Re: Problem when trying to upgrade htsjdk
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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