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.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