gatk-3.8

Author	SHA1	Message	Date
Eric Banks	9025567cb8	Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. Moved the merging utility methods into GenomeLoc and moved the unit tests around accordingly.	2013-01-30 10:45:29 -05:00
Mauricio Carneiro	2a4ccfe6fd	Updated all JAVA file licenses accordingly GSATDG-5	2013-01-10 17:06:41 -05:00
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