Identify initial code contributions

[heuermh]

No description provided.

[heuermh]

https://github.com/tomwhite/squark

[heuermh]

I'm willing to help migrate the following
https://github.com/bigdatagenomics/convert

and any of the modules in
https://github.com/heuermh/dishevelled-bio

Longer term, as scope increases, bits of the following might be fair game
https://github.com/bigdatagenomics/adam
https://github.com/bigdatagenomics/bdg-formats
https://github.com/bigdatagenomics/utils

Relicensing contributions from dishevelled-bio (LGPL 3.0) would be relatively easy, as it is single-author. adam, bdg-formatics, convert, and utils are all Apache 2 and multi-author, so the process would be more difficult (though easier if disq were also licensed Apache 2).

[tomwhite]

I would like to transfer https://github.com/tomwhite/disq over to here. One way would be to move the repository, which keeps the history. Alternatively I can prepare a PR.

[heuermh]

I would prefer a pull request so that we can code review on the way in.

[magicDGS]

In that case, would it be small PRs with concrete functionality for easier review or all the code at once?

[tomwhite]

I've opened #14. It's not obvious how to break it into pieces, so I would suggest looking at it as it stands.

[magicDGS]

Maybe README/pom/NOTICE/gitignore and non-code files could be separated; the samtools package can be in one PR (as it is independent) and then each package in a different one - #14 looks like a hard PR to review...

[tomwhite]

@magicDGS The samtools package does not really need reviewing (or at least not here) as it is a copy of the files in samtools/htsjdk#1138 - it's a short-term expedient until that PR gets reviewed and released.

I'll think a bit more about splitting up the packages, but I fear they are quite interconnected.

[heuermh]

Closed by #14.