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gatk-3.8/java/test/org/broadinstitute/sting/utils
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kshakir 673fa841a4 Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 
Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-12 20:14:28 +00:00
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bed Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
collections Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
genotype Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
interval Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 2010-11-12 20:14:28 +00:00
pileup Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
report Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
sam Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
threading Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
BaseUtilsUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
GenomeLocParserUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
GenomeLocSortedSetUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
GenomeLocUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
MathUtilsUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
PathUtilsUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
ReservoirDownsamplerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
UtilsUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00