[Debian-med-packaging] Bug#923428: fastqc: autopkgtest regression

[Sascha Steinbiss]

Hi Andreas,

> On Thu, Feb 28, 2019 at 10:38:52AM +0200, Graham Inggs wrote:
>> Control: found -1 0.11.7+dfsg-1
>> Control: title -1 fastqc: autopkgtest regression
>> Control: user -1 debian-ci at lists.debian.org
>> Control: usertags -1 regression
>> 
>> As per the link in the bug report, the autopkgtest failures coincided with
>> the upload of 0.11.7+dfsg-1.
> 
> Once you commited
> 
> commit ce4840ca8ec57c52fc144eb9b5695e8f02f0f5e5
> Author: Sascha Steinbiss <satta at debian.org>
> Date:   Thu Dec 8 19:04:06 2016 +0000
> 
>    add some BAM/SAM test data
> 
> 
> containing test data and commands to process these data.  This is
> failing since 0.11.7+dfsg-1 as Graham confirmed.  Can you please
> check whether there are some issues with these test data or whether
> the commands have changed?

The BAM/SAM files are just the SAM example from the samtools distribution [1] and its BAM equivalent. They should be fine (in face, I picked them for being provided as examples by the authors of the file format).
I can’t say whether they reflect real-life data or not as I am not too familiar with that. However, I can reproduce the issue here. Looks like a real bug introduced in 0.11.7 (or a dependency?)

Not sure what you mean with ’the commands have changed’…? I get the same issue in the GUI version of FastQC, so I guess it has nothing to do with the test suite call but rather with how these files are handled internally.

Cheers
Sascha

[1] https://raw.githubusercontent.com/samtools/samtools/develop/examples/toy.sam