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Geraldine Van der Auwera b42dc1624b Documentation fixes 
- Fix missing closing code block tag
	- SOR fix + minor fix to template
	- Minor typo fixes
	- Make no_cmdline_in_header arg visible in docs
	- Caveats for UG-only args that are difficult to move out of common collection
	- Reference -L and -XL in -gvcf documentation
	- Annotation doc fixes (dsde-docs#1289)
	- Unhide some ContEst args and make Advanced
	- Fix inputPrior error message
	- Update web urls
	- Add JEXL doc link
 		2016-12-05 14:09:44 -05:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.7 development 2016-06-01 17:21:48 -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 3.7 development 2016-06-01 17:21:48 -04:00
gatk-engine Documentation fixes 2016-12-05 14:09:44 -05:00
gatk-queue Replace SAMFileReader with calls to SamReaderFactory 2016-10-14 11:22:54 -04:00
gatk-queue-extensions-generator Replace SAMFileReader with calls to SamReaderFactory 2016-10-14 11:22:54 -04:00
gatk-queue-extensions-public Update pom versions to mark the start of GATK 3.7 development 2016-06-01 17:21:48 -04:00
gatk-root Remove sra group 2016-09-23 17:39:10 -04:00
gatk-tools-public Documentation fixes 2016-12-05 14:09:44 -05:00
gatk-utils Documentation fixes 2016-12-05 14:09:44 -05:00
gsalib Update pom versions to mark the start of GATK 3.7 development 2016-06-01 17:21:48 -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 3.7 development 2016-06-01 17:21:48 -04:00
repo Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -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 3.7 development 2016-06-01 17:21:48 -04:00