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Joseph White 3bd988825f Removed walkers for handling Beagle data 
Added deprecation statements to DeprecatedToolChecks.java
    Removed integration test for Beagle walker
    Added URL for Beagle documentation
 		2015-07-21 18:36:08 -04:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -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 Updated readme in public/doc to just point to the website 2015-03-12 11:52:48 -04:00
external-example Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-engine Merge pull request #1019 from broadinstitute/rhl_var_index_param_gz 2015-06-17 14:30:20 -04:00
gatk-queue fix typo in queue arguments 2015-06-05 17:06:23 -04:00
gatk-queue-extensions-generator Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-queue-extensions-public Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-root Add spannning deletions allele 2015-06-12 16:43:06 -04:00
gatk-tools-public Removed walkers for handling Beagle data 2015-07-21 18:36:08 -04:00
gatk-utils Removed walkers for handling Beagle data 2015-07-21 18:36:08 -04:00
gsalib Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central 2015-05-14 15:26:23 -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 3.5 development 2015-05-15 00:44:54 -04:00