aaron 026f68fb41 a couple of quick name changes ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@976 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-10 20:02:52 +00:00
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gatk	removed the requirement that a bam file list be present in the XML version of the command line arguments.	2009-06-10 20:01:13 +00:00
playground	a couple of quick name changes	2009-06-10 20:02:52 +00:00
secondarybase	More accessors. Can compute the sum of the quality scores in the read (useful for sorting) and can return a subset of itself.	2009-06-09 01:02:48 +00:00
utils	Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker	2009-06-10 17:31:00 +00:00