broadgsa/gatk-protected — pull request #6 by johnwallace123 (2014-06-11 19:41:46+00:00)
Title: Allele balance gvcf

Enclosed, please find fixes for 2 issues:
1- Enable "AB" annotation within the GVCF files
2- Fix NullPointerException when using AlleleBalance annotator and GenotypeGVCFs utility

For fix #1, note that I copied a large amount of code from the DepthPerAlleleBySample class from the protected repository, and the AlleleBalanceBySample is in the public.