Re: Problem when trying to upgrade htsjdk

[Andreas Tille <andreas@an3as.eu>]

On Tue, Sep 15, 2020 at 10:09:10AM +0200, olivier sallou wrote:
> On Sun, 2020-09-13 at 21:37 +0200, Pierre Gruet wrote:
> > 
> > - 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....

But the exit code is "fail" anyway.  What exactly is your suggestion to
do? 

Kind regards

      Andreas.

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