On Sun, 2020-09-13 at 21:37 +0200, Pierre Gruet wrote: > Hi Andreas, hi everyone, > > Le 11/09/2020 à 09:08, Andreas Tille a écrit : > > Hi, > > > > 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.testReadCRAMWithEmbeddedReferen > ce > outputs several messages like > > Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Read
this test and the other one shows "Ignoring SAM validation error" so I guess it is ok.... Olivier > 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 > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
