aaron f4cfb0f990 The first step in integrating Jim's tree based index scheme: ... - changed to a better method for getting headers from Codecs - some removal of old commented out code in the GATKAgrumentCollection - changes for the rename of FeatureReader to FeatureSource - removed the old Beagle ROD - cleaned up some of the code in SampleUtils git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3826 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-19 04:49:27 +00:00
..
CallableLociWalker.java	FindBugs fixes throughout the code base	2010-07-18 16:29:59 +00:00
CoarseCoverageWalker.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
CompareCallableLociWalker.java	a couple of small documentation fixes	2010-05-12 17:40:27 +00:00
CoverageUtils.java	Changes to Depth of Coverage:	2010-05-26 03:39:22 +00:00
DepthOfCoverageStats.java	Changes to Depth of Coverage:	2010-05-26 03:39:22 +00:00
DepthOfCoverageWalker.java	The first step in integrating Jim's tree based index scheme:	2010-07-19 04:49:27 +00:00