Re: Problem when trying to upgrade htsjdk

[Pierre Gruet <pgtdebian@free.fr>]

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