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Ron Levine 239151ac7b Do not process a variant if it is too large (> readLength), and log an error 
remove final keyword before refMap and altMap, constructHaplotype() changes their values

return ArtificialHaplotype from constructHaplotype instaed of passing as an argument

Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
 		2014-10-20 15:51:32 -04:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
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 Various fixes for package tests. 2014-09-04 15:30:31 -04:00
gatk-engine Do not process a variant if it is too large (> readLength), and log an error 2014-10-20 15:51:32 -04:00
gatk-queue Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gatk-queue-extensions-generator Moved arguments controlling options in output files into the engine 2014-09-05 21:18:11 -04:00
gatk-queue-extensions-public Updated license information 2014-10-14 17:10:12 -04:00
gatk-root Added -writeFullFormat engine-level argument 2014-09-17 08:25:27 -04:00
gatk-tools-public Throw UserException if input VCFs have duplicate samples but no genotypemergeoption is specified 2014-10-15 16:03:10 -04:00
gatk-utils Now passing in the path to the GATK directory to tests. 2014-09-02 01:40:59 +08:00
gsalib Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Various fixes for package tests. 2014-09-04 15:30:31 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Added -writeFullFormat engine-level argument 2014-09-17 08:25:27 -04:00
src/main/scripts/shell For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. 2014-06-25 02:32:15 +08:00
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00