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gatk-3.8/public/java/src/org/broadinstitute/sting/gatk
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Eric Banks ebd5404124 Fixed the add functionality of GenomeLocSortedSet. 
* Fixed GenomeLocSortedSet.add() to ensure that overlapping intervals are detected and an exception is thrown.
 * Fixed GenomeLocSortedSet.addRegion() by merging it with the add() method; it now produces sorted inputs in all cases.
 * Cleaned up duplicated code throughout the engine to create a list of intervals over all contigs.
 * Added more unit tests for add functionality of GLSS.
 * Resolves GSA-775.
 		2013-02-28 23:31:00 -05:00
..
arguments Added check that BaseRecalibrator is not being run on a reduced bam. 2013-02-06 10:14:27 -05:00
contexts Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
datasources Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
downsampling -Added Per-Sample Contamination Removal to UnifiedGenotyper: Added an @Advanced option to the StandardCallerArgumentCollection, a file which should 2013-02-04 18:24:36 -05:00
examples Archiving CoverageBySample 2013-02-26 13:49:00 -05:00
executive Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -05:00
filters Added better error message for BAMs with bad read groups. 2013-02-27 16:02:56 -05:00
io Making SplitReads output FastQ's instead of BAM 2013-01-27 02:36:31 -05:00
iterators Collapse the downsampling fork in the GATK engine 2013-01-28 01:50:30 -05:00
phonehome Extend AWS timeout for uploads of the GATK run reports to 30 seconds 2013-02-08 17:37:36 -05:00
refdata Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -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 ActivityProfile and ActiveRegions respects engine interval boundaries 2013-02-18 10:40:25 -05:00
walkers Cleanup and unit tests for QualityUtils 2013-02-16 07:31:37 -08:00
CommandLineExecutable.java Final cleanup and unit testing for GATKRunReport 2013-02-02 15:06:56 -05:00
CommandLineGATK.java Refactored GATKDocs categories some more ( GSATDG-62 ) 2013-02-13 16:49:18 -05:00
GenomeAnalysisEngine.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -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 Collapse the downsampling fork in the GATK engine 2013-01-28 01:50:30 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00