Remove JAXB dependency for better java 9+ compatibility.

[jrobinso]

As you know JAXB is not included with Java 9 and above. It can be used with command line switches, for now, but introduces another dependency. I have removed all uses of JAXB from IGV, and am looking at the htsjdk now. It looks like the only place it is used is the class SAMSequenceDictionary, however I'm not sure what its purpose is there. Are objects of that class serialized from somewhere? It would be strange to serialize this class only but it is the only class I can find with JAXB annotations.

[jrobinso]

BTW we are using the htsjdk with Java 11 with no issues, but would like to drop the JAXB switches.

[lindenb]

I wrote the jaxb bindings because I had the idea to use htshdk for webservices. But in the end, I did not use it . Unless someone else use it, I don't see any reason to keep the jaxb stuff in htsjdk.

I only see my code in github (or some forks..) : https://github.com/search?q=Unmarshaller+htsjdk&type=Code

[lbergelson]

Interesting, I'm surprised it works in 11, that's good to hear though.

It looks like we have xml binding annotations in:
SAMSequenceRecord
AbstractSAMHeaderRecord
SAMSequenceDictionary

And we have a single use of DatatypeConverter.printHexArrays() in EncodingParams

We could definitely remove the use of DatatypeConverter without any problems.

@lindenb I believe you added the xml binding annotations. Would you be opposed to removing them if it meant we could make htsjdk be more compatible with java 9+?

[lbergelson]

Oh, sorry, you wrote back before I finished my comment and I didn't see it. Please ignore...

[lindenb]

@lindenb I believe you added the xml binding annotations. Would you be opposed to removing them if it meant we could make htsjdk be more compatible with java 9+?

no, one can remove them

[lbergelson]

@jrobinso Sounds like we should remove it.

[jrobinso]

@lindenb Pierre is that you? You're everywhere.

I can remove these and send a PR if you want, I just removed several hundred of them from IGV.

[lbergelson]

@jrobinso You should be able to replace the Dataconverter.printHexBinary with StringUtil.bytesToHexString()