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
>
>
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