gatk-3.8/java
ebanks 6934f83cc7 Two changes to CombineVariants.
1. Fix: VCs were padded before the merge, but they were never unpadded afterwards.  This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-25 04:52:12 +00:00
..
config Provide a default logger, some config settings, and some doc updates. 2009-04-29 02:06:05 +00:00
src Two changes to CombineVariants. 2010-11-25 04:52:12 +00:00
test Two changes to CombineVariants. 2010-11-25 04:52:12 +00:00