hanna 5c6965575e Some refactoring that Mauricio and I worked through together. Changed filters ... to extend from org.broadinstitute.sting.gatk.filters.ReadFilter rather than directly from net.sf.picard.filter.SamRecordFilter, which allows us to add an initialize(GATKEngine) method so that filters can do any initialization they'd like based on CL arguments, SAM headers, etc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5760 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-04 19:29:08 +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	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
test	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00