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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Christopher Hartl 4a08e8ca6e Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) 
This is somewhat of an arbitrary decision, and is negotiable. I could see treating

GT:PL   ./.:.

differently from

GT:PL   .:0,3,6

but am not sure the worth of doing so.
 		2012-01-23 08:25:34 -05:00
..
datasources Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup. 2011-12-06 10:10:38 -05:00
executive Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
filters Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
iterators Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup. 2011-12-06 10:10:38 -05:00
refdata Merge with master 2011-11-19 09:56:06 -05:00
report Right aligning GATKReport numeric columns and updated MD5s in tests. 2011-12-05 23:22:15 -05:00
samples Added UnitTests for getFamilies() and getChildrenWithParents() 2011-12-09 15:57:07 +01:00
traversals First pass of the asynchronous block loader. 2011-11-18 15:02:59 -05:00
walkers Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) 2012-01-23 08:25:34 -05:00
EngineFeaturesIntegrationTest.java Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two. 2011-08-09 12:04:55 -04:00
GenomeAnalysisEngineUnitTest.java Allow processing of empty intervals, but warn user when this case is encountered. 2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant. 2011-08-10 12:20:18 -04:00