[Debian-med-packaging] Bug#844760: fastqc: Please temporarily drop support for fast5 files

[Gilles Filippini]

Source: fastqc
Version: 0.11.5+dfsg-4
Severity: important
Tags: patch

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Hi,

HDF5 1.10 is about to transition into unstable [1], and unfortunately a
FastQC build-dependency, libsis-jhdf5-java, doesn't support this new
release yet [2], and we have no information about its upstream schedule
wrt HDF5 1.10.

I've had a look at the FastQC code, and AFAIUI, libsis-jhdf5-java is
required only to support fast5 files from nanopore sequences.

Since these files can easily be converted to FastQ format using
poretools [3], I propose to temporarily drop fast5 support from FastQC
to avoid a removal from testing.

Please find attached a patch proposal to this end.

Thanks in advance,

_g.

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842177#40
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842815
{3] https://bioinfoexpert.com/2016/06/15/minion-fast5-to-fastq/

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