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gatk-3.8/java/test/org/broadinstitute/sting
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hanna acfe83920b '-L unmapped': adding integration tests for explicitly including (-L unmapped) 
unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting
the suite of unit tests already put in place.

'-L unmapped' seems safe to use; go for it, but please validate results against
samtools flagstat when the process finishes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-15 23:11:46 +00:00
..
alignment Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
commandline Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
datasources/pipeline Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
gatk 3 big changes that all kill the integration tests: 1. Don't cap the PLs by 255 anymore. 2. Move over to the 3state model as the only available base model for UG (no more base transition tables). 3. New QD implementation when GLs/PLs are available. 2010-12-15 16:24:28 +00:00
jna Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM. 2010-12-14 19:57:20 +00:00
oneoffprojects/walkers Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
playground/gatk/walkers consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation). 2010-11-30 00:01:56 +00:00
utils '-L unmapped': adding integration tests for explicitly including (-L unmapped) 2010-12-15 23:11:46 +00:00
BaseTest.java Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. 2010-11-22 22:59:42 +00:00
StingTextReporter.java Cleanup testng listener configuration. 2010-11-15 23:43:14 +00:00
WalkerTest.java Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. 2010-11-22 22:59:42 +00:00