Ryan Poplin 3503050a39 Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller ... -- Adding changes to CombineVariants to work with the Reference Model mode of the HaplotypeCaller. -- Added -combineAnnotations mode to CombineVariants to merge the info field annotations by taking the median -- Added new StrandBiasBySample genotype annotation for use in computing strand bias from single sample input vcfs -- Bug fixes to calcGenotypeLikelihoodsOfRefVsAny, used in isActive() as well as the reference model -- Added active region trimming capabilities to the reference model mode, not perfect yet, turn off with --dontTrimActiveRegions -- We only realign reads in the reference model if there are non-reference haplotypes, a big time savings -- We only realign reads in the reference model if the read is informative for a particular haplotype over another -- GVCF blocks will now track and output the minimum PLs over the block -- MD5 changes! -- HC tests: from bug fixes in calcGenotypeLikelihoodsOfRefVsAny -- GVCF tests: from HC changes above and adding in active region trimming		2013-09-06 16:56:34 -04:00
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commandline	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
gatk	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
jna	Fix pipeline tests that were not respecting the pipeline test dry run setting	2013-06-28 15:27:17 -04:00
utils	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00
BaseTest.java	Adaptations to accomodate Tribble API changes, comprising mostly of the following.	2013-08-19 15:52:47 -04:00
ExampleToCopyUnitTest.java	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
MD5DB.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
MD5Mismatch.java	Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements	2013-05-10 19:00:33 -04:00
StingTextReporter.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
WalkerTest.java	Reduce number of leftover temp files in GATK runs	2013-06-14 15:56:03 -04:00