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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Mark DePristo 4b206a3540 Check that -compress arguments are within range 0-9 
-- Although the original bug report was about SplitSamFile it actually was an engine wide error.  The two places in the that provide compression to the BAM write now check the validity of the compress argument via a static method in ReadUtils
-- delivers #49531009
 		2013-05-31 15:29:02 -04:00
..
datasources Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage 2013-05-29 12:07:12 -04:00
downsampling Require a minimum dcov value of 200 for Locus and ActiveRegion walkers when downsampling to coverage 2013-05-29 12:07:12 -04:00
executive Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Added check in the MalformedReadFilter for reads without stored bases (i.e. that use '*'). 2013-03-14 17:17:26 -04:00
iterators Refactor LIBS into utils.locusiterator before refactoring 2013-01-11 15:17:16 -05:00
refdata Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Trivial update to ceutrio.ped file to make it really the CEU trio sample names 2013-05-14 17:08:13 -04:00
traversals Count Reads should use a Long instead of an Integer for counts to prevent overflows. Added unit test. 2013-05-21 15:23:51 -04:00
walkers Fixes to get accurate read counts for Read traversals 2013-05-21 15:24:07 -04:00
CommandLineGATKUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java Check that -compress arguments are within range 0-9 2013-05-31 15:29:02 -04:00
GenomeAnalysisEngineUnitTest.java Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine. 2013-03-06 12:38:59 -05:00
MaxRuntimeIntegrationTest.java Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java Optimized counting of filtered records by filter. 2013-05-21 21:54:49 -04:00
WalkerManagerUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00