massie/adam — pull request #12 by chartl (2013-10-31 00:20:52+00:00)
Title: ADAM variant and genotype formats; and a VCF->ADAM converter

Introducing a Variant format and a converter VCF --> ADAM. Takes in a VC...F as a text file. It can be gzipped (I think Spark is smart enough for that).

The parsing is done manually. I attempted to adapt org.broad.tribble and org.broadinstitute.variant to help with a robust conversion; but the classes
rely too heavily on a flat text file (can't set the header manually), and are not serializable (so can't be broadcast). The problem runs so deep that
even with access to the source, I found it unworkable.

Currently the schema are nested:

ADAMVariant
... site-specific information ...
array
|
| .. genotype-specific information ..

however the info and format fields are rendered as strings rather than maps.