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Ron Levine 70b2575c29 Move htsjdk to ver 2.10.0 and picard to ver 2.9.2 2017-06-02 06:52:24 -04:00
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VectorPairHMM Update pom versions to mark the start of GATK 3.8 development 2016-12-12 08:53:23 -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 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 Move htsjdk to ver 2.10.0 and picard to ver 2.9.2 2017-06-02 06:52:24 -04:00
gatk-tools-public Changed calculation of rank sum so it's now the median of the per-sample rank sums (because the rank sum across all sample data did worse for biallelics). Now only called alt for 0/1s has rank sum, similar to old paradigm. Combined gVCF rank sums stored in Histogram, then median is taken once during genotyping. Histogram uses Integer keys to eliminate numerical precision mess 2017-05-10 09:04:42 -04:00
gatk-utils respond to review comments 2017-05-05 16:29:01 -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