David Roazen 19ceca5e86 Queue: add -qsub-broad argument ... When -qsub-broad is specified instead of -qsub, use the "h_vmem" parameter instead of "h_rss" to specify memory limit requests. Also cause the GridEngine native arguments to be output by default to the logger, instead of only when in debug mode.		2015-04-27 17:43:25 -04:00
..
VectorPairHMM	Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml	2015-01-06 10:32:11 -05:00
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	Added introductory CRAM support.	2015-01-26 14:47:39 -03:00
gatk-engine	Bypass reads with a bad CIGAR length	2015-04-21 11:55:56 -04:00
gatk-queue	Queue: add -qsub-broad argument	2015-04-27 17:43:25 -04:00
gatk-queue-extensions-generator	Added optional element "includeUnmapped" to the PartitionBy annotation	2015-01-31 15:47:57 -05:00
gatk-queue-extensions-public	since Picard mark duplicates moved to a different package, this class was broken. here's the fix. it would be good to have tests for all the scala picard-wrappers, but that is out of scope for this commit.	2015-04-13 08:44:30 -04:00
gatk-root	Upgrade SLF4J to allow new convient logging syntaxes	2015-03-02 17:01:10 -05:00
gatk-tools-public	Bypass reads with a bad CIGAR length	2015-04-21 11:55:56 -04:00
gatk-utils	Bypass reads with a bad CIGAR length	2015-04-21 11:55:56 -04:00
gsalib	Fixes the test that was failing due to gsalib build failure	2015-03-17 04:26:03 -04:00
java/config	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00
package-tests	Split all imports of tools|engine from utils, and all tools from engine.	2014-10-24 20:59:46 +08:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
repo	Bumping HTSJDK version to pickup a bug fix for CRAM.	2015-01-26 14:47:39 -03:00
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 3.4 development	2014-10-23 22:31:44 -04:00