aaron 96972c3a5c a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly. ... Also moved a buch of Lists over to Sets for consistancy. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-16 04:57:50 +00:00
..
gatk	Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially.	2009-10-16 04:11:34 +00:00
playground/gatk/walkers	changes to VCF output, and updated MD5's in the integration tests	2009-10-14 18:42:48 +00:00
utils	a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly.	2009-10-16 04:57:50 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	delete the integration test temp files when the test is over	2009-09-25 16:34:08 +00:00