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gatk-3.8/java/test/org/broadinstitute/sting/utils
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kshakir 787e5d85e9 Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. 
Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-22 22:59:42 +00:00
..
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 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
pileup Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes. 2010-11-19 19:59:05 +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 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