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Geraldine Van der Auwera 1cf66addaa Deprecate tools that were outdated or redundant 
ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)

Also deleted the java archive from the private repository (old junk we never use)
 		2015-11-20 22:49:40 -05:00
..
VectorPairHMM Updated licenses for 2015 2015-08-06 15:23:11 -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 Updated licenses for 2015 2015-08-06 15:23:11 -04:00
gatk-engine Move htsjdk & picard to version 1.141 2015-11-20 16:26:26 -05:00
gatk-queue Minor updates to previous ParallelShell commit. 2015-09-29 09:36:37 -03:00
gatk-queue-extensions-generator Updated licenses for 2015 2015-08-06 15:23:11 -04:00
gatk-queue-extensions-public Minor updates to previous ParallelShell commit. 2015-09-29 09:36:37 -03:00
gatk-root Move htsjdk & picard to version 1.141 2015-11-20 16:26:26 -05:00
gatk-tools-public Deprecate tools that were outdated or redundant 2015-11-20 22:49:40 -05:00
gatk-utils Deprecate tools that were outdated or redundant 2015-11-20 22:49:40 -05:00
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
repo Updated gatk so it compiles on java 8 2015-06-26 15:59:46 -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