gatk-3.8

Author	SHA1	Message	Date
depristo	c47a5ff5ab	Official parallel CountCovariates, passes all integration tests. Now poster-child example of parallelism in GATK (Matt H). Apparent general performance improvements throughout too. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3833 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-19 22:13:18 +00:00
depristo	b29eda83bb	Parallelized CountCovarites! percent_ref_called_var now a standard genotype concordance module (for validation!). Really much smarter merging of headers for combineVariants. VCF codecs now actually look at the file version and blow up if they are the wrong versions. setHeaderVersion() in VCFHeaderLine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3802 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-16 14:10:18 +00:00
hanna	c1e53d407d	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had unicode quote characters embedded in it. These characters were invisible inside IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason have a different default charset. Fixed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-20 15:26:32 +00:00
hanna	1bc26f69e9	An attempt to cleanup the Utils directory. Email to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-19 23:00:08 +00:00