[ch-10] Updates to ADAM code examples

[heuermh]

I noted some ADAM code examples in the 2nd edition need updating:

adam-submit transform → adam-submit transformAlignments

sc.broadcast(new TwoBitFile(...) → sc.loadReferenceFile

All the region join calls are different, joins are methods on GenomicRDD, e.g. reads.leftOuterRegionShuffleJoin(features)

adam-submit vcf2adam → adam-submit transformVariants or adam-submit transformGenotypes, for site-only VCF files or those with samples, respectively

ADAM docs are available at https://adam.readthedocs.io/en/latest/

ADAM is installable via Homebrew or Linuxbrew, Conda via BioConda, pip via PyPI, Docker via BioContainers, and hopefully soon in CRAN (once SparkR is back in CRAN, with the Spark 2.3 release perhaps?)

[srowen]

Do those changes work with the version used in the book? Does the book listing work with the version it used? Since we can't update paper copies and needs to stay consistent, not sure if this should be done

[heuermh]

Do those changes work with the version used in the book? Does the book listing work with the version it used?

For better or worse, the book builds from source off git HEAD. ADAM hasn't hit version 1.0 yet, so we haven't implemented semantic versioning. Breaking API changes between minor versions (e.g. 0.22.0 to 0.23.0, the last release) are common.

If you think it worth doing, I could create a pull request, or feel free to ping me later if a 3rd edition might happen.

[srowen]

I think updates to the source code here are fine as long as they continue to work with the text that was printed in the book. I don't think there will be any more printings. It's not impossible to let the source code vary if the updates were critical going forward, but ideal to avoid that.

[laserson]

If we can extract all the code from the book into a single document or "script", it may be worth keeping it updated with the latest ADAM version.

[srowen]

If updates would break text compatibility but are of significant use, just push them to a branch here.