Htsjdk Beta API first usage #1981
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This is an experiment to convert a tool to use the Htsjdk Beta codec registry.
@cmnbroad See the second commit for the changes I made. It's definitely more verbose than before, but a lot of it can be cleaned up by providing utilities with the picard specific defaults.
I also noticed that we didn't include a progress logger option which apparently SamWriters have. Maybe that could be factored out as a decorator. I'm not sure it's a core writer element.
Could you check this out and let me know if there is something I should have done differently?