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
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providers	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
reads	Fixed the add functionality of GenomeLocSortedSet.	2013-02-28 23:31:00 -05:00
reference	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
rmd	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