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gatk-3.8/public/java/src/org/broadinstitute/sting/gatk
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Mark DePristo b8b2b9b2de ManagingReferenceOrderedView optimization: don't allow a fresh RefMetaDataTracker in the frequent case where there's no reference meta data 2013-01-14 16:30:16 -05:00
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arguments Initial working version of new ActiveRegionTraversal based on the LocusIteratorByState read stream 2013-01-11 15:17:17 -05:00
contexts Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
datasources ManagingReferenceOrderedView optimization: don't allow a fresh RefMetaDataTracker in the frequent case where there's no reference meta data 2013-01-14 16:30:16 -05:00
downsampling ReservoirDownsampler optimizations 2013-01-14 16:30:16 -05:00
examples Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
executive LocusIteratorByState operates natively on GATKSAMRecords now 2013-01-11 15:17:18 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
iterators LocusIteratorByState operates natively on GATKSAMRecords now 2013-01-11 15:17:18 -05:00
phonehome Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
refdata ManagingReferenceOrderedView optimization: don't allow a fresh RefMetaDataTracker in the frequent case where there's no reference meta data 2013-01-14 16:30:16 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
resourcemanagement Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
samples Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
traversals LocusIteratorByState operates natively on GATKSAMRecords now 2013-01-11 15:17:18 -05:00
walkers Updating licenses to Eric's last commit 2013-01-11 14:33:00 -05:00
CommandLineExecutable.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
CommandLineGATK.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeAnalysisEngine.java Initial working version of new ActiveRegionTraversal based on the LocusIteratorByState read stream 2013-01-11 15:17:17 -05:00
ReadMetrics.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ReadProperties.java LIBS can now (optionally) track the unique reads it uses from the underlying read iterator 2013-01-11 15:17:16 -05:00
WalkerManager.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00