Ron Levine 08790e1dab Fix mmultiallelic info field annotation for VariantAnnotator ... Add multi-allele test for info field annotations Fix to process all types of INFO annotations roll back to previous version, removes INFO and FORMAT Correct @return for VariantAnnotatorEngine.getNonReferenceAlleles() Enhance comments and clean up multi-allelic logic, handle header info number = R only parse counts of A & R Add INFO for AC update MD5 Performance enhancement, only parse multiallelic with a count A or R Make argument final in getNonReferenceAlleles() Code cleanup, add exceptions for bad expression/allele size mismatch and missing header info for an expression Change exception to warning for expression value/number of alleles check remove adevertised exceptions		2014-12-17 22:21:00 -05:00
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VectorPairHMM	Add HaplotypeCaller argument so integration tests can specify the hardware dependent PairHMM sub-implementation	2014-11-25 21:53:53 -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	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
external-example	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00
gatk-engine	Catch RuntimeException and add the bad file name to the newly thown exception	2014-11-05 09:14:33 -05:00
gatk-queue	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00
gatk-queue-extensions-generator	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
gatk-queue-extensions-public	Disabling tests for Lsf706 specific functionality.	2014-11-04 01:31:18 +08:00
gatk-root	Merge pull request #768 from broadinstitute/pd_bcf_failures	2014-10-31 15:30:56 -04:00
gatk-tools-public	Fix mmultiallelic info field annotation for VariantAnnotator	2014-12-17 22:21:00 -05:00
gatk-utils	Add -output-file-extension option to GATKDoclet to produce html instead of php.	2014-12-01 18:06:36 -05:00
gsalib	Updated gsalib version to 2.1 for resubmitting with updated license to CRAN	2014-12-09 17:07:48 -05:00
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	Revved Picard/htsjdk	2014-10-30 21:16:25 -04:00
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