3 Commits (97d29f203e35fd98393f61a28e78134da2b84755)

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