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gatk-3.8/java/test/org/broadinstitute/sting/utils
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depristo 85553cf5cb V2 cleaner, easily testing, shared memory and distributed GATK job management. Serious unit testing. Very much cleaner processing. Some code cleanup remains in removing now unused classes but the system is ready for general testing. Confirmed that one can run the UG 100 ways parallel without error, but edge cases may remain. 
See documentation at:

http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK#Distributed_Parallelism_.28Experimental.29

for examples on how to run this, or the testing Scala script

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5032 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-20 12:58:13 +00:00
..
baq Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
bed Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
collections Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
fasta Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
genotype Moving GLF code to archive 2011-01-15 22:42:42 +00:00
interval Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
pileup Stop RBP.getPileupBySample() from throwing a NullPointerException if the 2010-11-23 05:17:06 +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 V2 cleaner, easily testing, shared memory and distributed GATK job management. Serious unit testing. Very much cleaner processing. Some code cleanup remains in removing now unused classes but the system is ready for general testing. Confirmed that one can run the UG 100 ways parallel without error, but edge cases may remain. 2011-01-20 12:58:13 +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 vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler. 2011-01-12 17:32:27 +00:00
GenomeLocUnitTest.java Getting back to '-L unmapped': 2010-12-14 18:24:18 +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 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