Re: Problem when trying to upgrade htsjdk
On Tue, 2020-09-15 at 10:44 +0200, Andreas Tille wrote:
> 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.testReadCRAMWithEmbeddedRef
> > > eren
> > > 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?
I just made a try to build based on latest code in git, and it worked
for me...
Olivier
>
> Kind regards
>
> Andreas.
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
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