hanna 2808fd4bbd Better support for required mutually exclusive options. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@199 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-26 03:22:30 +00:00
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gatk	Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process.	2009-03-25 16:01:58 +00:00
playground	massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified	2009-03-26 02:26:17 +00:00
utils	Better support for required mutually exclusive options.	2009-03-26 03:22:30 +00:00