HadoopGenomics/Hadoop-BAM — pull request #3 by jmthibault79 (2014-04-29 15:11:23+00:00)
Title: Untested: attempt to encode previously-decoded genotypes

The scope of my project is changing and I no longer have an immediate need for writing decoded VariantContexts as VariantContextWritables. Before I move on, I wanted to give you an update with what I've done so far.

VCFEncoder.addGenotypeData() and VCFEncoder.buildAlleleStrings() are now public in Picard's Variant JAR, for SVN revision 1943 (1.112.1943). This branch updates Picard to 1.112.1943 using a local repository. As we previously discussed, that's probably not the best way to go about upgrading. In addition, Picard is in the middle of a major reorganization of their code base. You may want to wait until they have completed their package renaming and transition to GitHub and Maven.

This branch is attempt to solve issue #1 by providing a means of supplying VCF headers to VariantContextWritables for use in encoding. It is untested.