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Valentin Ruano-Rubio 09ac3779d6 Added ReadLikelihoods component to substitute Map<String,PerReadAlleleLikelihoodMap>. 
It uses a more efficient java array[] based implementation and encapsulates operations perform with such a
read-likelihood collection such as marginalization, filtering by position, poor modeling or capping
worst likelihoods and so forth.

Stories:

          https://www.pivotaltracker.com/story/show/70222086
          https://www.pivotaltracker.com/story/show/67961652
 		2014-08-11 17:46:28 -04:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -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 Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
gatk-engine Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
gatk-queue Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
gatk-queue-extensions-generator Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
gatk-queue-extensions-public Update GATK to work with latest htsjdk 2014-07-30 12:05:14 -04:00
gatk-root Update GATK to work with latest htsjdk 2014-07-30 12:05:14 -04:00
gatk-tools-public Added ReadLikelihoods component to substitute Map<String,PerReadAlleleLikelihoodMap>. 2014-08-11 17:46:28 -04:00
gatk-utils Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00
gsalib Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -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 3.3 development 2014-07-17 12:09:33 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Update GATK to work with latest htsjdk 2014-07-30 12:05:14 -04:00
src/main/scripts/shell For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. 2014-06-25 02:32:15 +08:00
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00