[Debian-med-packaging] Bug#897109: fastqc: htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed

[Andreas Tille]

Hi Dylan,

On Tue, May 21, 2019 at 02:32:48PM +0200, Dylan Aïssi wrote:
> Control: severity -1 serious
> 
> Hi,
> I have tested the testsuite with the upstream binary (FastQC 0.11.8)
> and there is no error, so the testsuite is fine. This bug was probably
> hidden before we added the test of bam and sam files. Currently,
> fastqc from our package is unable to process bam and sam files which
> is very annoying for Buster. I guess we have to modify
> htsjdk-api.patch, but I admit I have no clue how to fix it. The
> easiest way should be to add SAMFileReader like suggested in [1]. Any
> suggestion?

Thanks for pointing out this issue.
No better suggestion than the naive one that I gave in issue #767.
May be FastQC contacting upstream is a good idea.

Kind regards

    Andreas.

> [1] https://github.com/samtools/htsjdk/issues/767#issuecomment-264843094

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