomyces_cerevisiae-S288C.fa chr1.fa

Results with (in version version 3.23~dfsg-3):
...
[Bases]
TotalBases                  12071326               230218
AlignedBases           572185(4.74%)        51864(22.53%)
UnalignedBases      11499141(95.26%)       178354(77.47%)
...
AvgIdentity                    97.65                97.65
...

Whereas in version 3.23~dfsg-2 we get something that's more expected:
...
[Bases]
TotalBases                  12071326               230218
AlignedBases           572185(4.74%)      230218(100.00%)
UnalignedBases      11499141(95.26%)             0(0.00%)
...
AvgIdentity                   100.00               100.00
...

We found this to happen in de novo assemblies of the W303 PacBio dataset,
as well as on a C. Elegans dataset, but not on E. Coli.

I'm attaching the sample reference I used in the example above.

P.S. The problem does not happen with the official Mummer 3.23 SourceForge
code.


Hope this helps,
Best regards,
Ivan.


-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages mummer depends on:
ii  gawk        1:4.1.1+dfsg-1
ii  libc6       2.19-18+deb8u6
ii  libgcc1     1:4.9.2-10
ii  libstdc++6  4.9.2-10
ii  perl        5.20.2-3+deb8u6

mummer recommends no packages.

mummer suggests no packages.
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