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gatk-3.8/public/java/src/org/broadinstitute/sting/gatk
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Mark DePristo 0fb238b61e TraverseActiveRegions Optimizations and Bugfixes: make sure to record position of current locus to discharge active regions when there's no data 
-- Now records the position of the current locus, as well as that of the last read.  Necessary when passing through regions with no reads.  The previous version would keep accumulating empty active regions, and never discharge them until end of traversal (if there was no reads in the future) or until a read was finally found
-- Protected a call to logger.debug with if ( logger.isDebugEnabled()) to avoid a lot of overhead in writing unseen debugger logging information
 		2013-01-27 14:10:06 -05:00
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arguments Re-committing the following changes from Dec 18: 2013-01-16 12:43:15 -05:00
contexts Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
datasources Optimization: LocusReferenceView now passes along the contig index to createGenomeLoc, speeding up their creation 2013-01-27 14:10:06 -05:00
downsampling Updating licenses of latest moved files 2013-01-26 13:46:52 -05:00
examples Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
executive Retire original TraverseActiveRegion, leaving only the new optimized version 2013-01-15 10:24:45 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
io Making SplitReads output FastQ's instead of BAM 2013-01-27 02:36:31 -05:00
iterators Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
phonehome Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
refdata Bug fix for VariantsToVCF: old dbSNP files can have '-' as reference base and those records always need to be padded. 2013-01-16 16:15:58 -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 TraverseActiveRegions Optimizations and Bugfixes: make sure to record position of current locus to discharge active regions when there's no data 2013-01-27 14:10:06 -05:00
walkers Updating licenses of latest moved files 2013-01-26 13:46:52 -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 Re-committing the following changes from Dec 18: 2013-01-16 12:43:15 -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