[Debian-med-packaging] Bug#923428: fastqc fails it's autopkg tests

[Matthias Klose]

Package: src:fastqc
Version: 0.11.8+dfsg-1
Severity: important
Tags: sid buster

fastqc fails it's autopkg tests according to
https://ci.debian.net/data/packages/unstable/amd64/f/fastqc/latest-autopkgtest/log.gz

ailed to process toy.sam
htsjdk.samtools.util.RuntimeIOException: java.io.IOException: Stream closed
	at
htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:448)
	at uk.ac.babraham.FastQC.Sequence.BAMFile.<init>(BAMFile.java:64)
	at
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:100)
	at
uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:152)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Caused by: java.io.IOException: Stream closed
	at java.base/java.io.BufferedInputStream.getInIfOpen(BufferedInputStream.java:165)
	at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252)
	at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292)
	at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
	at
htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:583)
	at
htsjdk.samtools.util.BlockCompressedInputStream.isValidFile(BlockCompressedInputStream.java:443)
	at htsjdk.samtools.SamStreams.isBAMFile(SamStreams.java:51)
	at
htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:374)
	... 6 more
autopkgtest [08:36:51]: test run-unit-test: -----------------------]
autopkgtest [08:36:51]: test run-unit-test:  - - - - - - - - - - results - - - -
- - - - - -
run-unit-test        FAIL non-zero exit status 1
autopkgtest [08:36:51]: @@@@@@@@@@@@@@@@@@@@ summary