bigdatagenomics/adam — pull request #13 by fnothaft (2013-12-04 10:54:55+00:00)
Title: Cleaning up VCF<->ADAM pipeline

Added internal ADAM variant context, that handles the unification of the core variant standard with additional variant/genotype annotations. This variant context also handles the unification of unnested variant and genotype info. In addition to this, the VCF<->ADAM conversion pipeline was upgraded to use Hadoop-BAM/GATK's VariantContext code, to eliminate text parsing. Also, an adam2vcf command was added.

This code is not yet ready to get merged in (it needs more testing), but the changes are pretty big both internally and to the schema for the variant/genotype formats, so I want to get the code out there. I will send a post about the format out to the developer list tomorrow to start discussion. Once this code gets further test coverage, I will update and we can merge, providing the community agrees.