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gatk3的最后一个经典版本3.8
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Valentin Ruano-Rubio 2914ecb585 Change the Map-of-maps-of-maps for an array based implementation ReadLikelihoods to hold read likelihoods. 
The array structure should be faster to populate and query (no properly benchmarked) and reduce memory footprint considerably.
    Nevertheless removing PairHMM factor (using likelihoodEngine Random) it only achieves a speed up of 15% in some example WGS dataset
    i.e. there are other bigger bottle necks in the system. Bamboo tests also seem to run significantly faster with this change.

    Stories:

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

    Changes:

       - ReadLikelihoods added to substitute  Map<String,PerSampleReadLikelihoods>
       - Operation that involve changes in full sets of ReadLikelihoods have been moved into that class.
       - Simplified a bit the code that handles the downsampling of reads based on contamination

    Caveats:

       - Still we keep Map<String,PerReadAlleleLikelihoodsMap> around to pass to annotators..., didn't feel like change the interface of so many public classes in this pull-request.
 		2014-08-11 17:46:28 -04:00
licensing deleted old license files 2013-07-02 16:36:47 -04:00
protected Change the Map-of-maps-of-maps for an array based implementation ReadLikelihoods to hold read likelihoods. 2014-08-11 17:46:28 -04:00
public Change the Map-of-maps-of-maps for an array based implementation ReadLikelihoods to hold read likelihoods. 2014-08-11 17:46:28 -04:00
settings/helpTemplates Various documentation improvements 2014-07-14 12:03:03 -04:00
.gitignore Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
README.md Update README file for the 2.6 release 2013-06-20 13:08:29 -04:00
ant-bridge.sh Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
pom.xml Update pom versions to mark the start of GATK 3.3 development 2014-07-17 12:09:33 -04:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/