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
..
BoundedReadIteratorUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
LocusIteratorByStateUnitTest.java	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
StingSAMIteratorAdapterUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
VerifyingSamIteratorUnitTest.java	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00