zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/java/test/org/broadinstitute/sting/gatk
History
rpoplin a6c7de95c8 By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4383 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-29 18:56:50 +00:00
..
arguments Removing the obsolete --hapmap and --hapmap_chip options 2010-08-31 16:57:05 +00:00
contexts/variantcontext Update integration tests to use the new ROD syntax. 2010-08-25 18:13:30 +00:00
datasources Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +00:00
executive A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
filters Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. 2010-09-12 15:07:38 +00:00
iterators Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
refdata one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry. 2010-09-21 18:47:20 +00:00
traversals Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
walkers By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout. 2010-09-29 18:56:50 +00:00