Geraldine Van der Auwera 071d82d1bf Un-exclude SD and TRA from HC annotators; resolves #966 ... Exclude MQ0BySample Move SD and TRA to new StandardUGAnnotation interface There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.		2015-05-03 00:45:53 +02:00
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VectorPairHMM	Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml	2015-01-06 10:32:11 -05:00
c	After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive.	2014-05-19 17:36:41 -04:00
chainFiles	The contig is named MT not M in b36. Delivers PT68890442.	2014-04-08 10:03:47 -04:00
doc	Updated readme in public/doc to just point to the website	2015-03-12 11:52:48 -04:00
external-example	Added introductory CRAM support.	2015-01-26 14:47:39 -03:00
gatk-engine	Numerous doc fixes; mostly formatting and clarifications	2015-05-03 00:28:46 +02:00
gatk-queue	Queue: add -qsub-broad argument	2015-04-27 17:43:25 -04:00
gatk-queue-extensions-generator	Added optional element "includeUnmapped" to the PartitionBy annotation	2015-01-31 15:47:57 -05:00
gatk-queue-extensions-public	since Picard mark duplicates moved to a different package, this class was broken. here's the fix. it would be good to have tests for all the scala picard-wrappers, but that is out of scope for this commit.	2015-04-13 08:44:30 -04:00
gatk-root	Upgrade SLF4J to allow new convient logging syntaxes	2015-03-02 17:01:10 -05:00
gatk-tools-public	Un-exclude SD and TRA from HC annotators; resolves #966	2015-05-03 00:45:53 +02:00
gatk-utils	Merge pull request #970 from broadinstitute/gg_minor_docfixes	2015-05-03 00:36:12 +02:00
gsalib	Fixes the test that was failing due to gsalib build failure	2015-03-17 04:26:03 -04:00
java/config	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
package-tests	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
repo	Bumping HTSJDK version to pickup a bug fix for CRAM.	2015-01-26 14:47:39 -03:00
src/main	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
pom.xml	Update pom versions to mark the start of GATK 3.4 development	2014-10-23 22:31:44 -04:00