Nanolyse autopkgtest broken - could someone provide a proper fastq file?

[Andreas Tille <andreas@an3as.eu>]

Hi,

by chance I realised that the autopkgtest of nanolyse was not
working on the provided dataset.  After fixing this[1] the test
breaks unfortunately[2]:

Traceback (most recent call last):
  File "/usr/bin/NanoLyse", line 33, in <module>
    sys.exit(load_entry_point('NanoLyse==1.2.0', 'console_scripts', 'NanoLyse')())
  File "/usr/lib/python3/dist-packages/nanolyse/NanoLyse.py", line 53, in main
    filter_reads(aligner, sys.stdin)
  File "/usr/lib/python3/dist-packages/nanolyse/NanoLyse.py", line 122, in filter_reads
    for record in SeqIO.parse(reads, "fastq"):
  File "/usr/lib/python3/dist-packages/Bio/SeqIO/Interfaces.py", line 74, in __next__
    return next(self.records)
  File "/usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py", line 1085, in iterate
    for title_line, seq_string, quality_string in FastqGeneralIterator(handle):
  File "/usr/lib/python3/dist-packages/Bio/SeqIO/QualityIO.py", line 950, in FastqGeneralIterator
    raise ValueError("Sequence and quality captions differ.")
ValueError: Sequence and quality captions differ.

The problem occures when reading the perfectly random fastq file which I
have shamelessly stolen from ncbi-blast+ package[3] and which is most
probably a bad choice.  It would be great if some educated person would
provide a better example data set.

Kind regards

        Andreas.


[1] https://salsa.debian.org/med-team/nanolyse/-/commit/847f0439ab66d47a512bab6fbea61268ffec4213
[2] https://salsa.debian.org/med-team/nanolyse/-/jobs/2498940
[3] https://salsa.debian.org/med-team/nanolyse/-/blob/master/debian/tests/data/README

-- 
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