fromer aa8cf25d08 Implemented fully symmetric sliding window read-backed phaser ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4104 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-24 21:12:32 +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	Implemented fully symmetric sliding window read-backed phaser	2010-08-24 21:12:32 +00:00
test	Some clean up for the variant recalibrator. Now uses @Input and @Output so that it can join the Queue party. Users now specify a -o, -clusterFile, -tranchesFile, and -reportDatFile. Example on the wiki. ApplyVariantCuts now has an integration test. Base quality recalibrator now requires a dbsnp rod or vcf file. Now that the base quality recalibrator is using @Output the PrintStream shouldn't be closed in OnTraversalDone.	2010-08-24 20:14:58 +00:00