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Author SHA1 Message Date
Mark DePristo 7d95176539 Bugfix to compareTo and equals in GenomeLoc 
-- Yes, GenomeLoc.compareTo was broken.  The compareTo function only considered the contig and start position, but not the stop, when comparing genome locs.
-- Updated GenomeLoc.compareTo function to account for stop.  Updated GATK code where necessary to fix resulting problems that depended on this.
-- Added unit tests to ensure that hashcode, equals, and compareTo are all correct for GenomeLocs
 2012-08-30 19:41:49 -04:00
Mark DePristo 3060a4a15e Support for list of known CNVs in VariantEval 
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
 2011-11-30 17:05:16 -05:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00