gatk-3.8

Commit Graph

Author	SHA1	Message	Date
Mark DePristo	7f166c3198	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 15:07:02 -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

Author

SHA1

Message

Date

Mark DePristo

7f166c3198

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 15:07:02 -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

3 Commits (72cf6bdd9f7d675797d0a76902907e3af05cea56)