Hi, I got compil and tests issues in the past, but were linked to jdk version available in debian vs their expected version. Those errors looks like context/data issues. I do not know the software itself so will be of little help....
Olivier Le lun. 14 sept. 2020 à 12:59, Andreas Tille <andr...@an3as.eu> a écrit : > Hi Pierre, > > I've added Olivier and Vincent explicitly to this conversation since > they cared in the past for this package. If they can not help here > we probably need to consult upstream. > > Thanks a lot for working on this package > > Andreas. > > On Sun, Sep 13, 2020 at 09:37:36PM +0200, Pierre Gruet wrote: > > > > > > I tried to upgrade htsjdk[1] but unfortunately I got some build time > > > test errors. It would be great if somebody could have a look. > > > > > > > I have looked and tried to build, which succeeded. Then I looked at the > > log and noticed, to sum up, 4 points: > > > > - many tests output to stdout or stderr because they are verbose but > > they succeed : no problem with them; > > > > - the test > > htsjdk.samtools.SAMSequenceDictionaryTest.testMergeDictionaries[7] > > outputs an error, but it's OK because it is expected to raise an > Exception; > > > > - the test > > htsjdk.samtools.CRAMReferencelessTest.testReadCRAMWithEmbeddedReference > > outputs several messages like > > > > Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read name > > 20FUKAAXX100202:2:1:20271:61529, Mate Alignment start (9999748) must be > > <= reference sequence length (200) on reference 20 > > > > I guess this is bad, but don't know what to do with it; > > > > - the tests htsjdk.samtools.SAMFileWriterFactoryTest.testMakeWriter* > > output lines like > > Ignoring SAM validation error: > > ERROR::HEADER_RECORD_MISSING_REQUIRED_TAG:File > > /work/testMakeWriterPathbam, Error parsing SAM header. @RG line missing > > SM tag. Line: @RG ID:1 > > > > I don't know either what to do with it. > > > > Does anyone have some experience with htsjdk to guide me? Inspecting the > > inputs of the tests is hard because many files are binary. > > > > > > > > Kind regards > > > > > > Andreas. > > > > > > > > > > Best regards, > > Pierre > > > > > > -- > http://fam-tille.de >
