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Ernesto Brau e8b42c4dfd Use GKL's implementation of Vector Logless Pair HMM 
Fixed MuTect2 tests by removing old -alwaysloadVectorHmm flag; upgraded to GKL 0.5.2; FASTEST_AVAILABLE pairhmm option; improved documenting comments in code

Made FASTEST_AVAIALABLE the default for the pairHMM cmdline argument

Make LOGLESS_CACHING the default pairHMM unified cmdline argument, fix error message if choose an unrecognized pairHMM

Updae MD5s
 		2017-06-07 13:33:32 -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 3.8 development 2016-12-12 08:53:23 -05:00
gatk-engine Copy Program Records (PG) from input BAM 2017-06-01 16:01:20 -04:00
gatk-queue Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
gatk-queue-extensions-generator Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
gatk-queue-extensions-public Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
gatk-root Use GKL's implementation of Vector Logless Pair HMM 2017-06-07 13:33:32 -04:00
gatk-tools-public Use GKL's implementation of Vector Logless Pair HMM 2017-06-07 13:33:32 -04:00
gatk-utils Use GKL's implementation of Vector Logless Pair HMM 2017-06-07 13:33:32 -04:00
gsalib Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -05:00
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 3.8 development 2016-12-12 08:53:23 -05:00
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 3.8 development 2016-12-12 08:53:23 -05:00