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

[Andreas Tille]

Hi Ivan,

On Tue, Nov 08, 2016 at 01:20:23PM +0100, Andreas Tille wrote:
> 
> 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
> ...

That's a very helpful observation.  My first suspicion is that the
patches I've taken over from mugsy that was featuring a code copy of
mummer are responsible for the diff.  I'd like to wait for some comments
from the Debian Med team.  In any case I can confirm that also the
version currently in Debian testing (3.23+dfsg-1) which is the release
candidate for the next stable distribution, is reproducing the issue:

$ dnadiff saccharomyces_cerevisiae-S288C.fa chr1.fa
$ grep -A3 '^\[Bases\]' out.report 
[Bases]
TotalBases                  12071326               230218
AlignedBases           572185(4.74%)        51931(22.56%)
UnalignedBases      11499141(95.26%)       178287(77.44%)

 
> 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.

That's very helpful to reproduce the issue.
 
> P.S. The problem does not happen with the official Mummer 3.23 SourceForge
> code.

Also a helpful hint which is targeting in the same direction as my
assumption that the code diff between 3.23~dfsg-2 and 3.23~dfsg-3 might
be responsible and should most probably be reverted.

Kind regards

      Andreas.

-- 
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