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Valentin Ruano-Rubio 9a9a68409e ReadLikelihoods class introduction final changes before merging 
Stories:

        https://www.pivotaltracker.com/story/show/70222086
        https://www.pivotaltracker.com/story/show/67961652

Changes:

  Done some changes that I missed in relation with making sure that all PairHMM implentations use the same interface; as a consequence we were running always the standard PairHMM.
  Fixed some additional bugs detected when running it on full wgs single sample and exom multi sample data set.
  Updated some integration test md5s.

Fixing GraphBased bugs with new master code
Fixed ReadLikelihoods.changeReads difficult to spot bug.
Changed PairHMM interface to fix a bug
Fixed missing changes for various PairHMM implementations to get them to use the new structure.
Fixed various bugs only detectable when running with full sample(s).
Believe to have fixed the lack of annotations in UG runs
Fixed integrationt test MD5s
Updating some md5s
Fixed yet another md5 probably left out by mistake
 		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 ReadLikelihoods class introduction final changes before merging 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