ebanks 28142408ff Refactoring so that all counting in UGv2 is done on the filtered context. In particular, tests for empty pileups and too many spanning deletions now use the correct counts. Also, -all_bases mode now trumps all; this one is for you, chartl. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4671 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-15 05:01:12 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Refactoring so that all counting in UGv2 is done on the filtered context. In particular, tests for empty pileups and too many spanning deletions now use the correct counts. Also, -all_bases mode now trumps all; this one is for you, chartl.	2010-11-15 05:01:12 +00:00
test	Updated ordering of integration tests. GVC > VR > AVC	2010-11-14 06:33:28 +00:00