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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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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
..
arguments A significant refactoring of the ROD system, done largely to simplify the process of 2010-12-31 04:52:22 +00:00
contexts/variantcontext Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test. 2010-12-08 17:22:29 +00:00
datasources A fix for Marian Thieme's NPE in the new sharding system. 2011-04-21 19:47:14 +00:00
executive Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
filters Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
iterators Some refactoring that Mauricio and I worked through together. Changed filters 2011-05-04 19:29:08 +00:00
refdata Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
report Added a utility method to retrieve the contig lengths for WG chunking. 2011-04-20 19:22:21 +00:00
traversals Fix requested by Lee Lichtenstein: first check to see whether it's time for 2011-04-20 03:22:48 +00:00
walkers Updating VariantGaussianMixtureModelUnitTest to use truth sensitivity cutting 2011-05-04 13:56:01 +00:00
CommandLineExecutableUnitTest.java Fix for bug GSA-441: BAM file list with blank lines gives a confusing error 2011-04-01 15:04:35 +00:00
GenomeAnalysisEngineUnitTest.java Fix for bug GSA-449: Intervals that are not in GATK format are not validated 2011-04-27 18:12:10 +00:00
WalkerManagerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00