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Geraldine Van der Auwera bf875974d1 Prep MuTect2 and ContEst for release 
Renamed M2 to MuTect2
    Renamed ContaminationWalker to ContEst
    Refactored related tests and usages (including in Queue scripts)
    Moved M2 and ContEst + accompanying classes from private to protected
    Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
 		2015-11-24 16:43:20 -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 Assorted documentation fixes, enhancements and reorganization. 2015-11-20 22:44:46 -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 Make the header sequence dictionary match reference 2015-11-21 19:12:37 -05:00
gatk-root Move htsjdk & picard to version 1.141 2015-11-20 16:26:26 -05:00
gatk-tools-public Prep MuTect2 and ContEst for release 2015-11-24 16:43:20 -05:00
gatk-utils Restore FindCoveredIntervals + add docs 2015-11-22 10:19:04 -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