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

[Dylan Aïssi]

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?

Best,
Dylan

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