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?)
I noted some ADAM code examples in the 2nd edition need updating:
adam-submit transform→adam-submit transformAlignmentssc.broadcast(new TwoBitFile(...)→sc.loadReferenceFileAll the region join calls are different, joins are methods on GenomicRDD, e.g.
reads.leftOuterRegionShuffleJoin(features)adam-submit vcf2adam→adam-submit transformVariantsoradam-submit transformGenotypes, for site-only VCF files or those with samples, respectivelyADAM 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?)