hanna cb144734c0 Getting rid of GenotypeWriter interface. Of note: ... - GATKVCFWriter deleted, to be replaced if absolutely necessary when VCF writing goes into Tribble. - VCFWriter is now an interface, for easier redirection. - VCFWriterImpl fleshes out the VCFWriter interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4026 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-13 16:33:22 +00:00
..
alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
oneoffprojects/walkers	fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!	2010-06-29 21:38:55 +00:00
playground	Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).	2010-08-11 21:58:26 +00:00
utils	Getting rid of GenotypeWriter interface. Of note:	2010-08-13 16:33:22 +00:00
BaseTest.java	Moving pointer to b36 reference from /broad/1KG to /humgen/1kg	2010-08-13 00:54:34 +00:00
WalkerTest.java	fix for feature source in Tribble; we need to check that the record coming back isn't null. Also in the GATK added code to set the default logging level in integration tests to WARN, with the default level change they were spewing a bunch of text.	2010-08-10 02:57:23 +00:00