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
..
alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Removing broken imports (boo)	2011-04-26 18:55:25 +00:00
playground/gatk/walkers	Moving VQSR v2 to core.	2011-05-03 20:20:06 +00:00
utils	Refactored IntervalUtils used to parse and scatter intervals for Queue.	2011-04-26 00:06:00 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00